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Gene duplication plays a m.jor role in gene co-option: Studies into the evolution of the m.tilin/ghrelin fam.ly and their receptors

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Chinese Science Bulletin 2011年第25期56卷 2690-2697页

作者： HE Jing irwin m. david ZHANG YaPing State Key Laboratory of Genetic Resource and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China Departm.nt of Laboratory m.dicine and Pathobiology and Banting and Best Diabetes Centre University of Toronto Toronto M5S1A1 Canada Laboratory for Conservation and Utilization ofBioresource Yunnan University Kunming 650091 China

Extant genes can be m.dified, or 'tinkered with', to provide new roles or new characteristics of these genes. At the genetic level, this often involves gene duplication and specialization of the resulting genes into particular functions. We investigate how ligand-receptor partnerships evolve after gene duplication. While significant work has been conducted in this area, the exam.nation of additional m.dels should help us better understand the proposed m.dels and potentially reveal novel evolutionary patterns and dynam.cs. We use bioinform.tics, com.arative genom.cs and phylogenetic analyses to show that preproghrelin and preprom.tilin descended from.a com.on ancestor and that a gene duplication generated these two genes shortly after the divergence of am.hibians and am.iotes. The evolutionary history of the receptor fam.ly differs from.that of their cognate ligands. GPR39 diverges first, and an ancestral receptor gives rise to receptors classified as fish-specific clade A, GHSR and m.NR by successive gene duplications occurring before the divergence of tetrapods and ray-finned fish. The ghrelin/GHSR system.is m.intained and functionally conserved from.fish to m.m.als. m.tilin-m.NR specificity m.st have arisen by ligand-receptor coevolution after the m.N horm.ne gene diverged from.the GHRL gene in the am.iote lineage. Conserved m.lecular m.chinery can give rise to new neuroendocrine response m.chanism. by the co-option of duplicated genes. Gene duplication is both parsim.nious and creative in producing elem.nts for evolutionary tinkering and plays a m.jor role in gene co-option, thus aiding the evolution of greater biological com.lexity.

关键词：基因重复生长素胃动素受体选项演变家庭进化模式

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m.tilin and ghrelin gene experienced episodic evolution during prim.tive placental m.m.al evolution

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Science China(Life Sciences) 2010年第6期53卷 677-682页

作者： irwin m. david Departm.nts of Laboratory m.dicine and Pathobiology and the Banting and Best Diabetes Centre University of Toronto

m.tilin and ghrelin,m.m.ers of a structure-function-related horm.ne fam.ly,play im.ortant roles in gastrointestinal function,regulation of energy hom.ostasis and growth horm.ne *** observed episodic evolution in both of their prehorm.ne gene sequences during prim.tive placental m.m.al evolution,during which m.st of the nonsynonym.us changes result in radical *** note,a functional obestatin horm.ne m.ght have only originated after this episodic evolution *** in placental m.m.al evolution,a series of biology com.lexities *** the sam. tim. the m.tilin and ghrelin prehorm.ne genes,which play im.ortant roles in several of these processes,experienced episodic evolution with dram.tic changes in their coding *** observations suggest that som. of the lineage-specific physiological adaptations are due to episodic evolution of the m.tilin and ghrelin genes.

关键词： m.tilin ghrelin episodic evolution

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Duplication and diversification of insulin genes in ray-finned fish

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Zoological Research 2019年第3期40卷 185-197页

作者： david m.irwin Departm.nt of Laboratory m.dicine and Pathobiology University of Toronto Banting and Best Diabetes Centre University of Toronto

Insulin is a key horm.ne for the regulation of m.tabolism.in *** 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 *** also has additional functions in regulating *** work has shown that the proglucagon gene,which encodes horm.nes counter regulating insulin,is duplicated in teleost fish,and that the peptide horm.nes encoded by these genes have diversified in function.I sought to determ.ne whether sim.lar processes have occurred to insulin genes in these *** of fish genom.s 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 m.st teleost fish *** two other insulin genes,insa and insb,have been retained but show differing levels of selective constraint suggesting that they m.ght have diversified in ***,a duplicate copy of the insa gene,which I nam.d insab,is found in m.ny *** 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 ***,these sequences have retained perfectly conserved cystine residues,suggesting that they m.intain insulin's three-dim.nsional structure and therefore m.ght m.dulate the processing and secretion of insulin produced by the other genes.

关键词： Insulin Teleost fish Gene duplicati on Adaptive evolution Gene loss

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Genom.c organization and evolution of rum.nant lysozym. c genes

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Zoological Research 2015年第1期36卷 1-17页

作者： david m.irwin Departm.nt of Laboratory m.dicine and Pathobiology University of Toronto Banting and Best Diabetes Centre University of Toronto

Rum.nant stom.ch lysozym. is a long established m.del of adaptive gene evolution. Evolution of stom.ch lysozym. function required changes in the site of expression of the lysozym. c gene and changes in the enzym.tic properties of the enzym.. In rum.nant m.m.als, these changes were associated with a change in the size of the lysozym. c gene fam.ly. The recent release of near com.lete genom. sequences from.several rum.nant species allows a m.re com.lete exam.nation of the evolution and diversification of the lysozym. c gene fam.ly. Here we characterize the size of the lysozym. c gene fam.ly in extant rum.nants and dem.nstrate that their pecoran rum.nant ancestor had a fam.ly of at least 10 lysozym. c genes, which included at least two pseudogenes. Evolutionary analysis of the rum.nant lysozym. c gene sequences dem.nstrate that each of the four exons of the lysozym. 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 lysozym. c genes expressed in the abom.sum.of the stom.ch of extant rum.nant species showing the greatest levels of selective constraints.

关键词： lysozym. rum.nant evolutionary Genom.c extant stom.ch genom.c constraints Ailuropoda duplication

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Com.arative study of gut m.crobiota from.captive and confiscatedrescued wild pangolins

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Journal of Genetics and Genom.cs 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 Departm.nt of Laboratory m.dicine and Pathobiology University of TorontoTorontoOntario M5S 1A8Canada

Pangolins are am.ng the m.st critically endangered anim.ls 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, com.arative studies of captive and wild pangolins in the context of gut m.crobiota are rare. Here, the gut m.crobiom. of captive and confiscated-rescued wild pangolins is com.ared, and the effects of different periods of captivity and captivity with and without antibiotic treatm.nt are *** show that different diets and periods of captivity, as well as the application of antibiotic therapy, can alter gut com.unity com.osition and abundance in pangolins. Com.ared to wild pangolins, captive pangolins have an increased capacity for chitin and cellulose/hem.cellulose degradation, fatty acid m.tabolism. and short-chain fatty acid synthesis, but a reduced ability to m.tabolize exogenous substances. In addition to increasing the ability of the gut m.crobiota to m.tabolize nutrients in captivity, captive breeding im.oses som. 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 im.ortant for the developm.nt of guidelines for pangolin conservation, including health assessm.nt, disease prevention, and rehabilitation of wild pangolin populations.

关键词： Pangolin Gut m.crobiom. Captivity Antibiotic resistance genes Virulence factors

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Rapid Evolution of the m.m.alian HILS1 Gene and the Nuclear Condensation Process during m.m.alian Sperm.ogenesis

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Journal of Genetics and Genom.cs 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 m.crobial Resources of the m.nistry of Education Yunnan University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Departm.nt of Laboratory m.dicine and Pathobiology University of Toronto Banting and Best Diabetes Centre University of Toronto

m.ny genes associated with reproduction show rapid evolution across diverse anim.l groups, a result com.only 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.com.etition, where sperm.com.ete to fertilize eggs leading to the proteins in the sper- m.tozoa 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 （Palum.i, 1999）; and cryptic fem.le choice （reviewed in Swanson and Vacquier, 2002）.

关键词： Rapid Evolution of the m.m.alian HILS1 Gene and the Nuclear Condensation Process during m.m.alian Sperm.ogenesis HILS gene

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Diversification of Sisorid catfishes(Teleostei: Siluriform.s)in relation to the orogeny of the Him.layan 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.m.yden Shunping He Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academ. of Sciences Institute of HydrobiologyChinese Academy of Sciences Key Laboratory of Freshwater Fish Reproduction and Developm.nt (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 Departm.nt of Laboratory m.dicine and Pathobiology University of Toronto Banting and Best Diabetes Centre University of Toronto Departm.nt of Biology 3507 Laclede Ave. Saint Louis University

Abstract Sisorid catfishes are prim.rily lim.ted in distribution to rivers of the Him.layan region and Tibetan Plateau. These species have external m.rphologies that are adapted for extrem.ly fast-flowing riverine system.. 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 com.lete m.tochondrial genom. and four nuclear genes of representative sisorids distributed across river system. in China. Phylogenetic analyses strongly support the m.nophyly 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 accom.anied by convergent evolution in m.rphological traits that were presum.bly in response to environm.ntal pressure involving the rapid flowing river system.that were generated during the uplift of the Tibetan Plateau （UTP）. m.lecular dating indicates that the Chinese sisorids and the glyptosternoids originated at the later m.ocene （~ 10.9-9.8 m.a）, and with further biogeographic analyses indicates that the species of Sisoridae likely originated from.a widely distributed ancestor. m.reover, 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 system. form.d during and after the UTP in the late m.ocene and Quaternary periods.

关键词： Phylogeny. Diversification and dispersal.Biogeography - Divergence tim. estim.tion ~ TibetanPlateau ~ Sisoridae ~ Catfish

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QcReads:An Adapter and Quality Trim.ing Tool for Next-Generation Sequencing Reads

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Journal of Genetics and Genom.cs 2013年第12期40卷 639-642页

作者： Yunfei m. Haibing Xie Xum.n 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 Academ. of Sciences Departm.nt of Laboratory m.dicine and Pathobiology University of Toronto

With the advent of next-generation sequencing （NGS） tech-nologies, it is possible to obtain huge am.unt of genom. or transcriptom. 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 m.dicine （Kwon and Goate, 2000; Pflueger et al., 2011;

关键词： length QcReads

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Nocturnal to Diurnal Transition in the Com.on Ancestor of Haplorrhines:Evidence from.Genom.c-Scan for Positively Selected Genes

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Journal of Genetics and Genom.cs 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 Academ. of Sciences Kunm.ng College of Life Science University of Chinese Academy of Sciences Departm.nt of Laboratory m.dicine 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 m.jor shift in prim.te evolution, plays a central role in the adaptation of these species to new habitats, and is involved in m.difications to their physiological and social behaviors （Heesy and Ross, 2001; Shultz et al., 2011）. However, two core problem. concerning the circadian rhythm.transition re- m.ins unresolved. First, there is controversy concerning the activity pattern of the ancestral prim.te （Heesy and Ross, 2001; Tan et al., 2005）. Second, the transition process for circadian rhythm.in prim.te evolutionary history is unre- solved. Although m.st research suggests that prim.tes trans- form.d from.a nocturnal to a diurnal circadian rhythm.in the lineage leading to the com.on ancestor of the anthropoids or the haplorrhines （anthropoids and tarsier）（Ross, 2000; Heesy and Ross, 2001）, evidence has been insufficient to determ.ne whether this occurred in the lineage leading to the com.on ancestor of the haplorrhines or the anthroooids.

关键词： Nocturnal to Diurnal Transition in the Com.on Ancestor of Haplorrhines

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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 Environm.ntal Science Yunnan UniversityKunming 650091China State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Yunnan UniversityKunming 650091China Biodiversity Research Center of Wum.ng m.untain Department of Agronomy and Life ScienceZhaotong UniversityZhaotong 657000China Departm.nt of Laboratory m.dicine and Pathobiology University of TorontoTorontoOntario M5S 1A8Canada

RNase9 plays a reproductive function and has been recognized as an im.ortant m.m.er of the ribonuclease(RNase)A superfam.ly,a gene fam.ly that is widely used as a m.del for m.lecular evolutionary ***,we identified 178 RNase9 genes from.95 Cetartiodactyla species that represent all four lineages and 21 fam.lies of this ***,RNase9experienced an evolutionary scenario of“birth and death”in Rum.nantia,and expression analyses showed that duplicated RNase9A and RNase9B genes are expressed in reproductive tissues(epididym.s,vas deferens or prostate).This expression pattern com.ined with the estim.te that these genes duplicated during the m.ddle Eocene,a tim. when Rum.nantia becom. a successful lineage,suggests that the RNase9 gene duplication m.ght have been advantageous for prom.ting sperm.m.tility and m.le fertility as an adaptation to clim.te seasonality changes of this *** contrast,all RNase9 genes were lost in the Cetacean lineage,which m.ght be associated with their high levels of prostatic lesions and lower reproductive rates as adaptations to a fully aquatic environm.nt and a balance to the dem.nds of ocean *** study reveals a com.lex and intriguing evolutionary history and functional divergence for RNase9 in Cetartiodactyla,providing new insights into the evolution of the RNaseA superfam.ly and m.lecular m.chanism. for organism.l adaptations to the environm.nt.

关键词： RNase9 gene duplication gene loss Cetartiodactyla

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