Comparative genomics reveals bamboo feeding adaptability in the giant panda (Ailuropoda melanoleuca)

He, Xin; Hsu, Walter H.; Hou, Rong; Yao, Ying; Xu, Qin; Jiang, Dandan; Wang, Longqiong; Wang, Hairui

doi:10.3897/zookeys.923.39665

Cited by 5 publications

(6 citation statements)

References 41 publications

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“…Mannans are a major group of hemicellulose, and bamboo contains a large amount of hemicellulose, which is difficult for giant pandas to digest and utilize. The hypomethylation and higher expression of these genes related to polysaccharides or oligosaccharides hydrolysis facilitate the digestion and absorption of hemicellulose components in bamboo for giant pandas, which is also similar to the result of He et al (2020).…”

Section: Discussionmentioning

confidence: 57%

Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet‐driven adaptive evolution

Chen,

Ma,

et al. 2024

Evolutionary Applications

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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.

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Section: Discussionmentioning

confidence: 57%

Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet‐driven adaptive evolution

Chen,

Ma,

et al. 2024

Evolutionary Applications

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“…The giant panda’s conversion to an herbivorous diet has produced unique adaptations in many aspects, for instance, pseudothumbs and a low energy metabolism rate, to accommodate to low-nutrient and low-energy consumption food [ 13 ]. The comparative genomic analysis revealed that the giant panda has similar genetic characteristics to carnivores in terms of olfaction [ 14 ]. The giant panda can use smell cues in urine and body odor to distinguish relatives from non-relatives.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of Olfactory Receptor Repertoires Sheds Light on the Diet Adaptation of the Bamboo-Eating Giant Panda Based on the Chromosome-Level Genome

Zhou

Liu

Zhao

et al. 2023

Animals

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The giant panda (Ailuropoda melanoleuca) is the epitome of a flagship species for wildlife conservation and also an ideal model of adaptive evolution. As an obligate bamboo feeder, the giant panda relies on the olfaction for food recognition. The number of olfactory receptor (OR) genes and the rate of pseudogenes are the main factors affecting the olfactory ability of animals. In this study, we used the chromosome-level genome of the giant panda to identify OR genes and compared the genome sequences of OR genes with five other Ursidae species (spectacled bear (Tremarctos ornatus), American black bear (Ursus americanus), brown bear (Ursus arctos), polar bear (Ursus maritimus) and Asian black bear (Ursus thibetanus)). The giant panda had 639 OR genes, including 408 functional genes, 94 partial OR genes and 137 pseudogenes. Among them, 222 OR genes were detected and distributed on 18 chromosomes, and chromosome 8 had the most OR genes. A total of 448, 617, 582, 521 and 792 OR genes were identified in the spectacled bear, American black bear, brown bear, polar bear and Asian black bear, respectively. Clustering analysis based on the OR protein sequences of the six species showed that the OR genes distributed in 69 families and 438 subfamilies based on sequence similarity, and the six mammals shared 72 OR gene subfamilies, while the giant panda had 31 unique OR gene subfamilies (containing 35 genes). Among the 35 genes, there are 10 genes clustered into 8 clusters with 10 known human OR genes (OR8J3, OR51I1, OR10AC1, OR1S2, OR1S1, OR51S1, OR4M1, OR4M2, OR51T1 and OR5W2). However, the kind of odor molecules can be recognized by the 10 known human OR genes separately, which needs further research. The phylogenetic tree showed that 345 (about 84.56%) functional OR genes were clustered as Class-II, while only 63 (about 15.44%) functional OR genes were clustered as Class-I, which required further and more in-depth research. The potential odor specificity of some giant panda OR genes was identified through the similarity to human protein sequences. Sequences similar to OR2B1, OR10G3, OR11H6 and OR11H7P were giant panda-specific lacking, which may be related to the transformation and specialization from carnivore to herbivore of the giant panda. Since our reference to flavoring agents comes from human research, the possible flavoring agents from giant panda-specific OR genes need further investigation. Moreover, the conserved motifs of OR genes were highly conserved in Ursidae species. This systematic study of OR genes in the giant panda will provide a solid foundation for further research on the olfactory function and variation of the giant panda.

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“…Nie et al argued that giant pandas maintain a low metabolic level through reductions in their activity levels, a shrinkage of major energy consuming organs, and a decline in thyroid hormone levels ( 2 ). Despite numerous studies on giant panda genomics ( 3 ), transcriptomics ( 4 , 5 ), and gut microbiome composition ( 6 ), it is unclear how pandas digest bamboo with a low metabolic rate. It is also uncertain how metabolic characteristics change with increasing age, particularly during the transitionary period from a milk-based diet in cubs to a bamboo-based diet in young pandas.…”

Section: Introductionmentioning

confidence: 99%

Age-related alterations in metabolome and microbiome provide insights in dietary transition in giant pandas

Liu,

Li,

Zhong

et al. 2023

mSystems

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We conducted UPLC-MS-based metabolomics, 16S rRNA, and metagenome sequencing on the fecal samples of 44 captive giant pandas ( Ailuropoda melanoleuca ) from four age groups (i.e., Cub, Young, Adult, and Old) to comprehensively understand age-related changes in the metabolism and gut microbiota of giant pandas. We characterized the metabolite profiles of giant pandas based on 1,376 identified metabolites, with 152 significantly differential metabolites (SDMs) found across the age groups. We found that the metabolites and the composition/function of the gut microbiota changed in response to the transition from a milk-dominant diet in panda cubs to a bamboo-specific diet in young and adult pandas. Lipid metabolites such as choline and hippuric acid were enriched in the Cub group, and many plant secondary metabolites were significantly higher in the Young and Adult groups, while oxidative stress and inflammatory related metabolites were only found in the Old group. However, there was a decrease in the α-diversity of gut microbiota in adult and old pandas, who exclusively consume bamboo. The abundance of bacteria related to the digestion of cellulose-rich food, such as Firmicutes, Streptococcus, and Clostridium, significantly increased from the Cub to the Adult group, while the abundance of beneficial bacteria such as Faecalibacterium , Sarcina, and Blautia significantly decreased. Notably, several potential pathogenic bacteria had relatively high abundances, especially in the Young group. Metagenomic analysis identified 277 CAZyme genes including cellulose degrading genes, and seven of the CAZymes had abundances that significantly differed between age groups. We also identified 237 antibiotic resistance genes (ARGs) whose number and diversity increased with age. We also found a significant positive correlation between the abundance of bile acids and gut bacteria, especially Lactobacillus and Bifidobacterium . Our results from metabolome, 16S rRNA, and metagenome data highlight the important role of the gut microbiota-bile acid axis in the regulation of age-related metabolism and provide new insights into the lipid metabolism of giant pandas. IMPORTANCE The giant panda is a member of the order Carnivora but is entirely herbivorous. The giant panda’s specialized diet and related metabolic mechanisms have not been fully understood. It is therefore crucial to investigate the dynamic changes in metabolites as giant pandas grow and physiologically adapt to their herbivorous diet. This study conducted UPLC-MS-based metabolomics 16S rRNA, and metagenome sequencing on the fecal samples of captive giant pandas from four age groups. We found that metabolites and the composition/function of gut microbiota changed in response to the transition from a milk-dominant diet in cubs to a bamboo-specific diet in young and adult pandas. The metabolome, 16S rRNA, and metagenome results highlight that the gut microbiota-bile acid axis has an important role in the regulation of age-related metabolism, and our study provides new insights into the lipid metabolism of giant pandas.

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Comparative genomics reveals bamboo feeding adaptability in the giant panda (Ailuropoda melanoleuca)

Cited by 5 publications

References 41 publications

Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet‐driven adaptive evolution

Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet‐driven adaptive evolution

Comparative Analysis of Olfactory Receptor Repertoires Sheds Light on the Diet Adaptation of the Bamboo-Eating Giant Panda Based on the Chromosome-Level Genome

Age-related alterations in metabolome and microbiome provide insights in dietary transition in giant pandas

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