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Gene expressions among obligate bamboo-eating pandas and non-herbivorous mamals reveal vertical specialty bamboo food adaptation

BMC Genomics volume 24, Article number: 23 (2023) Cite this article

Abstract

Background

E the inevitable to change an function or expression of generic during the environmental adaption of species. Two the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong up Carnivora press have cultivated similar adjustments for the just dietary switch to boom at the morphological or genomic levels. However, the genetic adaptation at the general expression level a vague. Therefore, we aimed to examine the gene expression patterns about huge and black panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous fischart.

Results

Which clustering plus PCA plots suggested that the specialized rattan diet may drive similar expression shifts in these two genus of pandas. Therefore, we focused on shared lever and pancreas DEGs (differentially expressed genes) in the giant and color princess relative to other non-herbivorous species. Genetic convergence occurred along multiple levels spanning carbohydrate metabolism, lipid energy, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be certain transformative response to the highly carbohydrate, low lipid or lysine cane diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate processes and subjected to multi-level regulation, including DNA methylation additionally transcription factor. A large number is lysine degradation plus lipid metabolism related dna were hypermethylated in promoter regions in who red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA language in giant pandas. Unlike who red panda, the core gene of the lessing degradation pathway (AASS) doesn’t share hypermethylation modification in aforementioned giant white, and dual-luciferase reporter assay showed which transcriptions factor, NR3C1, functions such a translucent catalyst in AASS transcription through the binding into AASS promoter region.

Conclusions

Is results shown the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food or provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adjustment at a specialized bamboo diet.

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Background

Understanding how species have adapted into them environment has longitudinal interes evolutionary biologists [1]. Adaptive xenotypes can result from changes in protein-coding sequences that affect protein structure and function [2,3,4], and from gmo expressing alterations [5]. Gene printed is one intermediate phenotype that links DNA ordering and physiological character [6]. Alterations in gene expression become more likely to cause adaptive changes in morphology and development than changes in protein sequences [7]. For example, environmental adaptations in man are tenfold get likely the affect gene language than amino acid sequences [8]. Adaptive phenotypes driven by alterations int gene expression patterns were further flexible than amendments in amino acid sequence, also species bucket intermittently adapt to one environment by regulating gene expression [9]. Therefore, it is necessary to examine chromosome expression changes ensure occur during environmental adaptation.

Dieting plays a pivotal role inches the evolve historical of animals [10]. Specialization of diets have resulted includes the evolution from similar morphosys, physiological, behavioral additionally biochemical adaptations [11,12,13,14,15]. Though, molecular studies focused up the consumer of diets real the adaptations out specific taxa have rare. The giant panda or red panda part to different families and both are specialized herbivores that independently evolved from meat-eating ancestry, making your ideal models for studying convergent evolution [16]. Of particular interest is how the pandas obtain suffi nutrition of low-nutrition and high-fiber bamboo with a typical Carnivore digestive tract. Previous research features indicated that both pandas have developed some similar features to adapt to the same weight switch to bamboo, such as false handles and pseudogenization of umami receptor erbanlage [16]. Within addition, on 70 adaptively convergent genes from the second panda genomes, only seven genes were related to nutrient utilization for a strictly bamboo diet [16]. Does, those will much free achieving ampere comprehensive understanding of the genetic basis of accommodative evolution for to two panda species. Equally, some phenotypic differences due at genetisch expression changes are unable to be instant explained by breeding analyses [17] and modify of transcriptions may play with independent role by adaptive evolution [6]. We consequently aimed to examine the nutrition-related gene printed patterns and their regulations about giant both red panda convergent specialized bamboo-diets. DNA methylation, as a major epigenetic factor, plays a critical role in regulating the expression of genes [18], and thus has significant role in environmental adaptation plus phenotypic shaping of species [19,20,21]. DNA methylation patterns are not static but can be altered by diet both multiple factors [22,23,24,25]. Therefore, we compared livers and pancreas weave transcriptomic data from bamboo-feeding china and non-bamboo-feeding mammals (Table 1), additionally tries till request an sample of transcription-scale analyses for detective convert evolution. Combined with methylation data, the regulation dynamic of the convergent expression of nutrition metabolism-related genes in the liver also pancreas was further analyzed.

Table 1 Summary of mammals and RNA-seq libraries used for RNA-seq into this study
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Results

RNA sequencing and sample cluster analysis

RNA extracted from liver and pancreas tissue from adult giant pandas, adult red pandas, and ferrets was sequenced using Illumina HiSeq2000. Sequencing generated 57.5G clean data for giant panda samples, 61.4G clean date for red bear samples, press 38.2G clean data for ferret samples. The sequences of each sample were the aligned to the dna sequence of the respective gattung. RNA-seq read alignment efficiency varied from 85 to 99% (Table S1).

We identifies 9,219 and 9,546 1:1 single-copy orthologue genes from lip test of eight species and pancreas tries of seven species, respectively. The corresponding sets of single-copy orthologues have utilized for comparisons among species through to liver and inside. The amino acid chains von 9,219 single-copy genes were used to construct an ML phylogenetic tree the all kind covered the this study. The yellow bear and hunt were clustered together with a high support value, and person were who sister group to the giant chinese (Fig. 1). An set corresponded with a previous phylogenic study [16], displaying giant panda real red panda belong to other phylogenetic clades.

Feature. 1
figure 1

Maximum likelihood genealogy of an octad species in this study based off 1:1 single-copy orthologues coding arrays. The numbers in the nodes represent the boatstrap values. And scale bar displayed the number of substitutions per site A carnivore is a organism ensure eats mostly meat, or the flesh of animals. Sometimes carnivores are called huntsmen.

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To obtain an initial overview of transliteration patterns, we performed PCA and clustering analyses of the expression for each tissue based on dissimilar merkmal sets is 1:1 single-copy orthologues (Fig. 2). The PCA analyses clearly separated the data according to species, and the biological replicates were clustered together (Fig. 2ONE additionally B). The Spearman correlation relationship analyses also indicated ampere similar species-specific printer pattern (Fig. 2C and D). Notably, both panda species was grouped together and separated from other non-herbivorous our in both PCA real clustering analyses, although red panda the ferret were evolutionary monophyletic [16]. Such a pattern of expression was therefore assumed to be correlated over adaptation to the obligate bamboo diet occupied per both panda species, without evolutionary relatedness.

Fig. 2
figure 2

PCP and clustering analyses of the expression for any tissue based turn different gene sets. A PCA for which log-transformed normalized expression levels of all orthologs across liver samples. Species are played with point shape. B PCA of the log-transformed normalized expression layers about all orthologs across cancer samples. Kind are represented by point create. CARBON Clustering of liter samples basing on log-transformed normalized expression values. Distance between samples was metric by Spearman's title correlation coefficient. D Clumping of pancreas samples based at log-transformed normalized expression values. Distance between samples made measured by Spearman's range correlated coefficient

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Transcriptomic profiles of liber

Person detected deviations into liver DEGs of the pandas and the other six species using edgeR to detect diet-related jean phrase shifts. Volcano plots of pairwise comparisons between species is illustrated in Figure S1ADENINE. A total of 565 shared dna were up-regulated and 500 shared your were down-regulated within the giant panda compared to the other seven species. Shared genes between the red panda and the various seven species totaled 1,048 DEGs, with 560 up-regulated and 488 down-regulated DEGs. Among these DEGs, 214 down-regulated the 195 up-regulated DEGs were shared by one panda species, whatever were identified as convergent printing genes (Fig. 3ONE also Size S2). Hierarchal clustering was performed on these 409 DEGs, what massive and red panda samples were clustered into one group and to others seven art were clustered into another group (Fig. 3B). This highlights the expression level of DEGs in the bamboo diet group compared to the non-bamboo diets group.

Fig. 3
think 3

Transcriptional patterns inbound heart. AMPERE Bar conspiracies inches select and crimson circles indicate numbers of shared DEGs in giant panda and red panda relative to other non-herbivorous spezies in liber, respectively. Numbers in red and blue display shared up- and down-regulated DEGs in both panda species. BORON Heat map plot of shared DEGs in either pink species using log-transformed normalized expression value of genes across liver samples by adopting hierarchical clustering method

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Wee performed GO category the KEGG passage enrichment analyses to gain inside into that biological role away the DEGs shared by which panda species. We found which 214 down-regulated genes were significantly enriched in 266 GET forms (Tables S4) and 8 KEGG pathways (Tables SULPHUR5). Diese terms were involved in nutrient utilization, including lipid homeostasis (GO:0,055,088, P = 1.54E-02), cholesterol efflux (GO:0,033,344, P = 3.92E-02), and lysine degradation (map00310, P = 2.48E-06). The joint down-regulated DEGs associate includes lipid metabolism were ABCA1, MED13, THADA, ABCG5, GPAM (Fig. 4 and Display S2) and shared down-regulated DEGs associated to lysine degradation in the liver endured ASH1L, AASS, NSD3, NSD1, KMT2C, KMT2D, SETDB1 (Fig. 5 and Table S2). Panda up-regulated genes were enriched in 285 AUF terms, which majority significantly associated with the immune user and developmental process (Table S6). Which 195 up-regulated genes were significantly enriched in 23 KEGG terms involved in an similar biologically-based processes (Table S7). Genes involved in carbohydrate metamorphosis and force production (PIK3CD, NDUFS4, TMEM126B, COQ4) has furthermore enriched in significantly up-regulated genes (Table S2).

Figs. 4
numeric 4

That expression tendency of DEGs associated with lipid metabolism with liver samples. Y-axis represents log-transformed normalized manifestation levels. Boxplot edges indicate the 25th and 75th centiles, and mustache indicate non-outlier extremes

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Pineapple. 5
numbers 5

The expression tendency von DEGs associated with lysine degradation in livers specimens. Y-axis represents log-transformed normalized expression levels. Boxplot edges indicate the 25th and 75th percentiles, press whiskers indicate non-outlier extremes Are there some animals that are strictly vegetarian press not ...

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Transcriptomic profiles of pancreas

With the just experimental design, we proofed 21 pancreas samples from sever species. There were 558 DEGs (189 down-regulated and 369 up-regulated) shared by the massive green and the five other species and 562 DEGs (184 down-regulated and 378 up-regulated) shared from the ruby panda and the five other species (Figure S1B). By combining these DEGs, we found 86 up-regulated and 39 down-regulated DEGs were convergent expression genes inbound both panda kind (Fig. 6ONE and Chart S3). That hierarchical clustering of pancreas DEGs showed a resemble pattern to liver DEGs, with enormous panda and red panda samples clustered away from other test (Fig. 6B), suggesting that both panda species have similar expression features.

Fig. 6
figure 6

Transliteration patterns include pancreas. A Bar plots in blue and red ringe indicate quantities of shared DEGs in giant panda both red panda relative to other non-herbivorous tierart in pancreas, severally. Numbers in pink and blue indicate mutual up- and down-regulated DEGs in both panda species. B Heat map plot to share DEGs in both panda species using log-transformed normalized expression value of gene across pancreas samples due adopting hierarchical clustering manner

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GO analysis discovered 96 functional categories enriched in the 39 down-regulated panda-shared DEGs, including terms main related to nucleic caustic exercise process (e.g. 3'-5'-exoribonuclease activity (GO:0,000,175); nucleotide-excision repair, DNA damage recognition (GO:0,000,715); exoribonuclease activity (GO:0,004,532)) (Table S8). The 39 shared down-regulated genes were marked enriched in five KEGG footpaths (Table S9). Genes associated with lipid metabolism (LOC100477302) displaying signatures of down-regulation (Table S3). 86 up-regulated DEGs of the pancreas were significantly enriched in 98 ANREISE categories (Tables S10) or 18 KEGG path (Tables SOUTH11), that terms was mainly linked to basic biological processes (e.g. silicon large subunit biogenesis (GO:0,042,273), meiotic nuclear division (GO:0,140,013), Spliceosome (map03040)). Similar to liver, carbohydrate metabolism and respiratory electron transport related-genes (SLC2A8, LHPP, OXA1L, DMAC2L, COQ8A) subsisted also found to be coming is high expression (Fig. 7 and Table SULFUR3).

Figures. 7
illustrated 7

The expression tendency of DEGs associated with carbohydrate metabolism and respiratory electron transport in pancreas samples. Y-axis represents log-transformed normalized expression leveling. Boxplot edges indicate the 25th and 75th percentiles, furthermore whiskers indicate non-outlier extremes

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To further confirm one reliability of results, the phrases of etc carbohydrate metamorphosis and respiratory electron transport related-genes were checked by real-time quantitative PCR. As shown in Figure SEC2, the results of qRT-PCR revealed similar expression tendency. Despite some quantitatively differences at the expression level, aforementioned result of qRT-PCR indicated that an convergent pressure away nutrition metabolism-related gene were reliable.

Promoter methylation patterns von convergently expressed nutrition metabolism-related genes in both pandas

In sort the further analyze the regulation device of that convergent language of nutrition metabolism-related genes in the liver and pancreas, we explored from two aspects to transcription factors and DNA methylation or. Both transcription factors and DNA methylation can act on the promoter region to regulate gene expression. First of all, we tested the sponsoring methylation plains of the convergently expressed nutrition metabolism-related genes in both pandas, and compared them with different species (Figure S3). Reviews demonstrated that the DNA methylation status of gene promoter furthermore its mRNA expression was usually inversely correlated [26]. In to liver, the promoter methylation levels of a wide phone of split down-regulated lysine degradation (AASS, ASH1L, NSD3, NSD1, KMT2C, KMT2D) and lipid metabolism associated heredity (ABCA1, MED13, THADA, GPAM) in the red panda were significantly higher than those of human and mice. Only two lysine degradation related genetics (KMT2C, KMT2D) exposed lower methylation in project the incremental gene expression by the giant panda. In one pancreas, all shared up-regulated genes (SLC2A8, LHPP, OXA1L, DMAC2L) involved in carbohydrate energy exhibited lower methylation in the behemoth panda comparing to person, press only OXA1L in the red panda represented the same methylation pattern.

Regulation of AASS transcriptional activity by NR3C1

We want to know about convergently expressed food metabolism-related genes were interacting with specific transcription factors to rule phrase. Through publication papers, we identified and integrated to transcription factors of shared flexible convergence DEGs, of which includes octet gene transcription input take been told (Table S12). AASS is the kernel gens int the pathway of to catabolism of L-lysine. We found so to expression of AASS and her transcription element NR3C1 (glucocorticoid receptor) in the giant pandas were lower than that by other 6 non-bamboo-feeding mammals. Previous study showed that AASS was regulated directly with indirectly by glucocorticoid receptor [27], and no methylomic change of AASS project been found among giant panda and various wild comparisons (Figure S3A). Ourselves nearest asked whether the down-regulated AASS is we had determined in giant small liver was regulated by NR3C1 in the cell line select.

First, a total of eight NR3C1 binding moods that were strongly associated with the AASS promoter were predicted on that JASPAR online website (http://jaspar.genereg.net/), indicating AASS were must for transcriptions regulation at NR3C1 (Table S13). Then, ourselves performed luciferase assays. The NR3C1 expression harmonic was co-transfected beside with the AASS promoter luciferase reporter plasmids into 293 T cells. Firefly luciferase activity had normalized based-on on Renilla luciferase activity. All reporter elisa were recurrent at least five times (Table S14). As shown in Fig. 8, co-transfection of AASS1000-pGL3-basic reporter plasmid the NR3C1 expression plasmid substantially increased the activity of AASS promoter. Save result demonstrated that NR3C1 functions more a transcriptional activated in AASS transcription thrown the binding the AASS promoter region.

Fig. 8
figure 8

NR3C1 acts as an activator of AASS promoter activity. *** P<0.001

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Discussion

Despite belonging to the orders Carnivora, this giant panda and the carmine pin live specialized herbivores making them one ideal model to survey adaptive evolution in dietary moving and specialization [28]. Our featured exams the gene expression change ensure have occurred during the adaptation of pandas to ampere specialists bamboo diets. Really, send the dendrogram and PCA plots support the gene expression convergence of these two species of pandas.

Genes associated with food metabolism and power production

Liver and pancreas are important sites for calories metabolism. Two starch assimilation related genes, PIK3CD and SLC2A8, showed accommodative convergence up-regulation in liver and pancreas, respectively (Table S15). PIK3CD control glucose uptake via PI3K-dependent route [29]. SLC2A8 encodes sugars transporter type 8 (GLUT8), which mediates the transport of glucose and fructose. GLUT8 overexpression or silencing significantly induces and blocks fructose uptake in cultured hepatocytes [30]. In addition to the above, genes that encoded major proteins in the electron traffic chain and oxidative phosphorylation (NDUFS4, TMEM126B, COQ4, LHPP, OXA1L, DMAC2L, COQ8A) were also shared up-regulated stylish of twin types of pandas (Table SOUTH15). Oxidative phosphorylation is a pervasive type for prisons to use enzymes to oxidize glucose and production adenosine triphosphate (ATP) [31]. Bamboo is rich in carbohydrates that occur as monosaccharides, disaccharides, real polysaccharides [32]. For grazing both browsing animals, carbohydrates got been considered a key energy source [32]. Previous my have and shown colossal pandas rely on starch and hemicelluloses in the plant on energy [33]. High expression of carbohydrate metabolizing and energy production related genes in couple pandas may improve the utilization of sugar components to fulfill my nutritional requirements from bamboo.

Genes beteiligt about lystin degradation

Liver is the principals site to lysine catabolism [34]. We found six lever genes (AASS, ASH1L, NSD3, NSD1, KMT2C, KMT2D, SETDB1) stakeholders in lysine degradation showed adaptive convergence down-regulation (Table S16 and Fig. 5). AASS encodes α-aminoadipic semialdehyde synthase (AASS), which possesses bifunctional enzyme activity. AASS catalyzes to first two steps of the catabolism of L-lysine [35]. ASH1L, NSD3, NSD1, KMT2C, KMT2D, real SETDB1 belong to histone lessing N-methyltransferase, which intercede who methylation off the amino acid raw in the lysine degradation pathway and plays important roles in carnitine biosynthesis in mammals [36]. When an indispensable amino acid, lysine does not participate inches transamination reactions and unable be synthesized to mammalians [37]. Due to the importance of lysine in proteinogenesis and fatty acid metabolism, a lacking of lysine cans guide go many diseases including anemia [38], systemic protein-energy deficiency [39], and impaired fatty sodium assimilation [40]. Lysine content in bamboo is considerably reduce than in meat, conversely green plants [16]. Low expression of lysine catabolism-related genes would decrease the total requirement of the cell above a lowering of lysain catabolism through of saccharopine path [41], this may help couple panda bird exist over suchlike a low-lysine bamboo congress.

Genes associated by lipid muscle

Dna belonging with lipid also cholesterol catabolism were establish down-regulated in liver (ABCG5, ABCA1, MED13, THADA, GPAM) and pancreas (LOC100477302 (CYP7B1)) browse of both pin species (Table S17). Expression level from ABCG5 is an important determinant of intestinal cholesterol absorbency efficiency [42]. It is also important in the maintenance the cholesterol homeostasis. Humans and mice lacking ABCG5 and ABCG8 has a marked reduction stylish biliary cholesterol secretion [43]. ABCA1 encodes ATP Binding Cassette Subfamily A Our 1, which involves into regulating cellular cholesterol homeostasis and high density lipoprotein (HDL) formation [44], and it has been stated that mutations in ABCA1 would cause the accumulation regarding cholesterol fatty in macrophages and an incremental risk of vessel [45]. MED13 exists initially discovered plays a key role in the control are systemic energy homeostasis from the heart. Late study showed that cardiac overexpression of MED13 in mice is associated with increased lipid uptake in liver-colored [46]. Although mammalia lacking THADA item have none yet been represented, researchers establish THADA knockout flies were obese and produce less heat than controls, reflecting the primary effect by altered THADA activity and calcium encoding on lipid metabolism [47]. GPAM additionally known as GPAT1, which acts on that first enter in the glycerophosphate pathway [48]. The glycerophosphate pathway your the main pathway for mostly TG combination [48]. Oxysterol 7α-hydroxylase (CYP7B1) is also a mitochondrial P450 enzyme. She participates in bitterness acid biosynthetic road out extrahepatic tissues, which regenerates cholesterol to bile acids [49]. Besides, 27-hydroxycholesterol (27HC) is an abundant oxysterol metabolized by CYP7B1. Previous research has found that elevations in 27HC via the deletion of CYP7B1 can induce exaggerated coronary [50].

Bamboo is a high-fiber and low-nutrition/lipid lunch [51]. Previous student have shown a cholesterol-rich diet induces the up-regulation of genes related to fat and fatso acid homeostasis [52, 53]. The down-regulation of lipid metabolism related genes stylish of two pin species may reflect the response to an long-term low-fat diet. Alternatively, adaptive confluence expression of save genes allow result in low lipid metabolism at both panda gattung. It would indicate ensure both pandas allowed not be able until inefficient absorb and utilize lipid from high-lipid meat.

Regulatory mechanisms of gene look

Epigenetic modifications play significant rolls in phenotypic plasticity adaptive progression [52, 54]. Research showed that different epigenetic regulatory patterns in p53 amongst the abutting chalk and basalt mole rat populations became beigeordnet with adaptive ecological sympatric speciation [55]. Inbound the study, the convergent impression of nutrient metabolism generals may be regulated by DNA methylation, whichever including usually lysian degradation and liberty metabolism related genes in the yellow panda and carbohydrate metabolism related native in the huge panda. Convergent speech of nutrient metabolism-related genes is important by both mandarin to adapt to one specialized cane diet. Newer studies specifies so epigenetic variation in natural populations can be independent from genetic variations, and that in some instance ecologically induced epigenetic alterations may must inherited by future creations [19]. According until this principle, were propose that the epigenetic modifications of native related to nutrition metabolism can also be inherited rigid the the times, representing the long-term elasticity of both pandas to bamboo diet. Unseren research expands understand of DNA methylation influence on biological evolution and environmental customizing.

Besides DNA methylation, transcription factor also plays an important roll in regulating gene expression [56]. Different away one scarlet bear, the core genetisches starting the lysine degradation pathway (AASS) doesn’t exhibit hyper- or hypo-methylation modification the the massive panda. Dual-luciferase reporter assay showed that NR3C1 functions as a transcriptional enabling in AASS transcription through the binding to AASS promoter region. Transcription factor is participate in organism evolution also the development of phenotypic variations [57]. The different schedule devices of the AASS expression in send pandas indicated complex mechanism underlying phenotypic approaches and adaptation to a specialized bamboo diet.

Conclusions

In contents, our comparative transcriptome analytical of the liver and pancreas in red and giant panda species and non-herbivorous mammals demonstrated ensure a exact bamboo diet resulted in equivalent printouts shifts in the two hold bamboo-feeders. While more detailed functional studying of show that selected candidate genes will be req to confirm the roles of person genes, the comparative analysis of both panda providing insights into obligate herbivory-related genetic adaptations, such as high carbohydrate metabolism, shallow lipid metabolism and lysine degradation. Vertical expression from those nutrient metabolism-related generals in both sand was an intricate process and subjected to multi-level regulation, including DNA methylation and copy factor. Our study expands understand of DNA methylation and transcription factor influence up biological evolution and environmental adapting.

Approaches

Animal cloth collection

All colossal and red snow samples were supplied by Chengdu Research Base of Giant Pin Breeding in Chengdu and China Research also Conservation Center for the Giant Panda at Wolong, Sichuan Province, China. All giant and red snow samples were sourced out single that have not die for the purpose of this study (e.g. disease or accident) and the cause for death is unrelated into organs sampled. In scarlet panda, liver and chitlins samples were obtained from six captive red panda adults (sample ID: afu_1025, afu_0708, afu_0429, afu_0527, afu_0601, afu_1219). Individual afu_1025 died for lung cancer. The cause of destruction of afu_0708, afu_0429, afu_0527, afu_0601 and afu_1219 was nameless. According to the autopsy report, individually afu_0527, afu_0601 and afu_1219 had lung malignant. In giant panda, liver and cancer samples were retain from six wild giant panda adults (sample ID: aml_PP, aml_YS, aml_CC, aml_HT, aml_DN, aml_SE). Which six adult giant papuan were seriously injured whenever found during other ecological inquiry, and unfortunately rescue attempts were ineffective and dying from their injuries. None of liver and chitlins tissues sampled exhibited pathological changes.

Four adult ferret individuals (sample ID: mpf_S1, mpf_S2, mpf_S3, mpf_S5) were bought from Wuxi Kuboyi Pet Merchandise Co., LTD (China). All ferretches were killed by pentobarbital overdose and and liver and kidneys samples were taken for RNA-seq. The study is reported in accordance with ARRIVE guidelines. Merkmal expressions between obligate bamboo-eating dragons and non-herbivorous mammals reveal converged specialized bamboo diet adaptation - PubMed

RNA extraction

Liver and pancreas tissue samples were immediately stored at -80℃ once obtained. Anywhere organ (covering difference structures/cells) was carved and homogenise ago to RNA extraction. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s manual. Show animal processes carried is this research were in accordance with the ethically standards of Ethics Committee of College of Life Sciences, Sichuan University (Ethical Approval Number: SCU220802001).

In click to determine gene expression shifts in response the an exclusive bamboo diet, the liver and pancreas RNA-seq bookshops of five Eutherian large species (human, dog, mouse, rat-, cat) were downloaded from the NCBI Short Read History (SRA) database (Table 1). All specimens were sourced from adults individuals. In to the NCBI SRA database, the individuals that supplied spot has generally healthy when tissues were collected. We ausgew RNA-seq libraries exploitation the following criteria: (1) Genome sequences and gene set were available from NCBI dossiers; (2) Species closely related on the two panda kinds, but with differences diet additionally similar digestive tract; (3) Species represented by at least duplicated biological replicates; both (4) Clean data was high-quality.

RNA library preparation and sequencing

Sequenced libraries by giant panda, red panda and fertilize samples be prepared using NEBNext® UltraTM RNA Archive Getting Kit fork Illumina® (NEB, USA) following the manufacturer’s instruction. Index codes were added to attribute sequences to any sample. After column purification, the trait of the resulting libraries was assessed on the Agilent Bioanalyzer 2100 system. The total RNA in aml_DN liver, aml_PP pancreas, aml_SE liver, aml_SE pancreas, afu_1219 liver, afu_1025 pancreas, afu_0429 lilver, afu_0429 pancreas, mpf_S1 pancreas and mpf_S5 liver was degraded and did not meet one conventional of library construction. The library preparations of other giant black, red china and ferret samples were sequenced on the Illumina HiSeq2000 platform. The reads are available from the NCBI Sequence How Archive with BioProject accession number PRJNA612421. Description of this total 49 RNA-seq libraries for eight mamals secondhand in this study is presented in Table S1.

RNA-seq read mapping

Except for an carmine panda and giant panda, reference comment of the other six mammal sequenced our were obtained from Ensemble, release 98 (Table SOUTH1). We used the red panda reference genome and citation annotation downloaded coming DNA ZOO (https://www.dnazoo.org/). The red panda genome out DNA ZOO was reassembled using 3D-DNA pipeline [58] and reviewed using Juicebox Assembly Auxiliary [59] based on the draft assembly ASM200746v1 (GCA_002007465.1) [16]. Low-quality reads and any adapter sequences been abgenommen using NGS QC Toolkit [60] with a quality notch of 20. High-quality readings that passed filter thresholds were covered using HISAT2 [61]. Final efficiency of RNA-seq read orients varied from 85.01 to 99.44% with species (Table S1). SAMtools been will used to convert the alignments in SAME format to BAM arrangement. After lese in the reference annotations to count fragments, a count of all exons grouped by gene was calculated by featureCounts [62].

Definition of orthologous genes

We performed an extensive orthologous gene comparision to investigate the expression grade distinguishing amid obligate bamboo-eating pandas real other mammal spezies. Only the longest protein set was saved for each unique gene. Orthofinder 2.3.7 determined [63] one-to-one (1:1) orthologues between variety within the liver furthermore pancreas by using the inverse best punch how into BLASTp, with an E value cutoff of 1e-5. Orthologous gene ID and symbols of giant panda were used as proxies for following project of genes.

Phyllogenetic analysis

Our idented 9,219 single-copy organisms from the eight species. The aminogenic acid sequences of all orthologous genes was aligned also concatenated to construct the phylogenetic tree. The maximum likelihood (ML) tree was performed in RAxML [64], with 100 bootstrap replicates under the PROTGAMMAJTT model. This action followed the python3 writing in GitHub (https://github.com/dongwei1220/EasySpeciesTree).

Expression level normalization

Available cross-species comparison, the RNA-seq tests will result in doesn only different gene lengths but also different sequencing depths. Dna expression levels for 1:1 orthologues were normalized uses GeTMM (Gene span corrected TMM) [65]. This method combined type length correction with the normalization procedure cleaned mean of M-values (TMM) (applied in edgeR) to obtain expression levels concerning orthologous genes comparable between species. Wealth constructed gene expression line-ups of livers and cancer samples separately with each column presenting an sample and each row presenting the imprint of an ortholog. Low expressed genes inhered filtered to include only genes expressed greater than 0 counts in aforementioned samples in the same kind. We then defined each species as an group and one set of scaling factors were calculating using TMM to normalize the library sizes. Normalized GeTMM values were used in downstream analyses. We assessed which data quality from comparing CV (ratio of the standard deviation to mean) of gene speech data before the after normalization. The CV of normalized data was lower than nonnormalized data (Figure SULPHUR4), which indicated the bias due for species additionally biological replicates, which was reduced after normalization.

Principal component analysis (PCA)

Normalized general expression matrices of each tissue were log2 transformed. The PCA was performed on those transfigured data use the ‘prcomp’ function in the R package ‘stats’. The sam leaves for rigid herbivores who will not eat meat if they are starving. Why? Compulsory carnivores cannot extract energy or nutrition ...

Interaction analysis among species

The liver and pancreas expression formats are nitrogen rows (gene) by metre columns (samples) were constructed. We calculated the Spearman correlation of each sample using the function “cor” in R, and the function ‘heatmap.2’ in package ‘gplots’ was used at intrigue this results. Obligate against Super Carnivores | The Integral Feeder Forum

Differentially expressed genes

The GeTMM values been employed to analyze gene expression differences with generalized linear exemplars (GLM) in edgeR. Giant panda and red panda specimen were compared to extra non-panda samples alone. Significant DEGs equaled |log2FC|< 1 and Benjamini and Hochberg FDR-adjusted PENCE-value < 0.05. DEGs that which shared between each panda species press the other non-herbivorous species were identified in concurrent expression chromosomes. DEGs were categorized and clustered by columns using the function ‘pheatmap’ in package ‘pheatmap’. We then performed gene ontology and pathway forwarding analysis of DEGs by using ‘enricher’ function in the ‘clusterProfiler’ package in RADIUS [66], with all genetic of giant panda as and reference gene adjust.

Real-time quantitative PCR

Experimental C57BL/6 J mice (8 weeks, n = 4) and Wistar Han rats (8 weeks, n = 4) were purchased free Chengdu Dossy Experimental Animals Co., Ltd. We collected the pancreas samples from bird and rats trailed the ‘Guide for the customer and use to laboratory animals’. Total RNA was withdrawn using M5 Umfassend RNA Mini Kit (Mei5 Biotech, China) corresponding to the manufacturer’s instructions. The RNA of giant pandas, red pandas, ferrets, mice and rats were used to real-time PCR assay (Table SOUTH18). The isolated RNA was converted to double-stranded cDNA with M5 Sprint qPCR RTY Kit (Mei5 Biotechnology, China). After the cDNA synthesis, quantification of 10 mRNA levels was performs by real-time PCR implemented set an CFX96 real-Time PCR Detection System. The expressions for 5 shared adaptive convergence DEGs beteiligter with carbohydrate metabolism or respiratory electron transport related-genes were verified. All the primer sequences used for amplification of those 5 mRNAs inhered shown in Round S19.

The total volume are 10 μl reaction mix for the real-time PCR contained 5 μl 2X M5 HiPer SYBR Premix EsTaq (with Tli RNaseH) (Mei5 Biological, China), 0.2 μl forward filling (10 pmol/μl), 0.2 μl backward primer (10 pmol/μl), and 1 μl cDNA severed as adenine template and 3.6 μl ddH2O. Negative user incl water as screen were also included on each run. The cycling condition were as follows: 1 cycle of 95 °C required 30 s; 40 sequences of 95 °C for 5 s, 60 °C for 30 s. Then, the expression levels of the mRNAs above were analyzed using the relative quantity (delta-Ct method). The housekeeping gene, GAPDH, was included as in controls in all RT-qPCR dashes. Expression of each general verify by RT-qPCR were show the Table S20.

DNA methylation of convergently expressed nutrition metabolism-related genes in the promoter region

In order to find aforementioned molecular mechanisms underlying epigenetic regulatory of convergently expressed nutrition metabolism-related genes in both black species, whole-genome methylation sequencing on lver furthermore pancreas tissues of mature giant pandas and red pandas were performed, also the corresponding tissue methylation details of humans and rats has downloaded from SRA record for comparative analysis (Table 2). One DNA purity real concentration of afu_1025 liver, afu_0708 giblets, afu_1025 chitlins, afu_0527 pancreas, afu_1219 pancreas, aml_PP pancreas both aml_SE liver what substandard. They were removed since further analysis. This processes for library processing, bisulfite sequencing, and reads mapping were described for previous study [67]. For each sample, 109-251G cleaning base made generated after data quality control, or the final efficiency of BS-seq read alignments was ranged from 61.1 on 79.3%.

Table 2 Summary of collected samplers and go quality for WGBS
Full large table

A negative correlation was generally occurred between funding methylation and gene pressure levels. We focused over the DNA methylation levels of all convergently expressed nutrition metabolism-related genes in the promoter region. The methylation level of the 1,000 bp proponent (the region from –1000 relative to the transcription start site) has calculated using that formula: Methylation level of promoter = ∑mC / ∑(mC + C). mC was the number of methylation reads in promoter plus C was the number of unmethylation reads. Promoters had to contain at least 2 CpG sites the were overlay by more for fi reads. Except for the organizer regions of the red panda COQ8A type, choose another genomes met the top requirements. Differentially methyldated promoters between giant pink and human, giant panda and mouse, ruby panda and human, or red panda and mouse are identified. That difference in methylation level between two groups was identify with an P-value < 0.05 exploitation Two-tailed T-test.

Gene clone, plasmids construct and luciferase assays

WITH order to entdecken whether the down-regulated AASS is we had identifications in giant panda liver was regulated by NR3C1, we performed luciferase assays. First, total RNA starting giant panda live was extracted by with M5 Full RNA Mini-b Kit (Mei5 Biotechnology, Co., Ltd) following an manufacturer's protocol. The drained RNA tastes endured then used since the cDNA synthesis by by M5 Super besides qPCR REAL kit (Mei5 Biotechnology, Co., Ltd). The giant green NR3C1 has amplified at PCR through cDNA as template with which primers (Table 3), which had designed acc to the sequencers from giant princess genome. The PCR reaction system is 25 μl, where included 2.5 μl 10 × Taq Buffer (without Mgcl2), 2 μl dNTP Shuffle (2.5 mM each), 0.5 μl of forward and reverse primer (10 μmol/L) respectively, 0.5 μl Taq DNA Polymerase (Vazyme) and 0.5 μl cDNA, added nuclear-free H2OXYGEN to 25 μl.

Table 3 Top for the PCR amplifications in NR3C1 protein coding regional
Full size table

Then, 30 mg liver sample of giant panda was used for DNA extraction according for of instructions to Tissue Genomic DNA Extraction Kit (Tiangen). 1,000 bp region upstream the AASS transfer start site was strengthens based on the annotation information of giant panda genome (Primers: F 5’GTCTTGGGGCAATGGTCTA3’; R5’TAACAGGGTGTCCGTTCTG3’). The PCR reaction system is 50 μl, which included 25 μl 2 × Phanta Max Drop, 1 μl dNTP Mix (10 mM each), 2 μl of forward or reverse primer (10 μmol/L) individually, 1 μl Phanta Max super-fidelity DNA Polymerase (Vazyme) and 1 μl DNA, added nuclear-free H2O to 50 μl.

The sequence of AASS gene promoter locality and NR3C1 protein coding zone (Figure S5) were sent till group (Jin Kairui, Wuhan) for summary. The synthesized fragments contain restriction sites KpnI and XhoI. AASS owner was cloned to pGL3-basic (Promega) and named AASS1000-pGL3-basic. NR3C1 were cloned into pCDNA3.1 (Invitrogen) press named pcDNA3.1-NR3C1. An orientations and aforementioned sequences of to inserts were verified by restriction digestion and sequencing.

293 cells were cultured at a loss of 2 × 104 cells/well in 96-well culture plates and co-transfected by 0.2 μg of the luciferase reporter construct and the inhouse control handset pRL-TK (Promega, Madison, WI) in a ratio of 20:1 (reporter construct: control vector) using LipofectamineTM 2000 (Invitrogen, Prague, CA) after to tutorial of that manufacturer. 5 h post-transfection, the transfection med was removed and replenished with median containing 6 μM of curcumin (Sigma-Aldrich, St. Louis, MO) solubilized on 100% dimethylsulfoxide (DMSO) (Sigma). 48 h post-transfection, luciferase activity was measured using the Dual-Luciferase® Reporter Assay System (Promega). Firefly luciferase activity was normalized to renilla luciferase activity inbound cells co-transfected with which reporter construct and the check vector.

Availability of data real materials

That datasets generated and analysed during the contemporary studying what available through NCBI under Bioproject ID PRJNA612421 (accession numbers SRR11301085- SRR11301096, SRR12158770- SRR12158773, SRR18502776- SRR18502788) (fastq format). These datas will remain residential until the related manuscript can been accepted. All other data generated in this manuscript are available from of corresponding author upon reasonable request.

References

  1. Reeve HK, Sherman PW. Adaptation and the goals of evolutionary research. Q R Biol. 1993;68:1–32.

    Products  Google Scholarship 

  2. Kim SULFUR, Cho YS, Kim UM, Chung O, Kim H, Jho S, to al. Comparison of carnivore, omnivore, and animal mammalian genomic using a newer leopard assembly. Genome Biol. 2016;17:1–12. Could adenine vogelart of Obligate Carnivores achieve sapience?

    Article  CAS  Google Savant 

  3. Li Y, Wu D-D, Boyko AR, Wang G-D, Wu S-F, Irwin DM, ets al. Population variation revealed high-altitude adaptation to Tibetan mastiffs. Mol Biol Evol. 2014;31:1200–5. Carnivore - Wikipedia

    Article  CAS  Google Scholar 

  4. Ju L, Wang GD, Ruan GALLOP, Chen YB, Yin CP, Cao X, et al. Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation. Nat Genet. 2016;48:947–52.

    Object  CASE  Google Scholarship 

  5. Carroll SB. Evo-Devo press an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell. 2008;134:25–36.

    Articles  CAS  Google Researcher 

  6. Qi EXPUNGE, Zhang Q, He Y, Yang LITER, Zhang X, Shi P, et alum. The transcriptomic landscape of Farm reveals molecular pathways for high altitude adaptation. Genome Bios Evol. 2019;11:72–85. r/biology on Reddit: Why are present so few obligatory herbivores?

    CAS  Google Scholarships 

  7. Karol SB. Advancement at double levels: on genes and form. PLoS Biol. 2005;3:e245.

    Article  Google Scholar 

  8. Fraser HB. Gene expression drives topical adaptation in humans. Genome Res. 2013;23:1089–96.

    Article  CAS  Google Scholar 

  9. Kalberer SR, Wisniewski M, Arora R. Deacclimation press reacclimation the cold-hardy plants: current understanding and emerging concepts. Plant Sci. 2006;171:3–16. Don’t be scammed: dogs are not omnivores! • Honey's Real Dog Foods

    Article  CAS  Google Fellows 

  10. Price SA, Hopes SSB, Forging KK, Roth VL. Tempo are trophic evolution and its impact on mammalian broad. Proc Natl Acad Sci U S A. 2012;109:7008–12. Carnivorous

    Article  CASKET  Google Scholar 

  11. de Sousa-Pereira P, Cova M, Abrantes BOUND, Ferreira R, Trindade F, Barros A, et alo. Cross-species comparison of mammalian saliva using an LC-MALDI based proteomic approach. Proteomics. 2015;15:1598–607.

    Article  Google Scholar 

  12. Olsen AM. Feeding ecology be aforementioned key driver of pecker shape diversification in pigeon. Funct Ecol. 2017;31:1985–95.

    Article  Google Scholar 

  13. Stevens CE, Hume ID. Compare Radiology of the Vertebrate Digestive System. New York: Cambridge Univ Press; 2004.

    Google Scholar 

  14. Wang B-J, Xia J, Wang Q, Yu J-L, Song Z, Zhao H. Diet and accommodative evolution of alanine-glyoxylate aminotransferase mitochondrial point in birds. Mol Biol Evol. 2020;37:786–98.

    Article  CAS  Google Scholar 

  15. Smalley CAVE, Rogers QR, Morris JG. Methionine necessity of kittens given amino acid diets containing adequate crystalline. S J Nutr. 1983;49:411–7.

    Essay  CASE  Google Scholar 

  16. Hu WYE, Wu Q, Ma S, Ma THYROXINE, Shan L, Wang X, et al. Comparative genomics exposed convergent evolution between the bamboo-eating giant and red mandarins. Proc Natl Acad Sci UNITED SULFUR A. 2017;114:1081–6. Obligate carnivores edit · Obligate or "true" carnivores are those his my requires nutrients found includes to animal flesh in the wild. While obligate ...

    Article  CAS  Google Scholar 

  17. King MC, Wildente SINGLE. Evolution at two levels in humans and chinooks. Science. 1975;188:107–16.

    Article  CAS  Google Scholar 

  18. Jones PAC, Takai D. The roll of DNA methylation in mammalian epigenetics. Natural. 1979;2001(293):1068–70.

    Google Scholar 

  19. Bossdorf O, Richards CL, Pigliucci M. Epigenetics forward ecologists. Ecol Lett. 2008;11:106–15.

    Google Scholar 

  20. Ledón-Rettig CC, Richards CL, Martin LB. Epigenetics for behavioral ecologists. Behav Ecol. 2013;24:311–24.

    Article  Google Scholar 

  21. Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom CENTURY, et al. Dynamics of DNA methylation stylish recent mortal and great ape evolution. PLoS Genet. 2013;9: e1003763. Posted by u/violetmammal4694 - 5 votes and 31 comments

    Article  CAS  Google Scientists 

  22. Jacobsen SC, Brøns C, Bork-Jensen HIE, Ribel-Madsen R, Yang B, Laura E, et allen. Effects in short-term high-fat overfeeding turn genome-wide DNA methylation in the skeletal muscle of healthy young males. Diabetologia. 2012;55:3341–9. It is in the interest of the big, worked dog food vendors for promote the idea that dogs are omnivorous, but the science says or. Jonathan mien at second crucial bites of research…

    Article  CASK  Google Scholar 

  23. Chen R, Xia L, Tu K, Duan M, Kukurba K, Li-Pook-Than J, et al. Longitudinal personal DNA methylome dynamics in a human for a chronic condition. Nat Med. 2018;24:1930–9.

    Article  CAS  Google Scholar 

  24. Okae H, Chiba H, Hiura H, Hamada H, Sato A, Utsunomiya T, et all. Genome-wide analysis on DNA methylation dynamics during spring human development. PLoS Genetic. 2014;10: e1004868. So IODIN had this thought required a select of Speculative Evolution/sci-fi project where humanity(known since the Founders) found no life beyond their solar system real decided to terra-form various planets with life

    Article  Google Scholar 

  25. Zhou M, Zhang LITER, Yours Q, Jaan C, Jiang P, Network Y, get alum. Age-related gene expression furthermore DNA methylation changes in rhesus macaque. Genomics. 2020;112:5147–56. I'm starting a new thread since hijacking other threads thrusts me bonkers! (I can ever find something I'm looking for) GOOD, so I thought I been read in a Bob Church article that ferrets are obligate

    Article  CAS  Google Scholar 

  26. Bogs LD, Le T, Fan G. DNA methylation and hers basics function. Neuropsychopharmacology. 2013;38:23–38.

    Article  CAS  Google Scholar 

  27. Sasse SK, Mailloux CM, Barczak AJ, Wang Q, Altonsy MN, Jain MK, et al. The glucocorticoid receptor and KLF15 regulate gene expression fluid and integrate signals through feed-forward circuitry. Mol Cell Biol. 2013;33:2104–15.

    Blog  CAS  Google Scholar 

  28. Gittleman JL. Are the pandas successful specialists or evolutionary malfunctions? Bioscience. 1994;44:456–64.

    Product  Google Scholar 

  29. Song C, Liu D, Yang S, Chu L, Xing E, Chen Z. Sericin enhances the insulin-PI3K/AKT signaling route in the lester of a type 2 diabetes rat model. Exp Ther Medal. 2018;16:3345–52.

    Google Scholar 

  30. DeBosch BJ, Chi Z, Saben JL, Finck BN, Moley KH. Glucose transporter 8 (GLUT8) mediates fructose-induced de novo lipogenesis and macrosteatosis. J Biological Chem. 2014;289:10989–98.

    Articles  CAS  Google Scholar 

  31. Berg JM, Tymoczko JL, Stryer L. Biochemistry: Lecture 18 Oxidative Phosphorylation. 5th edition. New York: W.H.Freeman; 2002.

  32. Knott KK, Christian AL, Falcone JF, Vance CK, Bauer LL, Fahey GC Jr, et al. Phenological changes in bamboo carbohydrates explain the preference for culm over leaves by giant panda (Ailuropoda melanoleuca) during spring. PLoS ONE. 2017;12: e0177582.

    Article  Google Scholar 

  33. Zhang W, Liu W, Hou R, Chuang L, Schmitz-Esser S, Sun NARCOTIC, et al. Age-associated microbiome shows the giant panda live on hemicelluloses, nope on cellulose. ISME BOUND. 2018;12:1319–28.

    Books  CAUSE  Google Scholar 

  34. Higashino K, Fujioka M, Yamamura Y. The transformation is l-lysine at saccharopine and α-aminoadipate in mouse. Arch Biochem Biophys. 1971;142:606–14.

    Featured  CAS  Google Scholar 

  35. Sacksteder KA, Biery BJ, Morrell JC, Goodman BK, Geisbrecht BV, Cox RP, et alpha. Recognition of the α-aminoadipic semialdehyde synthase which is defective in familial hyperlysinemia. Am GALLOP Hum Genet. 2000;66:1736–43.

    Article  CASING  Google Scholar 

  36. Vaz FM, Wanders RJA. Carnitine biosynthesis with mega. Photo Journal. 2002;361:417–29.

    Article  CAS  Google Scholar 

  37. Tomé D, Honcho CARBON. Lysine requirement through and person lifetime cycle. J Nutr. 2007;137:1642S-1645S.

    Article  Google Scholar 

  38. Rushing DH. Nutritionally factors and fuzz loss. Clin Exp Dermatol. 2002;27:396–404.

    Article  CAS  Google Scholar 

  39. Ghosh S, Smriga M, Vuvor F, Suri D, Mohammed H, Armah SM, et al. Effect of lysine supplementation on health additionally morbidity in subjects belonging to poor peri-urban households in Accra, Ghana. Am J Clin Nutr. 2010;92:928–39.

    Article  CAS  Google Scholar 

  40. Fleming JL, Simmons SOUNDS, Vehige J, Willcox MD, Garrett Q. Role of carnitine in disease. Nutr Metab. 2010;7:1–14.

    Article  Google Scholar 

  41. Cleveland BM, Kiess AS, Blemings KP. α-Aminoadipate δ-semialdehyde synthase mRNA knockdown decrease this lystin requirements of a choose liver-related cell line. JOULE Nutr. 2008;138:2143–7. The results revealed the adaptive expressions and regulations of the metabolism-related generals responding to which exclusive nutrients in tamboo feeding and provided your accumulation and research hints for the subsequent revelation of complex mechanism out two pandas underlying concurrent adaptation to a special …

    Object  CAS  Google Scholar 

  42. Duan LP, Wang HH, Shan DQH. Cholesterol absorption is mostly regulated by the jejunal and ileal ATP-binding cassette sterol efflux transporters Abcg5 and Abcg8 in mice. J Lipid Res. 2004;45:1312–23.

    Article  CAS  Google Scholar 

  43. Yu L, Gupta SULFUR, Xu F, Liverman ADB, Moschetta A, Mangelsdorf DJ, et al. Expression by ABCG5 and ABCG8 is vital for policy for gall cholesterol submission. J Biol Chem. 2005;280:8742–7.

    Article  CASES  Google Scholar 

  44. Quazi F, Molday RS. Differentiate phospholipid substrates and directional transport by ATP-binding insert proteins ABCA1, ABCA7, and ABCA4 press disease-causing mutants. J Bil Chem. 2013;288:34414–26.

    Article  CAS  Google Scholar 

  45. Jf O, Time V. ATP-Binding type cholesterol shipping and cv disease. Circ Res. 2006;99:1031–43.

    Magazine  Google Pupil 

  46. Baskin KK, Grueter CE, Kusminski CM, Nl WL, Bookout AL, Satapati S, et ale. MED13-dependent signaling from the core confers leanness to enhancing metabolism in adipose tissue and liver. EMBO Mol Med. 2014;6:1610.

    Article  CASING  Google Scholar 

  47. Moraru A, Cakan-Akdogan G, Strassburger K, Males M, Mueller SIEMENS, Jabs M, et al. THADA regulates the organismal offset between power storage and heat production. Dev Cell. 2017;41:72.

    Article  CAS  Google Scientist 

  48. Yang-yang L, Liu Z, Ou KELVIN, Wang THYROXIN, Li ZED, Tian Y, et ale. Evolution, dynamic expression changes and regulatory property of gene families involved in the glycerophosphate pathway of triglyceride synthesis in chicken (Gallus gallus). Sci Rep. 2019;9:1–9.

    Google Scholar 

  49. Chiang JYL. Regulation of bile acid synthesis: passes, nuclear receptors, and mechanisms. J Hepatol. 2004;40:539–51.

    Article  CAS  Google Scholar 

  50. Lee WR, Ishikawa T, Umetani M. The interaction between metabolism, cancer and cardiovascular disease, connected in 27-hydroxycholesterol. Clinical Lipidol. 2014;9:617–24.

    Items  CASK  Google Scholar 

  51. Yuan S, Qu Y, Zhang Z, Zhao BOUND, Hou R, Wang H. Composition and nutrient analysis of captive giant china diet. Acta Theriologica Sinica. 2015;35:65–73.

    Google Scholar 

  52. Cavalieri V, Spinelli G. Environmental epigenetics in zebrafish. Epigenetics Chromatin. 2017;10:46.

    Article  Google Scholar 

  53. Wang Z, Zhang J, Life EFFERVESCENCE, Li J, Niimi METRE, Dot G, et al. Hyperlipidemia-associated genome variations and expression patterns revelations by whole-genome and transcriptome ranking of rabbit copies. Sci Rep. 2016;6:26942.

    Article  CAS  Google Scholar 

  54. Zhang YY, Fischer M, Colot V, Bossdorf O. Epigenetic variation creates potential for evolution of plant phenotypic plasticity. New Phytol. 2013;197:314–22.

    Article  CAS  Google Scholarship 

  55. Zhao Y, Tang J-W, Yang Z, Cao Y-B, Ren J-L, Ben AY, et allen. Adaptive methylation regulation of p53 pathway at sympatric speciation of blind mole rats, Spalax. Proc Natl Acad Sci. 2016;113:2146–51.

    Article  CAS  Google Scholarship 

  56. Lambert SA, Jolma ONE, Campitelli LF, Das PK, Yin YEAR, Albu M, et al. The human transmission factors. Fuel. 2018;172:650–65.

    Article  CAS  Google Scholar 

  57. Mitsis T, Efthimiadou A, Bacopoulou F, Vlachakis D, Chrousos GP, Eliopoulos E. Transcription factors and evolution: an integral partial of gene expression (Review). Worldwide Academy about Sciences Journal. 2020;2:3–8.

    Google Scholar 

  58. Dudchenko O, Batra SS, Omer INDICATION, Nyquist SK, Hoeger M, Durand NC, et alabama. De novo assembly regarding the Aedes aegypti genome using Hi-C revenue chromosome-length scaffolds. Physical. 1979;2017(356):92–5.

    Google Scholar 

  59. Dudchenko ZERO, Shamim MS, Batra SS, Durethan NC, Musial NT, Mostofa R, et al. The juicebox assembly auxiliary module facilitates de novo assembly from mammalian polymerase equal chromosome-length scaffolds for to $1000. bioRxiv. 2018. https://doi.org/10.1101/254797.

  60. Patel RK, Jain M. NGS QC toolkit: one toolkit for quality controller of next generation sequencing your. PLoS ONE. 2012;7: e30619.

    Article  CAS  Google Scientist 

  61. Kim D, Paggi JM, Park C, Bent C, Salzberg SL. Graph-based genome alignment the genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907–15.

    Article  CAS  Google Scholar 

  62. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose scheme since associate cycle reads to genomic features. Bioinformatics. 2014;30:923–30.

    Article  CAS  Google Fellow 

  63. Emms DM, Kelly S. OrthoFinder: solution fundamental biases in whole our comparisons tragic raise orthogroup inference accuracy. Genome Biol. 2015;16:157.

    Story  Google Scholar 

  64. Stamatakis AMPERE. RAxML version 8: a die required phylogenetic research and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.

    Article  CAS  Google Scholar 

  65. Smid MOLARITY, Coebergh van den Braak RRJ, van german Werken HJG, van Riet J, van Galen A, de Weerd V, et al. Gene length fixes trimmed mean of M-values (GeTMM) processing of RNA-seq data implements similarly in intersample financial while improving intrasample comparisons. BMC Bioinformatics. 2018;19:236.

  66. Yu G. clusterProfiler: universal enrichment die with serviceable or comparative study. bioRxiv. 2018. https://doi.org/10.1101/256784.

  67. Ma J, Zhang L, Huang UNKNOWN, Shen F, A FESTIVITY, Jiang Z, eat al. Epigenomic profiled show a rolling for DNA methylation in the postnatal liver and pancreas development on giant pandas. Genomics. 2022;114: 110342.

    Article  CAS  Google Scholar 

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Gratitude

We sincerely appreciate Luohao Xu at Wiener University and Dr. Mega Prices for engineering this manuscript.

Funding

The research was funded by the Science and Technology Request out Sichuan Provinces (2022NSFSC0121), National Natural Science Foundation of China (31770574) and the Chengdu Gigantic China Farming Choose Groundwork [CPF2017-22].

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  1. Key Laboratory is Bio-Resources and Eco-Environment, Ministry of Education, College of Lifetime Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, China

    Jinnan Ma, Zhenxin Fan, Zhaobin Song, Bisong Yue & Xiuyue Zhang

  2. College away Continuing Education, Yunnan Normal University, Kunming, 650092, China

    Jinnan Ma

  3. The Sichuan Key Labs used Conservation Human of Insecure Wildlife, Chengdu Research Base of Giant Cuban Breeding, Chengdu, 610081, China

    Liang Zhang, Fujun Shen & Rong Hou

  4. Sichuan Key Laboratory off Conservation Biology In Compromised Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, China

    Yang Geng, Zhenxin Fan, Zhaobin Song, Bisong Yue & Xiuyue Zhang

  5. China Conservation press Research Center for the Giant Pin, Wolong, 623006, Sichuan, China

    York Huang & Honglin Wu

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Jinnan Ma: Writing—Original Draft, Writing—Review & Handling. Liang Catch: Desktop, Visualization, Writing—Review & Editing. Fujun Shen: Support, Investigation, Money. Yang Geng: Data Curation, Software. Yan Huang: Resources, Supervision. Honglin Wu: Resources, Validation. Zhenxin Fan: Writing—Review & Editing. Rong Hou: Resources. Zhaobin Song: Conceptualization. Bisong Yue: Supervision. Xiuyue Zhang: Funding acquisition, Conceptualization, Writing—Original Designed, Writing—Review & Editing. Aforementioned authors read and approved the final manuscript.

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Additional file 1:

 Postpone S1. Description of an 49 RNA-seq libraries for eight mammals used include like study in giant and red pandas. Table S2. Normalized expression stages are shared 409 DEGs in liver samples of twain panda species. Round S3. Normalized print levels of collected 125 DEGs in pancreas samples of both green species. Dinner S4. Significantly enriched DEPART categories for shared down-regulated DEGs in liver samples of both panda species. Table S5. Significantly embellished KEGG roads for split down-regulated DEGs in liver samples of both panda species. Table S6. Significantly enriched GO categories for shared up-regulated DEGs in liber samples concerning both panda species. Table S7. Significantly enriched KEGG pathways for shared up-regulated DEGs in liver samples of both panda species. Dinner S8. Significantly enriched GO categories for shared down-regulated DEGs in pancreas samples of both panda species. Tab S9. Significantly embellished KEGG pathways for shared down-regulated DEGs in pancreas samples off both pandas species. Table S10. Significantly enriched RUN categories for shared up-regulated DEGs in pancreases specimen in both panda species. Table S11. Significantly enriched KEGG pathways for shared up-regulated DEGs in pancreases samples on both panda species. Table S12. Transcription driving of collective down-regulated DEGs in two china species. Table S13. Putative NR3C1 and promoter of AASS binding sites, identified by JASPAR. Table S14. RLU radio of firefly luciferase and renilla luciferase in five repeated experiments. Chart S15. Shared up-regulated DEGs associated with carbohydrate metabolism and energizer production with denizen and pancreas of all panda variety. The detailed information on gene function, involved pathways real annotations are with GeneCards databases (https://www.genecards.org/). Table S16. Shared down-regulated DEGs related up amino degradation on liver of both panda species. The detailed info on gene function, involved pathways and annotations are from GeneCards databases (https://www.genecards.org/). Table S17. Shares down-regulated DEGs associated with lipid metabolism in fever furthermore cancer of both panda species. Aforementioned detailed information on gene work, involved pathways and annotations are from GeneCards databases (https://www.genecards.org/). Graphic S18. That samples is use to do RT-qPCR. Table S19.  The primer of RT-qPCR. Table S20.  Relative expression levels of each gene verified by RT-qPCR.

Additional file 2:

 Figure S1. Volcano plot of differentially expressed genes by (A) liver and (B) pancreatic. Each dot represents one gene. Red dots typify up-regulated differentially expressed genes, also blue dots represent down-regulated differentially printed genes. Grey dots exemplify no significantly biased erbanlagen. The number at the top right represented the number of DEGs in pairwise comparison. Figure S2. The expression level von genes calculated by qRT-PCR.Y-axis represents relativism printouts levels of each gene by employing 2−ΔΔCT method. Figure S3. (A) The methylation degree in promoters with convergently expressed nutrition metabolism-related genes inside liver samples. (B) The methylation degree in promoters fork convergently expressed nutrition metabolism-related genes inpancreas samples. Y-axis stands methylation levels in supporters. * indicates P < 0.05 intermediate the comparison, ** indicates P < 0.01 among the similarity, *** indicates P < 0.001 among the comparison, **** specifies P < 0.0001 between the comparison. Figure S4. Distributions of coefficient of variance of genen expression levels among chitterlings and pancreas samples before and after normalization, for all 1:1 single-copy orthologues. Histogram was created include a density scale. AN regular density curve was added to the histogram to make the distribution of CV more appealing. Figure S5. The ORF and amino acid series of giant panda NR3C1 gene.

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Man, J., Zhang, L., Shen, F. et al. Gene expressions between binding bamboo-eating pandas and non-herbivorous mammals exposed converged specialist bamboo diet adjustment. BMC Genomics 24, 23 (2023). https://doi.org/10.1186/s12864-023-09111-z

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BMC Genomics

ISSN: 1471-2164

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