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Genome-wide phylogenetic tree of giant and red pandas, and their convergent pseudothumbs. (A) Phylogenomic tree, divergence time (blue), and expansion (purple, +) and contraction (red, ‒) of gene family in red and giant pandas, and other six Eutherian species. Three divergence times (red node) were used as the calibration points for estimating divergence time. The estimated divergence times were showed with 95% confidence intervals (in parentheses). The posterior probabilities for each branch of the tree were showed. (B) Diagram of pseudothumb (pt) of red panda (Upper) and giant panda (Lower).
Source publication
Significance
The giant panda and red panda are obligate bamboo-feeders that independently evolved from meat-eating ancestors and possess adaptive pseudothumbs, making them ideal models for studying convergent evolution. In this study, we identified genomic signatures of convergent evolution associated with bamboo eating. Comparative genomic analyse...
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... 326 genes with convergent amino acid substitutions and excluding the third codon positions of exons, the constructed genome-wide phylogenetic tree confirmed recent molecular conclusions (7-9) that the giant panda belongs to the family Ursidae together with the polar bear, whereas the red panda and ferret belong to the superfamily Musteloidea ( Fig. 1). Based on the 133 genes evolving under the strict molecular clock, a divergence time of 47.5 Mya (95% confidence interval, 39.5∼54.4 Mya) between giant and red pandas was derived by using three calibration points ( Fig. 1). This result was slightly higher than previous molecular-based estimate of 43 Mya ...
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... to the family Ursidae together with the polar bear, whereas the red panda and ferret belong to the superfamily Musteloidea ( Fig. 1). Based on the 133 genes evolving under the strict molecular clock, a divergence time of 47.5 Mya (95% confidence interval, 39.5∼54.4 Mya) between giant and red pandas was derived by using three calibration points ( Fig. 1). This result was slightly higher than previous molecular-based estimate of 43 Mya ...
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... on homologous gene annotations by syntenic alignment across the eight species ( Fig. 1), 14,254 orthologous genes were used for genomic convergence and positive selection analyses. First, convergent amino acid substitutions between both pandas were identified based on Zhang and Kumar's method (19). Considering noise resulting from chance amino acid substitutions (6,20), we performed a statistical test to compare the ...
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... mice (SI Appendix, Table S25), high- lighting the uniqueness of these variations and their potential functional importance in pseudothumb development. Similarly, the centrosomal coiled-coil protein PCNT is also involved in primary cilia assembly by forming a complex with IFT proteins (e.g., IFT20, IFT57, IFT88) (Fig. 2C, Table 1, and SI Appendix, Fig. S10). PCNT modification could affect basal body localization of IFT proteins, thus inhibiting primary cilia assembly (30). We propose that con- vergent amino acid substitutions in the two genes may work syner- gistically for pseudothumb development in both pandas, although their effects on other aspects of skeletal development remain elu- ...
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... meet this nutritional challenge, pandas need to improve efficiency of nutrient absorption and utilization and, therefore, signatures of adaptive convergence related to essential nutrient utilization might be observed. Three genes (PRSS1, PRSS36, and CPB1) involved in dietary protein digestion showed adaptive convergence (Table 1 and SI Appendix, Fig. S10). All of these proteins belong to serine proteases and are secreted by the pancreas into the small intestine. Interestingly, both PRSS1 and PRSS36 are endopeptidases for proteolytic cleavage of Lys or Arg residues from the carboxyl ter- minal, whereas CPB1 is an exopeptidase and acts on preferential release of Lys or Arg from ...
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... and arachidonic acid are essential nutrients, they are either absent or their content in bamboo is much lower than in meat, nuts, or green plants ( SI Appendix, Tables S27 and S28). Four genes (ADH1C, CYP3A5, CYP4F2, and GIF) in- volved in utilization of these nutrients were identified to be under adaptive convergence (Table 1 and SI Appendix, Fig. S10). ADH1C and CYP3A5 are involved in the regulation of vitamin A metabo- lism that is essential to dark vision maintenance. ADH1C catalyzes conversion between retinal and retinol, whereas CYP3A5 is in- volved in the degradation of retinoic acids to prevent detrimental accumulation of excessive vitamin A (31). Vitamin A is needed by the ...
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... at night (10,33). Because vitamin A exists only in meat foods, both pandas must absorb dietary β-carotene as the source of vitamin A, although the content in bamboo is low. Therefore, the adaptive convergence of the two genes may improve the utilization of vitamin A, which may function to meet the need of maintaining dark vision (SI Appendix, Fig. ...
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... absorption efficiency (34). The cytochrome P450 enzyme CYP4F2 can catalyze arachidonic acid into 20-hydroxyeicosatetraenoic acid, an important bioactive substance for regulating vascular endothelial cells with antiangio- sclerosis activity (36), thus potentially alleviating the physiological consequences of vitamin B12 deficiency (SI Appendix, Fig. ...
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... TAS1R3 is an intact gene rather than a pseudogene in both pandas. Based on the change in the rate ratio (ω) of nonsynonymous to synonymous substitutions (SI Appendix, SI Materials and Methods), we infer that the functional constraint on TAS1R1 in red pandas was relaxed approximately 1.58 Mya (95% confidence interval, 0.1 ∼4.36 Mya) (SI Appendix, Fig. S12). The fossil records from sister lineages of the red panda (Pristinailurus bristoli and the genus Parailurus) suggest that the ailurines were partially herbivorous from the late Miocene (7 ∼4.5 Mya) (33). Thus, pseudogenization of TAS1R1 in red pandas may have occurred after its diet was at least partially herbivorous, as in giant ...
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... evolution has long interested evolutionary biologists. Classic examples include the wings of bats and birds, echolocation in bats and dolphins, and adaptation of marine mammals to ex- treme marine environments (1-3). Although the functional nature Table 1. ...
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... of Positively Selected Genes. Based on the MAF alignment se- quences from six Carnivora species (red panda, giant panda, polar bear, ferret, dog, and tiger), positive selections in the red panda and giant panda were tested under the reconstructed phylogenomic tree (Fig. 1A) by using PAML 4.8 (23). The branch- site model of codon evolution (53) was used with model = 2 and NSsites = 2. We compared model A (allows sites to be under positive selection; fix_omega = 0) with the null model A1 (sites may evolve neutrally or under purifying selection; fix_omega = 1 and omega = 1), with likelihood ratio tests (LRT) ...
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... Convergence Analysis. Convergent sites include both "parallel" and "convergent" sites as defined in ref. 19. In this study, ancestral protein se- quences were reconstructed for 14,254 orthologs among eight Eutherian spe- cies (Fig. 1A) by using the Codeml program in PAML 4.7. We identified convergent amino acid sites between giant and red pandas with the following Fig. 3. Convergent pseudogenization of umami receptor gene TAS1R1 between the giant and red pandas, as opposed to the polar bear, ferret, dog, and tiger. The giant panda has one 2-bp insertion on the third ...
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... Pseudogene Identification. To identify common pseudogenes in the red and giant panda genomes, we work with the precompiled MAF alignment file across eight Eutherian species (Fig. 1A). The MAF alignments with (i) at least five species present including two pandas, (ii) minimal sequence identity of 80%, and (iii) corresponding to human coding exon, were retrieved to check the presence of SNPs or indels that introduce premature stop codon or frame-shift mutation, and genomic positions with known heterozygous SNP or ...
Citations
... Despite belonging to Carnivora, they have both transitioned from a carnivorous diet to a specialized bamboo diet, a remarkable shift that has led to the emergence of convergent adaptive features. Notably, both species have developed pseudothumbs, enhancing their ability to grasp bamboo efficiently, a morphological convergence that underscores the profound impact of dietary specialization on evolutionary trajectories (Hu et al., 2017). This adaptation is paralleled by molecular convergences, such as the pseudogenization of taste receptor genes, the evolution of digestive enzymes, and adaptations of the gut microbiome to bamboo cellulose digestion and cyanide detoxification (Hu et al., 2017;Huang et al., 2018Huang et al., , 2021Li et al., 2010Li et al., , 2015McKenney et al., 2018;Zhang et al., 2018;Zhu et al., 2018). ...
... Notably, both species have developed pseudothumbs, enhancing their ability to grasp bamboo efficiently, a morphological convergence that underscores the profound impact of dietary specialization on evolutionary trajectories (Hu et al., 2017). This adaptation is paralleled by molecular convergences, such as the pseudogenization of taste receptor genes, the evolution of digestive enzymes, and adaptations of the gut microbiome to bamboo cellulose digestion and cyanide detoxification (Hu et al., 2017;Huang et al., 2018Huang et al., , 2021Li et al., 2010Li et al., , 2015McKenney et al., 2018;Zhang et al., 2018;Zhu et al., 2018). ...
... Extensively documented, the shared dietary specialization of giant and red pandas in bamboo, despite their belonging to different families, highlights convergent evolutionary outcomes driven by identical ecological pressures (Hu et al., 2017;Roberts & Gittleman, 1984;Wei et al., 1999). This offers a unique perspective on how environmental factors shape evolutionary paths across disparate lineages. ...
Epigenetic regulation plays an important role in the evolution of species adaptations, yet little information is available on the epigenetic mechanisms underlying the adaptive evolution of bamboo‐eating in both giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens). To investigate the potential contribution of epigenetic to the adaptive evolution of bamboo‐eating in giant and red pandas, we performed hepatic comparative transcriptome and methylome analyses between bamboo‐eating pandas and carnivorous polar bears (Ursus maritimus). We found that genes involved in carbohydrate, lipid, amino acid, and protein metabolism showed significant differences in methylation and expression levels between the two panda species and polar bears. Clustering analysis of gene expression revealed that giant pandas did not form a sister group with the more closely related polar bears, suggesting that the expression pattern of genes in livers of giant pandas and red pandas have evolved convergently driven by their similar diets. Compared to polar bears, some key genes involved in carbohydrate metabolism and biological oxidation and cholesterol synthesis showed hypomethylation and higher expression in giant and red pandas, while genes involved in fat digestion and absorption, fatty acid metabolism, lysine degradation, resistance to lipid peroxidation and detoxification showed hypermethylation and low expression. Our study elucidates the special nutrient utilization mechanism of giant pandas and red pandas and provides some insights into the molecular mechanism of their adaptive evolution of bamboo feeding. This has important implications for the breeding and conservation of giant pandas and red pandas.
... Both pandas consume high-nutrient milk during the suckling period, while they exclusively consume low-nutrient bamboo during the adult period. Their morphology, genome, gut microbiota, and gene expression patterns exhibit many convergent evolutionary characteristics [13][14][15][16][17][18][19]. Research on giant pandas showed that the high expression levels of genes related to cholesterol metabolism and protein digestion and absorption in their early stages of development may help meet their high energy needs for rapid growth and development, while the high expression levels of genes related to metabolism of carbohydrate, amino acid, and protein during the adult period may indicate their high metabolic levels [9]. ...
Red pandas evolved from carnivores to herbivores and are unique within Carnivora. Red pandas and carnivorous mammals consume milk during the suckling period, while they consume bamboo and meat during the adult period, respectively. Red pandas and carnivorous mammal ferrets have a close phylogenetic relationship. To further investigate the molecular mechanisms of dietary changes and nutrient utilization in red pandas from suckling to adult, comparative analysis of the whole transcriptome was performed on stomach tissues from red pandas and ferrets during the suckling and adult periods. The main results are as follows: (1) we identified ncRNAs for the first time in stomach tissues of both species, and found significant expression changes of 109 lncRNAs and 106 miRNAs in red pandas and 756 lncRNAs and 109 miRNAs in ferrets between the two periods; (2) up-regulated genes related to amino acid transport regulated by lncRNA-miRNA-mRNA networks may efficiently utilize limited bamboo amino acids in adult red pandas, while up-regulated genes related to amino acid degradation regulated by lncRNAs may maintain the balance of amino acid metabolism due to larger daily intakes in adult ferrets; and (3) some up-regulated genes related to lipid digestion may contribute to the utilization of rich nutrients in milk for the rapid growth and development of suckling red pandas, while up-regulated genes associated with linoleic acid metabolism regulated by lncRNA-miRNA-mRNA networks may promote cholesterol decomposition to reduce health risks for carnivorous adult ferrets. Collectively, our study offers evidence of gene expression adaptation and ncRNA regulation in response to specific dietary changes and nutrient utilization in red pandas during suckling and adult periods.
... Here, the evidence of convergent selection on the two genes based on SVs further substantiated their important roles in regulating reproductive traits. In fact, associations between convergently selected genes and the same or similar phenotypic traits of related species have been observed in several crops and animals, such as CHST11 and SDCCAG8 for fertility in goats and sheep [120], DYNC2H1 and PCNT for pseudothumb development in the giant panda and red panda [122], and KRN2 and OsKRN2 for grain yield in maize and rice [123]. Through integrated analyses of molecular evolution, GWAS, gene expression, and experimental validation data, we independently associated previously undetected SVs (e.g., deletions) in BMPR2 and BMPR1B to generate a two-stage evolutionary pattern of reproduction traits in sheep and goats. ...
Background
Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution.
Results
We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats.
Conclusions
Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
... By comparing the genomic structural characteristics of species occupying different positions in the evolutionary tree of life, researchers can obtain the sequence of nearest common ancestor. The study of sequence variation during species evolution, we can analyze the relationship of species evolution (Hu et al. 2017). Simultaneously, comparative genomes are also of great significance in explaining gene function, elucidating its role in adaptive evolution, and identifying the relationship between genotypes and phenotypes (Alfoldi and Lindblad-Toh 2013). ...
Lithocarpus litseifolius (Hance) Chun (L. litseifolius 1837) is an evergreen tree of the Fagaceae. It is commonly known as sweet tea and is a natural sweetener with high levels of dihydrochalcone. In addition, L. litseifolius is a precious medicinal material, and its phlorizin has a unique role in the treatment of diabetes. This investigation aimed to assemble and scrutinize the entire mitochondrial (mt) genome of L. litseifolius. The circular mt genome of L. litseifolius spans 573,177 bp and has a GC content of 45.61%. The mt genome of L. litseifolius comprises 61 genes, of which 21 are tRNA genes, 3 are rRNA genes, 36 are protein-coding genes (PCGs), and 1 is a pseudogene. Tetramer repeats made up 32.57% of all identified simple repeat sequences (SSRs), making them the most abundant type of SSR. 35 PCGs with a combined length of 32,208 bp were predicted to include a total of 461 RNA editing sites in the L. litseifolius mt genome. Besides, nine homologous genes between the chloroplast and mt genomes of L. litseifolius were identified. Furthermore, this study demonstrated that while plant mt genome sizes vary considerably, the GC content of these genomes has remained largely constant. The most conservative genes are atp6, rps1, ccmC, rpl2, nad4, nad7, and trnY-GTA. The phylogenetic analysis confirmed that L. litseifolius was genetically more closely related to Quercus variabilis. This study establishes the groundwork for investigations on the systematic evolution, genetic variability, and breeding of L. litseifolius.
... High-throughput sequencing nowallows usto address whether, and to what degree, convergent phenotypes at different degrees of similarityevolve along the same genomic pathways (Sackton and Clark 2019), with varying results from insular avian systems (Lamichhaney et al. 2015;Estandía et al. 2023b) as well as other animals (Foote et al. 2015;Hu et al. 2017;Kratochwil et al. 2018;Winchell et al. 2023). This will also allow us to better understand complex differentiation and speciation scenarios, where in situ evolutionary radiation can be hard to distinguish from intricate scenarios of repeated island colonization (Warren et al. 2003;Sangster et al. 2022;Stervander et al. 2022) or where introgressive hybridization can lead to the incorrect inference of evolutionary history Stervander et al. 2022). ...
... In order to adapt to exclusive feeding on bamboo, which is a low-fat, relatively poorquality food, the red panda has undergone a series of adaptive changes in morphology, behaviour, ecology, genetics and intestinal microbes, including the development of pseudothumbs, well-developed zygomatic arches, modified sweet taste receptor gene TAS1R1 and the consumption of high-nutrient-content bamboo leaves and bamboo shoots [29,31,44,45]. The red panda has not only adapted to feeding on high-fibre, low-nutrient bamboo by optimizing the composition and function of its gut microflora but has also formed special gut microbes to adapt to the consumption of bamboo with high secondary metabolite contents [18,29,31]. ...
Animals can adapt to unique feeding habits through changes in the structure and function of the gut microflora. However, the gut microflora is strongly influenced by the evolutionary relationships between the host, nutritional intake, intake of microorganisms, etc. The red panda (Ailurus fulgens), an herbivorous carnivore, has adapted to consuming bamboo through seasonal foraging strategies and optimization of the composition and function of its gut microflora during long-term evolution. However, to date, studies of the gut bacteria of the red panda have mainly focused on the composition, diversity and function of the gut microflora of captive individuals. There are a lack of studies on how the wild red panda adapts to the consumption of bamboo, which is high in fibre and low in nutrients, through the gut microflora. This paper reviews the technology and methods used in published studies investigating the gut microflora of the red panda, as well as the composition, diversity and function of the identified microbes and the influencing factors. Furthermore, this paper suggests future research directions regarding the methodology employed in analyzing the red panda gut microflora, the interplay between gut microflora and the health of the red panda, the red panda’s adaptation to its gut microflora, and the implications of these studies for the management and conservation of wild red pandas. The goal of this review is to provide a reference for the protection of wild red pandas from the perspective of the gut microflora.
... This phenomenon of convergent phenotypic evolution serves as a powerful framework to uncover the genetic underpinnings of adaptations to specific environments, as these phenotypic convergences commonly emerge due to parallel selective pressures. With the increasing accessibility of genomic datasets of diverse species, a growing body of recent studies on convergent phenotypic evolution has unveiled remarkable genomic similarities across distinct lineages [3][4][5][6][7][8][9]. Convergent phenotypic evolution is hypothesized to be associated with various genetic mechanisms of genomic convergences. ...
... For instance, a recent comparative genomics study between bamboo-eating giant and red pandas identified convergent amino acid substitutions in two limb development genes, DYNC2H1 and PCNT. Specifically, one of the two convergent amino acid sites is R3128K in DYNC2H1, and the amino acid K only occurs in giant and red pandas [7]. Extensive studies aimed at identifying molecular evolutionary patterns linked to convergent phenotypic evolution have yielded different levels of genomic convergences. ...
... For decades, studies on genomic convergences have primarily concentrated on the evolutionary dynamics of proteincoding genes [1][2][3][4][7][8][9]. By contrast, recent comparative genomic studies have begun to focus on the molecular evolution of non-coding regions across the genomes of diverse species, Figure 1. ...
... The microbial composition is influenced by host genetic factors (Kurilshikov et al., 2021), disease (Sanchez et al., 2015), diet, and gender (He et al., 2019). Bamboo rats mainly feed on bamboo, a low-nutrition food with approximately 70-80% of its composition being lignocellulosic components (Hu et al., 2017) that the single-stomach mammal cannot digest. Their ability to digest cellulose and lignin in bamboo largely depends on the composition of their gut microbiota (Xiao et al., 2022), which, consequently, may play an important role in their adaptation to digesting lignocellulose-based diets. ...
Introduction
Bamboo rats are rodents that eat bamboo, and their robust capacity for bamboo digestion is directly correlated with their gut flora. Chinese bamboo rat (Rhizomys sinensis) is a common bamboo rat in Chinese central and southern regions. As a single-stomach mammal, bamboo rats are a famous specificity bamboo-eating animal and their intestinal microbial composition may also play a key role in the digestion of cellulose and lignin. So, the gut microbiota of bamboo rat may play an important role in the adaptation of bamboo rats for digesting lignocellulose-based diet.
Methods
To study the microbiome differences of bamboo rats from different sexes, the microbial genomic DNA was extracted from each fecal sample and the V4 region of 16S rRNA genes was amplified and sequencing on an IlluminaHiSeq6000 platform. The operational taxonomic units (OTUs) were classified, the OTUs in different sexes was identified and compared at phylum and genus levels. For isolation and screening of cellulose degradation bacteria from bamboo rats, fresh feces from randomly selected bamboo rats were collected and used for the isolation and screening of cellulose degradation bacteria using Luria Bertani (LB) Agar medium containing Carboxymethyl cellulose. The cellulase activity, biochemical characterization and phylogenetic analysis of the purified bacteria strains were characterized.
Results and discussion
A total of 3,833 OTUs were classified. The total microbial diversity detected in the female and male rats was 3,049 OTUs and 3,452 OTUs, respectively. The Shannon index revealed significant differences between the two groups (p < 0.05), though they were all captive and had the same feeding conditions. At the phylum level, Firmicutes, Bacteroidota, and Proteobacteria were prominent in the microbial community. At the genus level, the microbial community was dominated by Lachnospiraceae, Lactobacillus, Bacteroides, and Prevotella, but there was a significant difference between the two groups of bamboo rats; ~90 bacteria genus in the female group was significantly higher than the male group. Among them, Bacteroides, Colidextribacter, and Oscillibacter were significantly higher genera, and the genera of Lachnoclostridium, Oscillibacter, and Papillibacter had the highest FC value among the male and female bamboo rats. The KEGG function annotation and different pathways analysis revealed that membrane transport, carbohydrate metabolism, and amino acid metabolism were the most enriched metabolic pathways in the two groups, and multiple sugar transport system permease protein (K02025 and K02026), RNA polymerase sigma-70 factor (K03088), and ATP-binding cassette (K06147) were the three different KEGG pathways (p < 0.05). Two cellulose degradation bacteria strains—Bacillus subtilis and Enterococcus faecalis—were isolated and characterized from the feces of bamboo rats.
... For the CCS method, ancestral protein sequences were first reconstructed for single-copy orthologs detected among eight species using the Codeml program in the PAML (v4.8) (Yang 2007) package. Observed convergent amino acid sites among M. electricus, E. electricus, and P. kingsleyae with rules as follow (Hu et al. 2017): (i) the amino acid residues of both the extant target lineages were identical; (ii) amino acid change was inferred to have occurred between the extant target lineages and the most recent common ancestor (MRCA) of each two of them. ...
The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes.
Supplementary Information
The online version contains supplementary material available at 10.1007/s42995-023-00197-8.
... Although giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) both are carnivores, they shifted to feeding on bamboo about the late Miocene (around 4.5 Mya) (Zhao et al., 2010;Hu et al., 2017). Bamboo is an exceptional food, with high fiber and low fat as well as a deficiency of some essential nutrients such as lysine (Hu et al., 2017). ...
... Although giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) both are carnivores, they shifted to feeding on bamboo about the late Miocene (around 4.5 Mya) (Zhao et al., 2010;Hu et al., 2017). Bamboo is an exceptional food, with high fiber and low fat as well as a deficiency of some essential nutrients such as lysine (Hu et al., 2017). In addition, bamboo is rich in plant secondary metabolites (Zhu et al., 2018). ...
... In addition, bamboo is rich in plant secondary metabolites (Zhu et al., 2018). After shifting from a meat diet to a specialized bamboo diet, giant and red pandas have evolved many adaptive physiological features, such as well-developed jaw muscles and molars (Figueirido et al., 2012), pseudogenization of the fresh taste receptor gene (T1R1) on the genome of giant and red pandas (Li et al., 2010), the six-finger structure of giant and red pandas to facilitate grasping bamboo stems (Hu et al., 2017), and adaptive evolution of intestinal flora (Zhu et al., 2018). In any case, giant and red pandas still retain carnivore digestive features, such as having a simple digestive system and not evolving a herbivore-specific digestive tract such as the ruminant stomach and cecum (Li et al., 2010;Hu et al., 2017;McKenney et al., 2018;Zhu et al., 2018). ...
The changes in the expression of genes related to digestion and metabolism may be various in different dietary mammals from juvenile to adult, especially, the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), which were once carnivores but have shifted to being specialized bamboo eaters, are unique features of their changes are more unclear. To elucidate the changing patterns of gene expression related to digestion and metabolism from juvenile to adult in different dietary mammals, we performed transcriptome analysis of the liver or pancreas in giant and red pandas, herbivorous rabbits (Oryctolagus cuniculus) and macaques (Macaca mulatta), carnivorous ferrets (Mustela putorius furo), and omnivorous mice (Mus musculus) from juvenile to adult. During the transition from juvenile to adulthood, giant and red pandas, as well as rabbits and macaques, show significant upregulation of key genes for carbohydrate metabolism, such as starch hydrolysis and sucrose metabolism, and unsaturated fatty acid metabolism, such as linoleic acid, while there is no significant difference in the expression of key genes for fatty acid β-oxidation. A large number of amino acid metabolism related genes were upregulated in adult rabbits and macaques compared to juveniles. While adult giant and red pandas mainly showed upregulation of key genes for arginine synthesis and downregulation of key genes for arginine and lysine degradation. In adult stages, mouse had significantly higher expression patterns in key genes for starch hydrolysis and sucrose metabolism, as well as lipid and protein metabolism. In contrast to general expectations, genes related to lipid, amino acid and protein metabolism were significantly higher expressed in adult group of ferrets, which may be related to their high metabolic levels. Our study elucidates the pattern of changes in the expression of genes related to digestion and metabolism from juvenile to adult in different dietary mammals, with giant and red pandas showing adaptations associated with specific nutritional limitations of bamboo.
