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| 1 | Genomic organization and evolution of ruminant lysozyme c genes显示文摘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. | David M.IRWIN | 2015 | Zoological Research2015，36，1： | 5 |
| 2 | Diversification of Sisorid catfishes(Teleostei: Siluriformes)in relation to the orogeny of the Himalayan Plateau显示文摘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 evolutionary 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(*10.9–9.8Mya), 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 consistent 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. | Chuanjiang Zhou Xuzhen Wang Xiaoni Gan Yaping Zhang David M.Irwin Richard L.Mayden Shunping He | 2016 | Science Bulletin2016，61，13： | 4 |
| 3 | Establishment of an optimized CTC detection model consisting of EpCAM,MUC1 and WT1 in epithelial ovarian cancer and its correlation with clinical characteristics显示文摘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(P<0.05).The detection rate of CTC;and CTC;was significantly higher in chemo-resistant patients(26.3%vs.11.9%;26.4%vs.13.4%,P<0.05).The median 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 CTC;and CTC;had predictive value for chemotherapy resistance,and the detection of CTC;suggested poor prognosis. | 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 | 2022 | Chinese Journal of Cancer Research2022，34，2： | 2 |
| 4 | Nocturnal to Diurnal Transition in the Common Ancestor of Haplorrhines:Evidence from Genomic-Scan for Positively Selected Genes显示文摘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 | Xue Cao Yan-Bo Sun David M.Irwin Guo-Dong Wang Ya-Ping Zhang | 2015 | Journal of Genetics and Genomics2015，42，1： | 1 |
| 5 | Comparative population genomics reveals genetic basis underlying body size of domestic chickens显示文摘Body size is the most important economic trait for animal production and breeding.Several hundreds of loci have been reported to be associated with growth trait and body weight in chickens.The loci are mapped to large genomic regions due to the low density and limited number of genetic markers in previous studies.Herein,we employed comparative population genomics to identify genetic basis underlying the small body size of Yuanbao chicken(a famous ornamental chicken)based on 89 whole genomes.The most significant signal was mapped to the BMP10 gene,whose expression was upregulated in the Yuanbao chicken.Overexpression of BMP10 induced a significant decrease in body length by inhibiting angiogenic vessel development in zebrafish.In addition,three other loci on chromosomes 1,2,and 24 were also identified to be potentially involved in the development of body size.Our results provide a paradigm shift in identification of novel loci controlling body size variation,availing a fast and efficient strategy.These loci,particularly BMP10,add insights into ongoing research of the evolution of body size under artificial selection and have important implications for future chicken breeding. | Ming-Shan Wang Yong-Xia Huo Yan Li Newton OOtecko Ling-Yan Su Hai-Bo Xu Shi-Fang Wu Min-Sheng Peng He-Qun Liu Lin Zeng David M.Irwin Yong-Gang Yao Dong-Dong Wu Ya-Ping Zhang | 2016 | Journal of Molecular Cell Biology2016，8，6： | 1 |
| 6 | Genome-wide identification of functional enhancers and their potential roles in pig breeding显示文摘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. | Yinqiao Wu Yuedong Zhang Hang Liu Yun Gao Yuyan Liu Ling Chen Lu Liu David M.Irwin Chunhui Hou Zhongyin Zhou Yaping Zhang | 2022 | Journal of Animal Science and Biotechnology2022，13，6： | 1 |
| 7 | Birth-and-death evolution of ribonuclease 9 genes in Cetartiodactyla显示文摘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. | Datian Lang Xiaoping Wang Chunbing Liu Weihang Geng David M.Irwin Shanyuan Chen Chunqing Li Li Yu Heng Xiao | 2023 | Science China(Life Sciences)2023，66，5： | 1 |
| 8 | Duplication and diversification of insulin genes in ray-finned fish显示文摘Insulin is a key hormone for the regulation of metabolism in vertebrates.Insulin is produced by pancreatic islet cells in response to elevated glucose levels and leads to the uptake of glucose by tissues such as liver and adipose tissue to store energy.Insulin also has additional functions in regulating development.Previous work has shown that the proglucagon gene,which encodes hormones counter regulating insulin,is duplicated in teleost fish,and that the peptide hormones encoded by these genes have diversified in function.I sought to determine whether similar processes have occurred to insulin genes in these species.Searches of fish genomes revealed an unexpected diversity of insulin genes.A triplication of the insulin gene occurred at the origin of teleost fish,however one of these three genes,insc,has been lost in most teleost fish lineages.The two other insulin genes,insa and insb,have been retained but show differing levels of selective constraint suggesting that they might have diversified in function.Intriguingly,a duplicate copy of the insa gene,which I named insab,is found in many fish.The coding sequenee encoded by insab genes is under weak selective constraint,with its predicted protein sequences losing their potential to be processed into a two-peptide hormone.However,these sequences have retained perfectly conserved cystine residues,suggesting that they maintain insulin's three-dimensional structure and therefore might modulate the processing and secretion of insulin produced by the other genes. | David M.Irwin | 2019 | Zoological Research2019，40，3： | 1 |
| 9 | Comparative study of gut microbiota from captive and confiscatedrescued wild pangolins显示文摘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. | Chunbing Liu Jingyang Hu Yajiang Wu David M.Irwin Wu Chen Zhigang Zhang Li Yu | 2021 | Journal of Genetics and Genomics2021，48，9： | 1 |
| 10 | Integrating Genomic and Transcriptomic Data to Reveal Genetic Mechanisms Underlying Piao Chicken Rumpless Trait显示文摘Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail feathers.So far,the molecular mechanisms underlying tail absence in this breed remain unclear.In this study,we comprehensively employed comparative transcriptomic and genomic analyses to unravel potential genetic underpinnings of rumplessness in Piao chicken.Our results reveal many biological factors involved in tail development and several genomic regions under strong positive selection in this breed.These regions contain candidate genes associated with rumplessness,including Irx4,Il18,Hspb2,and Cryab.Retrieval of quantitative trait loci(QTL)and gene functions implies that rumplessness might be consciously or unconsciously selected along with the high-yield traits in Piao chicken.We hypothesize that strong selection pressures on regulatory elements might lead to changes in gene activity in mesenchymal stem cells of the tail bud.The ectopic activity could eventually result in tail truncation by impeding differentiation and proliferation of the stem cells.Our study provides fundamental insights into early initiation and genetic basis of the rumpless phenotype in Piao chicken. | Yun-Mei Wang Saber Khederzadeh Shi-Rong Li Newton Otieno Otecko David M.Irwin Mukesh Thakur Xiao-Die Ren Ming-Shan Wang Dong-Dong Wu Ya-Ping Zhang | 2021 | Genomics, Proteomics & Bioinformatics2021，19，5： | 1 |
| 11 | Single-cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-genesis in Pigs显示文摘Development of thoracolumbar vertebra(TLV)and rib primordium(RP)is a common evolutionary feature across vertebrates,although whole-organism analysis of the expression dynamics of TLV-and RP-related genes has been lacking.Here,we investigated the single-cell transcriptome landscape of thoracic vertebra(TV),lumbar vertebra(LV),and RP cells from a pig embryo at 27 days post-fertilization(dpf)and identified six cell types with distinct gene expression signatures.In-depth dissection of the gene expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and RP development.Further analysis of cell type-specific and strand-specific expression uncovered the extremely high level of HOXA103′-UTR sequence specific to osteoblasts of LV cells,which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV transition.Thus,this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell type-specific resolution,which serves as a comprehensive view on the transcriptional profile of animal embryo development. | Jianbo Li Ligang Wang Dawei Yu Junfeng Hao Longchao Zhang Adeniyi C.Adeola Bingyu Mao Yun Gao Shifang Wu Chunling Zhu Yongqing Zhang Jilong Ren Changgai Mu David M.Irwin Lixian Wang Tang Hai Haibing Xie Yaping Zhang | 2021 | Genomics, Proteomics & Bioinformatics2021，19，3： | 1 |
| 12 | Rapid Evolution of the Mammalian HILS1 Gene and the Nuclear Condensation Process during Mammalian Spermiogenesis显示文摘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 | Yanhua Su Dongdong Wu Weiping Zhou David M.Irwin Yaping Zhang | 2013 | Journal of Genetics and Genomics2013，40，1： | 0 |
| 13 | QcReads:An Adapter and Quality Trimming Tool for Next-Generation Sequencing Reads显示文摘With the advent of next-generation sequencing(NGS)technologies,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;Manske et al.,2012;Xu et al.,2012;Jia et al.,2013).However,these sequencing technologies still exhibit some limitations。 | Yunfei Ma Haibing Xie Xuman Han David M.Irwin Ya-Ping Zhang | 2013 | Journal of Genetics and Genomics2013，40，12： | 0 |
| 14 | Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity显示文摘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 traits.However,the adaptation profile of each attribute and the selective role of solar energy as a whole during human evolution remain elusive.Here,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 data.We 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 immunity.In 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);P<0.005),immunity,metabolic syndrome,and cancer(χ^(2);P<0.05).For these adaptive SNPs,balancing selection was evident in Euro-Asians,whereas obvious positive and/or purifying selection was observed in Africans.Taken together,our study indicates that CAT is the most important attribute of solar energy that has driven genetic adaptation in development and immunity among global human populations.It also supports the non-neutral hypothesis for the origin of disease-predisposition alleles in common diseases. | Lindan Ji Dongdong Wu Haibing Xie Binbin Yao Yanming Chen David M.Irwin Dan Huang Jin Xu Nelson L.S.Tang Yaping Zhang | 2020 | Genomics, Proteomics & Bioinformatics2020，18，5： | 0 |
| 15 | c-Cbl介导了hSef的泛素化和降解(英文)显示文摘Sef(similar expression to fgf genes)作为FGF信号通路中可诱导的拮抗分子相继在斑马鱼,小鼠,和人类中被鉴定出来,并进行了相应的功能研究.目前对于Sef蛋白本身稳定性的研究还未见报道.对c-Cbl对Sef稳定性的影响进行了研究.免疫荧光实验表明Sef能够和c-Cbl蛋白在细胞中发生共定位,随后的免疫共沉淀实验证明Sef能够和c-Cbl发生相互作用.体内泛素化实验表明c-Cbl能够使Sef发生明显的泛素化作用.这种泛素化最终导致了Sef本身的剂量依赖性的降解.针对c-Cbl的siRNA表达也使Sef稳定细胞系的表达水平得到恢复.结果表明,c-Cbl对Sef的泛素化及降解可能作为一种调控拮抗因子的蛋白质水平从而最终调节信号通路的一种机制. | 任永明 荣知立 李智勇 程龙 李颖华 王银银 任芳丽 David M.Irwin 常智杰 | 2008 | 生物化学与生物物理进展2008，35，1： | 0 |
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