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The new chimeric chiron genes evolved essential roles in zebrafish embryonic development by regulating NAD+ levels

Science China(Life Sciences) 2021年第11期64卷 1929-1948页

作者： Chengchi Fang Xiaoni Gan Chengjun Zhang Shunping He The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China Kunming Institute of Botany Chinese Academy of ScienceKunming 650201China University of Chinese Academy of Sciences Beijing 100039China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China Huazhong Agricultural University Wuhan 430070China

The origination of new genes is important for generating genetic novelties for adaptive evolution and biological diversity.However, their potential roles in embryonic development, evolutionary processes into ancient networks, and contributions to adaptive evolution remain poorly investigated. Here, we identified a novel chimeric gene family, the chiron family, and explored its genetic basis and functional evolution underlying the adaptive evolution of Danioninae fishes. The ancestral chiron gene originated through retroposition of nampt in Danioninae 48–54 million years ago(Mya) and expanded into five duplicates(chiron1–5) in zebrafish 1–4 Mya. The chiron genes(chirons) likely originated in embryonic development and gradually extended their expression in the testis. Functional experiments showed that chirons were essential for zebrafish embryo development. By integrating into the NAD^(+) synthesis pathway, chirons could directly catalyze the NAD^(+) rate-limiting reaction and probably impact two energy metabolism genes(nmnat 1 and naprt) to be under positive selection in Danioninae fishes. Together,these results mainly demonstrated that the origin of new chimeric chiron genes may be involved in adaptive evolution by integrating and impacting the NAD^(+) biosynthetic pathway. This coevolution may contribute to the physiological adaptation of Danioninae fishes to widespread and varied biomes in Southeast Asian.

关键词： new chimeric genes essential function NAD^(+)rate-limiting enzyme coevolution

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3D landscape reorganization in response to feeding preferences adaptation in the youngest split Gymnocypris fish

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Journal of Genetics and Genomics 2023年第4期50卷 289-292页

作者： Ning Sun Cheng Wang Wenqi Lv Xiaoni Gan Liandong Yang Shunping He Chengchi Fang State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhanHubei 430072China University of Chinese Academy of Sciences Beijing 100049China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China

Divergence in feeding preference is one of the main mechanisms that lead to the emergence of new species.However,little is known about the underlying genetic mechanism of feeding preference adaptation,especially in the three-dimensional(3D)chromatin organization regulation.Gymnocypris eckloni scoliostomus(GS)and G.eckloni eckloni(GE)are two sister species of G.eckloni(Cyprinidae:Schizothoracinae:Gymnocypris).

关键词： species fish Cyprinidae

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Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

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Science China(Life Sciences) 2016年第11期59卷 1149-1165页

作者： Xuzhen Wang Xiaoni Gan Junbing Li Yiyu Chen Shunping He Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences

Origin and diversification of the Tibetan polyploid cyprinids(schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift. The unusual diversification shifts were located to branches subtending the clades of Tibetan polyploid cyprinids. Our analyses suggested that(i) phylogeny of Cyprininae recovered two independent origins of the Tibetan polyploidy schizothoracins;(ii) diversifications of the schizothoracins were closely related to the Neogene uplift of the Tibetan plateau in the following ways: the relatively ancient Late Oligocene-Middle Miocene adaptive radiation may be associated with the uplift of the southern Tibet and Himalaya; the Middle Miocene-Early Pleistocene lineage-specific diversification broadly coincident with major phase of the Neogene Tibetan uplift; and the most recent Pleistocene diversification shift in Schizothorax closely coincident with the successive Kunlun-Huanghe and Gonghe movements of the Tibetan uplift and the glaciation-induced climate oscillations on the plateau.

关键词： Cyprininae polyploid schizothoracins the Tibetan Plateau diversifications

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Molecular phylogeny and divergence time estimates using the mitochondrial genome for the hadal snailfish from the Mariana trench

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Science Bulletin 2017年第16期62卷 1106-1108页

作者： Yanjun Shen Wei Dai Zhaoming Gao Guoyong Yan Xiaoni Gan Shunping He The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China University of Chinese Academy of Sciences Beijing 100039China Institute of Deep-sea Science and Engineering Chinese Academy of SciencesSanya 572000China

Snailfishes are an important component of the hadal fish fauna[1].Based on osteological and other morphological characters,Kido[2]recognized the Cyclopteridae as a sister group to the Liparidae and the superfamily Cot... 详细信息

关键词：狮子鱼分子系统发育马里亚纳海沟线粒体基因组时间估计超深分化分子数据

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Pseudo-chromosome–length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation

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Science China(Life Sciences) 2023年第6期66卷 1379-1391页

作者： Jie Chen Honghui Zeng Wenqi Lv Ning Sun Cheng Wang Wenjie Xu Mingliang Hu Xiaoni Gan Lisheng He Shunping He Chengchi Fang Institute of Deep-Sea Science and Engineering Chinese Academy of SciencesSanya572000China State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan430072China University of Chinese Academy of Sciences Beijing100049China School for Ecological and Environmental Sciences Northwestern Polytechnical UniversityXi’an710072China

High hydrostatic pressure,low temperature,and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments.Here,we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel(MAE,Ilyophis brunneus,captured below a depth of 3,500 m)by using Illumina,Pac Bio,and Hi-C sequencing.We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes.The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes.Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species,European eel,~111.9 Mya and experienced a rapid evolution.The genome evolutionary analyses primarily revealed the following:(i)under high hydrostatic pressure,the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability;ACOX1 may enhance the fluidity of cell membrane and maintain transport activity;the expansion of ABCC12 gene family may enhance the integrity of DNA;(ii)positively selected HARS likely maintain the transcription ability at low temperatures;and(iii)energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and m TOR signaling pathways.

关键词： Ilyophis brunneus genome evolution deep sea adaption high hydrostatic pressure

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Genomic features for adaptation and evolutionary dynamics of four major Asian domestic carps

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Science China Life Sciences 2024年第6期67卷 1308-1310页

作者： Cheng Wang Liandong Yang Yongrui Lu Chengchi Fang Xiaoni Gan Yiyu Chen Shunping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of Chinese Academy of Sciences Academy of Plateau Science and Sustainability Qinghai Normal University National Natural Science Foundation of China Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences

Dear Editor,The coexistence of various species in a shared natural environment often results in the differentiation of their ecological niches, as they adapt to specific ecological roles(Jani?ová et al., 2018), this process leads to the development of distinct phenotypic traits and dietary preferences(Li et al., 2021). Studying this adaptive evolution, the four major Asian domestic carps, namely Ctenopharyngodon idella(grass carp), Mylopharyngodon piceus(black carp),

关键词： SPECIATION

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Monsoon boosted radiation of the endemic East Asian carps

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Science China(Life Sciences) 2023年第3期66卷 563-578页

作者： Chenguang Feng Kun Wang Wenjie Xu Liandong Yang Kunyuan Wanghe Ning Sun Baosheng Wu Feixiang Wu Lei Yang Qiang Qiu Xiaoni Gan Yiyu Chen Shunping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China School of Ecology and Environment Northwestern Polytechnical UniversityXi'an 710072China Key Laboratory of Adaptation and Evolution of Plateau Biota of Chinese Academy of Sciences Northwest Institute of Plateau BiologyChinese Academy of SciencesXining 810008China University of Chinese Academy of Sciences Beijing 100039China Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China Florida Museum of Natural History University of FloridaGainesvilleFL 32611USA National Natural Science Foundation of China Beijing 100085China Center for Excellence in Animal Evolution and Genetics Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China

Major historical events often trigger the rapid flourishing of a few lineages,which in turn shape established biodiversity patterns.How did this process occur and develop?This study provides a window into this issue.The endemic East Asian carps(EEAC)dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems.A series of evidence,including ecogeography,phylogenetics,and macroevolution,suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities.We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting(e.g.,marine transgression and regression and glacial-interglacial cycle)have further reshaped the distribution patterns of EEAC’s members.Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting,which boosted radiation.Overall,this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.

关键词： adaptive radiation Xenocyprididae east Asian monsoon genomes macroevolution phylogenomics

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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

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.

关键词：喜马拉雅地区西藏高原造山运动多样化亲缘关系分析河流系统线粒体基因组系统发育分析

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Methodology for fish biodiversity monitoring with environmental DNA metabarcoding:The primers,databases and bioinformatic pipelines

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Water Biology and Security 2022年第1期1卷 63-72页

作者： Fan Xiong Lu Shu Honghui Zeng Xiaoni Gan Shunping He Zuogang Peng State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan430072China Key Laboratory of Freshwater Fish Reproduction and Development(Ministry of Education) Southwest University School of Life SciencesChongqing400715China

Environmental DNA(eDNA)originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled and monitored using metabarcoding technology,which is revolutionizing fish biodiversity monitoring.Several reviews concerning fish eDNA have focused on standard sampling methods and its applications,though a systematic review focused on marker genes,databases,and bioinformatic pipelines has not yet been published.Here,we present a comprehensive literature review of studies applying metabarcoding technology to fish eDNA for the purpose of fish biodiversity monitoring.We systematically provide the available universal primers used to amplify barcoding sequences from fish eDNA,and then discuss reference barcoding databases,relevant bioinformatic analyses,as well as developed pipelines.The performances of universal primers and their relevant reference databases are summarized.Combined use of multiple primer pairs targeted for more than one gene marker(e.g.,12S,16S,Cytb,COI),and use of both local and public databases are recommended as approaches to improve the sensitivity and reliability of fish eDNA analyses.We also compare the effectiveness of eDNA metabarcoding to traditional approaches for monitoring fish biodiversity and highlight challenges and future perspectives associated with this new tool.Ultimately,we advocate for greater incorporation of eDNA analysis into fish biodiversity assessments to assist environmental managers.

关键词： Environmental DNA Fish biodiversity Metabarcoding Methodology

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Sympatric or micro-allopatric speciation in a glacial lake?Genomic islands support neither

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National Science Review 2022年第12期9卷 37-49页

作者： Ning Sun Liandong Yang Fei Tian Honghui Zeng Ziwen He Kai Zhao Cheng Wang Minghui Meng Chenguang Feng Chengchi Fang Wenqi Lv Jing Bo Yongtao Tang Xiaoni Gan Zuogang Peng Yiyu Chen Shunping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of Chinese Academy of Sciences Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau Biology Chinese Academy of Sciences State Key Laboratory of Biocontrol Guangdong Key Lab of Plant Resources School of Life Sciences Sun Yat-sen University School of Ecology and Environment Northwestern Polytechnical University Institute of Deep-Sea Science and Engineering Chinese Academy of Sciences Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences National Natural Science Foundation of China Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences

Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation.One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence,wherein divergent DNA segments are interspersed with low-divergence segments.Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow.Sympatric divergence of endemic fishes is known from isolated saline,crater,postglacial,and ancient lakes.Two morphologically distinct cyprinid fishes,Gymnocypris eckloni scoliostomus(GS) and G.eckloni eckloni(GE),in a small glacial lake on the Qinghai-Tibet Plateau,Lake Sunmcuo,match the biogeographic criteria of sympatric speciation.In this study,we examined genome-wide variation in 46individuals from these two groups.The divergence time between the GS and GE lineages was estimated to be 20-60 Kya.We identified 54 large genomic islands(≥100 kb) of speciation,which accounted for 89.4%of the total length of all genomic islands.These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes.Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation,they were too large to support the hypothesis of sympatric speciation.Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands(as small as a few kilobases in size).Thus,the observed pattern is consistent with the extensive evidence on parapatric speciation,in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation.We suggest that many,if not most,of the reported cases of sympatric speciation are likely to be micro-parapatric speciation.

关键词： sympatric speciation gene flow genomic islands micro-parapatric speciation selection olfaction

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