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

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          Abstract

          The giant panda ( Ailuropoda melanoleuca ) is one of the world’s most endangered mammals and remains threatened as a result of intense environmental and anthropogenic pressure. The transformation and specialization of the giant panda’s diet into a herbivorous diet have resulted in unique adaptabilities in many aspects of their biology, physiology and behavior. However, little is known about their adaptability at the molecular level. Through comparative analysis of the giant panda’s genome with those of nine other mammalian species, we found some genetic characteristics of the giant panda that can be associated with adaptive changes for effective digestion of plant material. We also found that giant pandas have similar genetic characteristics to carnivores in terms of olfactory perception but have similar genetic characteristics to herbivores in terms of immunity and hydrolytic enzyme activity. Through the analysis of gene family expansion, 3752 gene families were found, which were enriched in functions such as digestion. A total of 93 genes under positive selection were screened out and gene enrichment identified these genes for the following processes: negative regulation of cellular metabolic process, negative regulation of nitrogen compound metabolic process, negative regulation of macromolecule metabolic process and negative regulation of metabolic process. Combined with the KEGG pathway, it was found that genes such as CREB3L1, CYP450 2S1, HSD11B2, LRPAP1 play a key role in digestion. These genes may have played a key role in the pandas’ adaptation to its bamboo diet.

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          Most cited references 28

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          PAML: a program package for phylogenetic analysis by maximum likelihood

           Ziheng Yang (1997)
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            A cellular microRNA mediates antiviral defense in human cells.

            In eukaryotes, 21- to 24-nucleotide-long RNAs engage in sequence-specific interactions that inhibit gene expression by RNA silencing. This process has regulatory roles involving microRNAs and, in plants and insects, it also forms the basis of a defense mechanism directed by small interfering RNAs that derive from replicative or integrated viral genomes. We show that a cellular microRNA effectively restricts the accumulation of the retrovirus primate foamy virus type 1 (PFV-1) in human cells. PFV-1 also encodes a protein, Tas, that suppresses microRNA-directed functions in mammalian cells and displays cross-kingdom antisilencing activities. Therefore, through fortuitous recognition of foreign nucleic acids, cellular microRNAs have direct antiviral effects in addition to their regulatory functions.
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              The KEGG database.

              KEGG (http://www.genome.ad.jp/kegg/) is a suite of databases and associated software for understanding and simulating higher-order functional behaviours of the cell or the organism from its genome information. First, KEGG computerizes data and knowledge on protein interaction networks (PATHWAY database) and chemical reactions (LIGAND database) that are responsible for various cellular processes. Second, KEGG attempts to reconstruct protein interaction networks for all organisms whose genomes are completely sequenced (GENES and SSDB databases). Third, KEGG can be utilized as reference knowledge for functional genomics (EXPRESSION database) and proteomics (BRITE database) experiments. I will review the current status of KEGG and report on new developments in graph representation and graph computations.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2020
                01 April 2020
                : 923
                : 141-156
                Affiliations
                [1 ] Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
                [2 ] Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
                [3 ] Sichuan Academy of Giant Panda, Chengdu, 610081, China
                [4 ] Department of Biomedical Sciences, Iowa State University, Ames 50011, IA, USA
                Author notes
                Corresponding author: Hairui Wang ( wang200108143@ 123456aliyun.com )

                Academic editor: J. Maldonado

                Article
                39665
                10.3897/zookeys.923.39665
                7142162
                Xin He, Walter H. Hsu, Rong Hou, Ying Yao, Qin Xu, Dandan Jiang, Longqiong Wang, Hairui Wang

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Funding
                Giant Panda Breeding Research Foundation Sichuan Science and Technology Program
                Categories
                Research Article
                Ailuropodidae
                Carnivora
                Chordata
                Placentalia
                Theria
                Genetics
                Molecular Genetics
                Cenozoic
                Asia
                Central Asia
                China

                Animal science & Zoology

                adaptation, bamboo diet, dietary transition, digestion, feeding habits

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