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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 studies.Here,we identified 178 RNase9 genes from 95 Cetartiodactyla species that represent all four lineages and 21 families of this clade.Unexpectedly,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 period.In 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 resources.This 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 research.Enhancers are critical regulatory elements that have fundamental functions in evolution,development and disease.Genome-wide quantification of functional enhancers in the pig is needed.Results: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 enhancers.most of these enhancers were located in repetitive sequences and were enriched within silent and lowly expressed genes.Enhancers 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 histones.This 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 stages.Additionally,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 enhancers.Conclusions: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

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

Establishment of an optimized CTC detection model consisting of EpCAm,mUC1 and WT1 in epithelial ovarian cancer and its correlation with clinical characteristics

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Chinese Journal of Cancer Research 2022年第2期34卷 95-108页

作者： Tongxia Wang Yan Gao Xi Wang Junrui Tian Yuan Li Bo Yu Cuiyu Huang Hui Li Huamao Liang david m.irwin Huanran Tan Hongyan Guo Department of Obstetrics and Gynecology Peking University Third HospitalBeijing 100191China Department of Pharmacology School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China Department of Laboratory medicine and Pathobiology University of TorontoToronto M5S1A8Canada

Objective:Emerging studies have demonstrated the promising clinical value of circulating tumor cells(CTCs)for diagnosis,disease assessment,treatment monitoring and prognosis in epithelial ovarian cancer.However,the clinical application of CTC remains restricted due to diverse detection techniques with variable sensitivity and specificity and a lack of common standards.methods:We enrolled 160 patients with epithelial ovarian cancer as the experimental group,and 90 patients including 50 patients with benign ovarian tumor and 40 healthy females as the control group.We enriched CTCs with immunomagnetic beads targeting two epithelial cell surface antigens(EpCAm and mUC1),and used multiple reverse transcription-polymerase chain reaction(RT-PCR)detecting three markers(EpCAm,mUC1 and WT1)for quantification.And then we used a binary logistic regression analysis and focused on EpCAm,mUC1 and WT1 to establish an optimized CTC detection model.Results:The sensitivity and specificity of the optimized model is 79.4%and 92.2%,respectively.The specificity of the CTC detection model is significantly higher than CA125(92.2%vs.82.2%,P=0.044),and the detection rate of CTCs was higher than the positive rate of CA125(74.5%vs.58.2%,P=0.069)in early-stage patients(stage I and II).The detection rate of CTCs was significantly higher in patients with ascitic volume≥500 mL,suboptimal cytoreductive surgery and elevated serum CA125 level after 2 courses of chemotherapy(Pmo-resistant patients(26.3%vs.11.9%;26.4%vs.13.4%,Pmedian progression-free survival time for CTC;patients trended to be longer than CTC;patients,and overall survival was shorter in CTC;patients(P=0.043).Conclusions:Our study presents an optimized detection model for CTCs,which consists of the expression levels of three markers(EpCAm,mUC1 and WT1).In comparison with CA125,our model has high specificity and demonstrates better diagnostic values,especially for early-stage ovarian cancer.Detection of

关键词： Circulating tumor cells epithelial ovarian cancer optimized detection model diagnosis and prognosis

Hologenomic insights into mammalian adaptations to myrmecophagy

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National Science Review 2023年第4期10卷 24-36页

作者： Shao-Chen Cheng Chun-Bing Liu Xue-Qin Yao Jing-Yang Hu Ting-Ting Yin Burton K.Lim Wu Chen Guo-Dong Wang Cheng-Lin Zhang david m.irwin Zhi-Gang Zhang Ya-Ping Zhang Li Yu State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Department of Natural History Royal Ontario Museum Guangzhou Zoo Center for Excellence in Animal Evolution and Genetics Kunming Institute of ZoologyChinese Academy of Sciences Beijing Zoo Department of Laboratory medicine and Pathobiology University of Toronto

Highly specialized myrmecophagy(ant-and termite-eating) has independently evolved multiple times in species of various mammalian orders and represents a textbook example of phenotypic evolutionary convergence. We explored the mechanisms involved in this unique dietary adaptation and convergence through multi-omic analyses, including analyses of host genomes and transcriptomes, as well as gut metagenomes, in combination with validating assays of key enzymes’ activities, in the species of three mammalian orders(anteaters, echidnas and pangolins of the orders Xenarthra, monotremata and Pholidota, respectively) and their relatives. We demonstrate the complex and diverse interactions between hosts and their symbiotic microbiota that have provided adaptive solutions for nutritional and detoxification challenges associated with high levels of protein and lipid metabolisms, trehalose degradation, and toxic substance detoxification. Interestingly, we also reveal their spatially complementary cooperation involved in degradation of ants’ and termites’ chitin exoskeletons. This study contributes new insights into the dietary evolution of mammals and the mechanisms involved in the coordination of physiological functions by animal hosts and their gut commensals.

关键词： myrmecophagy adaptive evolution hologenome genomics metagenomics convergent evolution

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

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 considered.We 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

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