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Revisiting the evolutionary history of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree

Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1040-1052页

作者： Mingpeng Zhang Qiang Yang Huashui Ai Lusheng Huang State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchang 330045China

The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary ***,we estimated the de novo mutation rate of pigs as 3.6×10-9 per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and *** this mutation rate,we re-investigated the evolutionary history of *** estimated divergence time of~10 kiloyears ago(KYA)between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological ***,other divergence events inferred here were not as ancient as previously *** estimates suggest that Sus speciation occurred~1.36 million years ago(MYA);European wild pigs split from Asian wild pigs only~219 KYA;and south and north Chinese wild pigs split~25 ***,our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao Plain,northern China,approximately 20 KYA,supporting the possibly independent domestication in northern China along the middle Yellow *** also found that the maximum effective population size of pigs was~6 times larger than estimated *** archaic migration from other Sus species originating~2 MYA to European pigs was detected during western colonization of pigs,which may affect the accuracy of previous demographic *** de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.

关键词： Pig De novo mutation rate Three-generation pedigree evolutionary history Archaic migration

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Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway

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mLife 2022年第2期1卷 198-209页

作者： Jian-Yu Jiao Zheng-Han Lian Meng-Meng Li Nimaichand Salam En-Min Zhou Lan Liu Hong Ming Guoxing Nie Wensheng Shu Guoping Zhao Brian P.Hedlund Wen-Jun Li State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)School of Life SciencesSun Yat-Sen UniversityGuangzhouChina International Joint Research Center for Karstology School of Earth SciencesYunnan UniversityKunmingChina Synthetic Biology Engineering Laboratory of Henan Province College of Life Sciences and TechnologyXinxiang Medical UniversityXinxiangChina College of Fisheries Henan Normal UniversityXinxiangChina Institute of Ecological Science School of Life ScienceSouth China Normal UniversityGuangzhouChina Institute of Synthetic Biology Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina School of Life Sciences University of NevadaLas VegasNevadaUSA Nevada Institute of Personalized Medicine University of NevadaLas VegasNevadaUSA State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina

Biological denitrification is a crucial process in the nitrogen biogeochemical cycle,and Thermus has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal ***,neither the denitrification potential nor the evolutionary history of denitrification genes in the genus Thermus or phylum Deinococcota is well ***,we performed a comparative analysis of 23 Thermus genomes and identified denitrification genes in 15 Thermus *** confirmed that Thermus harbors an incomplete denitrification pathway as none of the strains contain the nosZ *** character state reconstructions and phylogenetic analyses showed that narG,nirS,and norB genes were acquired by the last common ancestor of Thermales and were inherited *** contrast,nirK of Thermales was acquired via two distinct horizontal gene transfers from Proteobacteria to the genus Caldithermus and from an unknown donor to the common ancestor of all known Thermus species except Thermus *** study expands our understanding of the genomic potential for incomplete denitrification in Thermus,revealing a largely vertical evolutionary history of the denitrification pathway in the Thermaceae,and supporting the important role for Thermus as an important heterotrophic denitrifier in geothermal environments.

关键词： comparative genomics denitrification evolutionary history Thermus

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Comparative Studies on the Genome and evolutionary history of Domestic Bactrian Camel

Comparative Studies on the Genome and Evolutionary History o...

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提升骆驼产业科技含量，打造骆驼行业知名品牌——第二届（...

作者： Siriguleng Yu Jirimutu Temuulen Ming Linag Yi Li Sirendalai Sanchir Sarentuya Key Laboratory of Dairy Biotechnology and Engineering Ministry of Education College of Food Science and EngineeringInner Mongolia Agricultural University Inner Mongolia Camel Protection Association College of Veterinary Science Inner Mongolia Agricultural University

INTRODUCTION The factual origin of the domestic bactrian camel remain *** the archaeozoological record shows that fully domesticated bactrian camels were present in the third millennium BC and subsequently spread into much of Central ***,our knowledge about the origins and migration history of domestic bactrian camels remains ***,camels have acquired many special

关键词： Domestic bactrian camel Genome evolutionary history

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Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds

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Zoological Research 2022年第3期43卷 423-441页

作者： Jia-Qi Chen Ming-Peng Zhang Xin-Kai Tong Jing-Quan Li Zhou Zhang Fei Huang Hui-Peng Du Meng Zhou Hua-Shui Ai Lu-Sheng Huang State Key Laboratory for Swine Genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchangJiangxi 330045China

In pig-to-human xenotransplantation,the transmission risk of porcine endogenous retroviruses(PERVs)is of great ***,the distribution of PERVs in pig genomes,their genetic variation among Eurasian pigs,and their evolutionary history remain *** scanned PERVs in the current pig reference genome(assembly Build 11.1),and identified 36 long complete or near-complete PERVs(lc PERVs)and 23 short incomplete PERVs(si PERVs).Besides three known PERVs(PERV-A,-B,and-C),four novel types(PERV-JX1,-JX2,-JX3,and-JX4)were detected in this *** to evolutionary analyses,the newly discovered PERVs were more ancient,and PERV-Bs probably experienced a bottleneck~0.5 million years ago(Ma).By analyzing63 high-quality porcine whole-genome resequencing data,we found that the PERV copy numbers in Chinese pigs were lower(32.0±4.0)than in Western pigs(49.1±6.5).Additionally,the PERV sequence diversity was lower in Chinese pigs than in Western *** the lc PERV copy numbers,PERV-A and-JX2 in Western pigs were higher than in Chinese ***,Bama Xiang(BMX)pigs had the lowest PERV copy number(27.8±5.1),and a BMX individual had no PERV-C and the lowest PERV copy number(23),suggesting that BMX pigs were more suitable for screening and/or modification as xenograft ***,we identified 451 PERV transposon insertion polymorphisms(TIPs),of which 86 were shared by all 10 Chinese and Western pig *** findings provide systematic insights into the genomic distribution,variation,evolution,and possible biological function of PERVs.

关键词： PERVs Chinese and Western pigs Copy number variation evolutionary history Biological function prediction

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Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution

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Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1092-1105页

作者： Qian Zhao Longqing Shi Weiyi He Jinyu Li Shijun You Shuai Chen Jing Lin Yibin Wang Liwen Zhang Guang Yang Liette Vasseur Minsheng You State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou 350002China Institute of Rice Fujian Academy of Agricultural SciencesFuzhou 350018China Tea Research Institute Fujian Academy of Agricultural SciencesFuzhou 350001China Center for Genomics and Biotechnology Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biological Sciences Brock UniversitySt.CatharinesON L2S 3A1Canada

Tea green leafhopper(TGL),Empoasca onukii,is of biological and economic *** numerous studies,the mechanisms underlying its adaptation and evolution remain ***,we use previously untapped genome and population genetics approaches to examine how the pest adapted to different environmental variables and thus has expanded *** complete a chromosome-level assembly and annotation of the *** genome,showing notable expansions of gene families associated with adaptation to chemoreception and *** signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse *** of genetic variations among 54 *** samples unveil the population structure and evolutionary history across different tea-growing regions in *** results demonstrate that the genomic changes in key pathways,including those linked to metabolism,circadian rhythms,and immune system functions,may underlie the successful spread and adaptation of *** work highlights the genetic and molecular basis underlying the evolutionary success of a species with broad economic impacts,and provides insights into insect adaptation to host plants,which will ultimately facilitate more sustainable pest management.

关键词： Tea green leafhopper Genomic variation Population genetics Local adaptation evolutionary history

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Conservation priority of global Galliformes species based on phylogenetic diversity

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Integrative Zoology 2014年第3期9卷 340-348页

作者： Youhua CHEN Department of Zoology University of British ColumbiaVancouverBCCanada Department of Renewable Resources University of AlbertaEdmontonAB T6G 2H1Canada

In this study,based on phylogenetic diversity(PD),I develop a conservation strategy for Galliformes species around the world.A cladogram of 197 Galliformes species derived from a previous study was used for calculating PD *** length is an important aspect of the phylogenetic information a tree can convey,but 2 traditionally-used metrics,the number of phylogenetic groups to which a taxon belongs(I)and the proportion that each taxon contributes to the total diversity of the group(W),are fully node-based and do not take branch length into ***,to measure PD more appropriately,I combined a branch-related metric,pendant edge(P),in addition to I and W.A final combined rank for Galliformes species was obtained by summing the ranks of the 3 *** results showed that the 5%top priority species for conserving evolutionary potential were Galloperdix lunulata,Haematortyx sanguiniceps,Margaroperdix madagarensis,Syrmaticus soemmerringii,Coturnix pectoralis,Polyplectron napoleonis,Alectoris melanocephala,Xenoperdix udzungwensis,Afropavo congensis and Syrmaticus *** current species priority ranking based on pylogenetic diversity and the official International Union for Conservation of Nature(IUCN)ranking of Galliformes species was significantly correlated when considering the 5 categories of IUCN(critical endangered,endangered,vulnerable,near threatened and least concern).This indicated the feasibility of introducing the PD index into the network of IUCN regional Red List *** 5%top priority countries selected using the complementarity principle possessing diversified Galliformes genetic resources were China,Indonesia,Mexico,India,Colombia,Australia,Brazil,Angola,Congo and Japan(in descending order).China,Indonesia,Mexico,Brazil,India and Colombia are consistently selected among the 4 top priority sets of richness,rarity,endemicity and *** result indicated that the priority result from PD is highly congruent with conventio

关键词： complementarity conservation priority evolutionary history IUCN Red List

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Birth of the Yangtze River: age and tectonic-geomorphic implications

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National Science Review 2015年第4期2卷 438-453页

作者： Hongbo Zheng CAS Center for Excellence in Tibetan Plateau Earth Sciences School of Geography Science Nanjing Normal UniversityXianlin University Town

Large river systems are an integral and essential component of Earth dynamics. he development of large river systems in Asia is closely linked to the evolving topography driven by both near-ield and far-ield efects of the interplay among Indian, Eurasian and Paciic plates. Plate tectonics together with climatic changes during the Cenozoic is therefore believed to have determined the evolution of Asian large rivers,yet the age of the Yangtze, the largest in Asia, has been strongly debated over a century, with estimates ranging from 40–45 Ma to a more recent initiation postdating 750 ka. In this paper, I atempt to review the competing views about the age of the Yangtze, and evaluate the estimated pre-Miocene birth of the river based on the provenance of the luvial sediments from the lower reaches. I further present new geological evidence from the upper stream in southeastern Tibetan Plateau to show the existence of a possible southward paleo-Jinshajiang during the Paleogene, and exploit when and how it might deviated eastward to give birth to the modern Yangtze River. I propose that the present Yangtze River system formed in response to the continental-scale gradient driven by upliting Tibetan Plateau and regional extension throughout eastern China, synchronous with surface uplit in southeastern Tibet and strengthening of Asian summer monsoon.

关键词： Yangtze River evolutionary history Tibetan Plateau Oligocene/Miocene tectonic geomorphology

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Mitochondrial phylogenomics reveal the origin and adaptive evolution of the deep-sea caridean shrimps(Decapoda:Caridea)

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Journal of Oceanology and Limnology 2021年第5期39卷 1948-1960页

作者： Shao’e SUN Zhongli SHA Yanrong WANG Deep Sea Research Center Institute of OceanologyChinese Academy ofSciencesQingdao 266071China Laboratory for Marine Biology and Biotechnology Pilot NationalLaboratory for Marine Science and Technology(Qingdao)Qingdao 266237China Center for Ocean Mega-Science Chinese Academy of SciencesQingdao266071China University of Chinese Academy of Sciences Beijing 100049China

The deep-sea is considered as the most extensive ecosystem on the *** is meaningful for elucidating the life origins by exploring the origin and adaptive genetic mechanisms of the large deepsea *** shrimps have colonized and successfully adapted to deep-sea *** provide an ideal model to analyze the origin and adaptive evolution of modern deep-sea ***,we conducted the phylogenetic analyses of mitocho ndrial genomes(mitogenomes)from carideans,including 11 newly sequences reported in this investigation to explore the habitat origins,divergence times,and adaptive evolution of deep-sea(seamounts and hydrothermal vents)caridean *** results showed that the species of deep-sea Caridea formed a monophyletic *** analysis supported that the deepsea caridean shrimps may originated from shallow *** hydrothermal vents alvinocaridid shrimps and Lebbeus shinkaiae from Thoridae underwent a second range expansion from seamounts to vent *** of divergence time showed that the caridean shrimps invaded into deep-sea at 147.75 *** divergence of most of the modern seamount and hydrothermal vent species are in the late Cretaceous/early *** may associate with the geological events of the Western Pacific,the climate change,and the global deep-water anoxic/dysoxic events during this ***-two potentially important adaptive residues were detected in the deep-sea shrimp lineage,which were located in atp6,atp8,cox1,cox3,cytb,nad2,nad4 l,and *** investigation adds our understanding of the evolutionary history of deep-sea caridean shrimps,and provides insights into the mitochondrial genetic basis of deep-sea adaptation in this group.

关键词： hydrothermal vents seamounts Caridea mitochondrial genome phylogenetic analysis evolutionary history

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Distinct evolution process among type I interferon in mammals

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Protein & Cell 2013年第5期4卷 383-392页

作者： Lei Xu Limin Yang Wenjun Liu CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China China-Japan Joint Laboratory of Molecular Immunology and Molecular Microbiology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Interferon (IFN) is thought to play an important role in the vertebrate immune system, but systemic knowledge of IFN evolution has yet to be elucidated. To evaluate the phylogenic distribution and evolutionary history of type I IFNs, 13genomes were searched using BLASTn program, and a phylogenetic tree of vertebrate type I IFNs was constructed. In the present study, an IFNδ-like gene in the human genome was identified, refuting the concept that humans have no IFNδ genes, and other mammalian IFN genes were also identified. In the phylogenetic tree, the mammalian IFNβ, IFNɛ, and IFNκ formed a clade separate from the other mammalian type I IFNs, while piscine and avian IFNs formed distinct clades. Based on this phylogenetic analysis and the various characteristics of type I IFNs, the evolutionary history of type I IFNs was further evaluated. Our data indicate that an ancestral IFNα-like gene forms a core from which new IFNs divided during vertebrate evolution. In addition, the data suggest how the other type I IFNs evolved from IFNα and shaped the complex type I IFN system. The promoters of type I IFNs were conserved among different mammals, as well as their genic regions. However, the intergenic regions of type I IFN clusters were not conserved among different mammals, demonstrating a high selection pressure upon type I IFNs during their evolution.

关键词： type I IFN evolutionary history vertebrate gene cluster

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