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Genomic organization and evolution of ruminant lysozyme c genes

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Zoological Research 2015年第1期36卷 1-17页

作者： david m.irwin Department of Laboratory medicine and Pathobiology University of Toronto Banting and Best Diabetes Centre University of Toronto

Ruminant stomach lysozyme is a long established model of adaptive gene evolution. Evolution of stomach lysozyme function required changes in the site of expression of the lysozyme c gene and changes in the enzymatic properties of the enzyme. In ruminant mammals, these changes were associated with a change in the size of the lysozyme c gene family. The recent release of near complete genome sequences from several ruminant species allows a more complete examination of the evolution and diversification of the lysozyme c gene family. Here we characterize the size of the lysozyme c gene family in extant ruminants and demonstrate that their pecoran ruminant ancestor had a family of at least 10 lysozyme c genes, which included at least two pseudogenes. Evolutionary analysis of the ruminant lysozyme c gene sequences demonstrate that each of the four exons of the lysozyme c gene has a unique evolutionary history, indicating that they participated independently in concerted evolution. These analyses also show that episodic changes in the evolutionary constraints on the protein sequences occurred, with lysozyme c genes expressed in the abomasum of the stomach of extant ruminant species showing the greatest levels of selective constraints.

关键词： lysozyme ruminant evolutionary Genomic extant stomach genomic constraints Ailuropoda duplication

Comparative study of gut microbiota from captive and confiscatedrescued wild pangolins

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Journal of Genetics and Genomics 2021年第9期48卷 825-835页

作者： Chunbing Liu Jingyang Hu Yajiang Wu david m.irwin Wu Chen Zhigang Zhang Li Yu State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan UniversityKunming 650091China Guangzhou Zoo&Guangzhou Wildlife Research Center Guangzhou 510070China Department of Laboratory medicine and Pathobiology University of TorontoTorontoOntario M5S 1A8Canada

Pangolins are among the most critically endangered animals due to widespread poaching and worldwide trafficking. Captive breeding is considered to be one way to protect them and increase the sizes of their populations. However, comparative studies of captive and wild pangolins in the context of gut microbiota are rare. Here, the gut microbiome of captive and confiscated-rescued wild pangolins is compared, and the effects of different periods of captivity and captivity with and without antibiotic treatment are *** show that different diets and periods of captivity, as well as the application of antibiotic therapy, can alter gut community composition and abundance in pangolins. Compared to wild pangolins, captive pangolins have an increased capacity for chitin and cellulose/hemicellulose degradation, fatty acid metabolism, and short-chain fatty acid synthesis, but a reduced ability to metabolize exogenous substances. In addition to increasing the ability of the gut microbiota to metabolize nutrients in captivity, captive breeding imposes some risks for survival by resulting in a greater abundance of antibiotic resistance genes and virulence factors in captive pangolins than in wild pangolins. Our study is important for the development of guidelines for pangolin conservation, including health assessment, disease prevention, and rehabilitation of wild pangolin populations.

关键词： Pangolin Gut microbiome Captivity Antibiotic resistance genes Virulence factors

Rapid Evolution of the mammalian HILS1 Gene and the Nuclear Condensation Process during mammalian Spermiogenesis

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Journal of Genetics and Genomics 2013年第1期40卷 55-59页

作者： Yanhua Su Dongdong Wu Weiping Zhou david m.irwin Yaping Zhang Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for microbial Resources of the ministry of Education Yunnan University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Department of Laboratory medicine and Pathobiology University of Toronto Banting and Best Diabetes Centre University of Toronto

many genes associated with reproduction show rapid evolution across diverse animal groups, a result commonly due to adaptive evolution driven by positive selection （Swanson and Vacquier, 2002）. Different theories have been proposed to explain the elevated rates of evolution （Swanson and Vacquier, 2002）, including sperm competition, where sperm compete to fertilize eggs leading to the proteins in the sper- matozoa adaptively evolving to increase their ability to fertilize eggs; sexual conflict, where the egg experiences a loss of fitness when sperm are too abundant; sexual selection, where eggs bind sperm carrying adaptive alleles （Palumbi, 1999）; and cryptic female choice （reviewed in Swanson and Vacquier, 2002）.

关键词： Rapid Evolution of the mammalian HILS1 Gene and the Nuclear Condensation Process during mammalian Spermiogenesis HILS gene

Diversification of Sisorid catfishes(Teleostei: Siluriformes)in relation to the orogeny of the Himalayan Plateau

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Science Bulletin 2016年第13期61卷 991-1002页

作者： Chuanjiang Zhou Xuzhen Wang Xiaoni Gan Yaping Zhang david m.irwin Richard L.mayden Shunping He Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of HydrobiologyChinese Academy of Sciences Key Laboratory of Freshwater Fish Reproduction and Development (Southwest University) Ministry of EducationSchool of Life Science Southwest University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences College of Fisheries Henan Normal University Department of Laboratory medicine and Pathobiology University of Toronto Banting and Best Diabetes Centre University of Toronto Department of Biology 3507 Laclede Ave. Saint Louis University

Abstract Sisorid catfishes are primarily limited in distribution to rivers of the Himalayan region and Tibetan Plateau. These species have external morphologies that are adapted for extremely fast-flowing riverine systems. Given the diversity of the group and the above qualities of these catfishes, this lineage serves as an ideal group for inferring the geological history of this region based on their phylogenetic relationships reflecting evolu- tionary history. We sequenced the complete mitochondrial genome and four nuclear genes of representative sisorids distributed across river systems in China. Phylogenetic analyses strongly support the monophyly of the Sisoridae and the glyptosternoids. An analysis of the reconstructed ancestral states derived from inferred genealogical relationships suggests that the evolution of this lineage was accompanied by convergent evolution in morphological traits that were presumably in response to environmental pressure involving the rapid flowing river system that were generated during the uplift of the Tibetan Plateau （UTP）. molecular dating indicates that the Chinese sisorids and the glyptosternoids originated at the later miocene （~ 10.9-9.8 mya）, and with further biogeographic analyses indicates that the species of Sisoridae likely originated from a widely distributed ancestor. moreover, the divergence of the Sisoridae in China can be divided into two phases consis- tent with the UTP. All of these results indicate that the diversification and dispersal events in this lineage occurred as a result of drainage systems formed during and after the UTP in the late miocene and Quaternary periods.

关键词： Phylogeny. Diversification and dispersal.Biogeography - Divergence time estimation ~ TibetanPlateau ~ Sisoridae ~ Catfish

QcReads:An Adapter and Quality Trimming Tool for Next-Generation Sequencing Reads

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Journal of Genetics and Genomics 2013年第12期40卷 639-642页

作者： Yunfei ma Haibing Xie Xuman Han david m.irwin Ya-Ping Zhang School of Life Sciences University of Science and Technology of China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences University of Chinese Academy of Sciences Department of Laboratory medicine and Pathobiology University of Toronto

With the advent of next-generation sequencing （NGS） tech-nologies, it is possible to obtain huge amount of genome or transcriptome sequence with high coverage. NGS technologies are now extensively used in various fields such as genetics （Feuillet et al., 2011; Young et al., 2012; Ling et al., 2013） and clinical medicine （Kwon and Goate, 2000; Pflueger et al., 2011;

关键词： length QcReads

Nocturnal to Diurnal Transition in the Common Ancestor of Haplorrhines:Evidence from Genomic-Scan for Positively Selected Genes

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Journal of Genetics and Genomics 2015年第1期42卷 33-37页

作者： Xue Cao Yan-Bo Sun david m.irwin Guo-Dong Wang Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology University of Chinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences Department of Laboratory medicine and Pathobiology University of TorontoI King's College CircleTorontoOntario M5S 1A8Canada Laboratory for Conservation and Utilization of Bio-resources Yunnan University

Transition from a nocturnal to a diurnal lifestyle represents a major shift in primate evolution, plays a central role in the adaptation of these species to new habitats, and is involved in modifications to their physiological and social behaviors （Heesy and Ross, 2001; Shultz et al., 2011）. However, two core problems concerning the circadian rhythm transition re- mains unresolved. First, there is controversy concerning the activity pattern of the ancestral primate （Heesy and Ross, 2001; Tan et al., 2005）. Second, the transition process for circadian rhythm in primate evolutionary history is unre- solved. Although most research suggests that primates trans- formed from a nocturnal to a diurnal circadian rhythm in the lineage leading to the common ancestor of the anthropoids or the haplorrhines （anthropoids and tarsier）（Ross, 2000; Heesy and Ross, 2001）, evidence has been insufficient to determine whether this occurred in the lineage leading to the common ancestor of the haplorrhines or the anthroooids.

关键词： Nocturnal to Diurnal Transition in the Common Ancestor of Haplorrhines

Birth-and-death evolution of ribonuclease 9 genes in Cetartiodactyla

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Science China(Life Sciences) 2023年第5期66卷 1170-1182页

作者： Datian Lang Xiaoping Wang Chunbing Liu Weihang Geng david m.irwin Shanyuan Chen Chunqing Li Li Yu Heng Xiao School of Life Sciences Yunnan UniversityKunming 650500China School of Ecology and Environmental Science Yunnan UniversityKunming 650091China State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Yunnan UniversityKunming 650091China Biodiversity Research Center of Wumeng mountain Department of Agronomy and Life ScienceZhaotong UniversityZhaotong 657000China Department of Laboratory medicine and Pathobiology University of TorontoTorontoOntario M5S 1A8Canada

RNase9 plays a reproductive function and has been recognized as an important member of the ribonuclease(RNase)A superfamily,a gene family that is widely used as a model for molecular evolutionary ***,we identified 178 RNase9 genes from 95 Cetartiodactyla species that represent all four lineages and 21 families of this ***,RNase9experienced an evolutionary scenario of“birth and death”in Ruminantia,and expression analyses showed that duplicated RNase9A and RNase9B genes are expressed in reproductive tissues(epididymis,vas deferens or prostate).This expression pattern combined with the estimate that these genes duplicated during the middle Eocene,a time when Ruminantia become a successful lineage,suggests that the RNase9 gene duplication might have been advantageous for promoting sperm motility and male fertility as an adaptation to climate seasonality changes of this *** contrast,all RNase9 genes were lost in the Cetacean lineage,which might be associated with their high levels of prostatic lesions and lower reproductive rates as adaptations to a fully aquatic environment and a balance to the demands of ocean *** study reveals a complex and intriguing evolutionary history and functional divergence for RNase9 in Cetartiodactyla,providing new insights into the evolution of the RNaseA superfamily and molecular mechanisms for organismal adaptations to the environment.

关键词： RNase9 gene duplication gene loss Cetartiodactyla

Genome-wide identification of functional enhancers and their potential roles in pig breeding

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Journal of Animal Science and Biotechnology 2022年第6期13卷 1690-1702页

作者： Yinqiao Wu Yuedong Zhang Hang Liu Yun Gao Yuyan Liu Ling Chen Lu Liu david m.irwin Chunhui Hou Zhongyin Zhou Yaping Zhang State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223YunnanChina Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204YunnanChina State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan Yunnan UniversityKunming 650091YunnanChina School of Life Science Yunnan UniversityKunming 650091YunnanChina Institute of Physical Science and Information Technology Anhui UniversityHefei 230601AnhuiChina Department of Laboratory medicine and Pathobiology University of TorontoTorontoCanada Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223YunnanChina

Background:The pig is an economically important livestock species and is a widely applied large animal model in medical *** are critical regulatory elements that have fundamental functions in evolution,development and ***-wide quantification of functional enhancers in the pig is ***:We performed self-transcribing active regulatory region sequencing(STARR-seq)in the porcine kidney epithelial PK15 and testicular ST cell lines,and reliably identified 2576 functional *** of these enhancers were located in repetitive sequences and were enriched within silent and lowly expressed *** poorly overlapped with chromatin accessibility regions and were highly enriched in chromatin with the repressive histone modification H3K9me3,which is different from predicted pig enhancers detected using ChIP-seq for H3K27ac or/and H3K4me1 modified *** suggests that most pig enhancers identified with STARR-seq are endogenously repressed at the chromatin level and may function during cell type-specific development or at specific developmental ***,the PPP3CA gene is associated with the loin muscle area trait and the QKI gene is associated with alkaline phosphatase activity that may be regulated by distal functional ***:In summary,we generated the first functional enhancer map in PK15 and ST cells for the pig genome and highlight its potential roles in pig breeding.

关键词： Breeding Functional enhancers Pig STARR-seq

Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity

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Genomics, Proteomics & Bioinformatics 2020年第5期18卷 489-500页

作者： Lindan Ji Dongdong Wu Haibing Xie Binbin Yao Yanming Chen david m.irwin Dan Huang Jin Xu Nelson L.S.Tang Yaping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Department of Biochemistry Medical School of Ningbo UniversityNingbo 315211China Department of Preventive medicine Medical School of Ningbo UniversityNingbo 315211China Department of Laboratory medicine and Pathobiology University of TorontoTorontoON M5S 1A8Canada Banting and Best Diabetes Centre University of TorontoTorontoON M5S 1A8Canada Department of Chemical Pathology and Laboratory for Genetics of Disease SusceptibilityLi Ka Shing Institute of Health SciencesFaculty of MedicineThe Chinese University of Hong KongHong Kong Special Administrative RegionChina KIZ/CUHK Joint Laboratory of Bioresources and molecular Research in Common Diseases Kunming 650223China Laboratory for Conservation and Utilization of Bio-resource Yunnan UniversityKunming 650091China

Solar energy,which is essential for the origin and evolution of all life forms on Earth,can be objectively recorded through attributes such as climatic ambient temperature(CAT),ultraviolet radiation(UVR),and sunlight duration(SD).These attributes have specific geographical variations and may cause different adaptation ***,the adaptation profile of each attribute and the selective role of solar energy as a whole during human evolution remain ***,we performed a genome-wide adaptation study with respect to CAT,UVR,and SD using the Human Genome Diversity Project-Centre Etude Polymorphism Humain(HGDP-CEPH)panel *** singled out CAT as the most important driving force with the highest number of adaptive loci(6 SNPs at the genome-wide 1×10^(-7)level;401 at the suggestive 1×10^(-5)level).Five of the six genomewide significant adaptation SNPs were successfully replicated in an independent Chinese population(N=1395).The corresponding 316 CAT adaptation genes were mostly involved in development and *** addition,265(84%)genes were related to at least one genome-wide association study(GWAS)-mapped human trait,being significantly enriched in anthropometric loci such as those associated with body mass index(χ^(2);Pmmunity,metabolic syndrome,and cancer(χ^(2);Pmost important attribute of solar energy that has driven genetic adaptation in development and immunity among global human *** also supports the non-neutral hypothesis for the origin of disease-predisposition alleles in common diseases.

关键词： Solar radiation Ambient temperature Natural selection Development Immunity