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Convergent evolution of AP2/ERF Ⅲ and IX subfamilies through recurrent polyploidization and tandem duplication during eudicot adaptation to paleoenvironmental changes

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Plant Communications 2022年第6期3卷 74-88页

作者： Liangyu Guo Shuo Wang Yuqi Nie Yirong Shen Xiaoxue Ye Wenwu Wu State Key Laboratory of Subtropical Silviculture School of Forestry and BiotechnologyZhejiang A&F UniversityLin’anHangzhou 311300China Institute of Tropical Biosciences and Biotechnology Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

Whole-genome duplication(WGD or polyploidization)has been suggested as a genetic contributor to angiosperm adaptation to environmental ***,many eudicot lineages did not undergo recent WGD(R-WGD)around and/or after the Cretaceous-Paleogene(K-Pg)boundary,times of severe environmental changes;how those plants survived has been largely ***,we collected 22 plants from major branches of the eudicot phylogeny and classified them into two groups according to the occurrence or absence of R-WGD:12 R-WGD-containing plants(R-WGD-Y)and 10 R-WGD-lacking plants(R-WGD-N).Subsequently,we identified 496 gene-rich families in R-WGD-Y and revealed that members of the AP2/ERF transcription factor family were convergently over-retained after R-WGDs and showed exceptional cold *** evolutionary trajectories of the AP2/ERF family were then compared between R-WGD-Y and R-WGD-N to reveal convergent expansions of the AP2/ERF Ⅲ and IX subfamilies through recurrent independent WGDs and tandem duplications(TDs)after the radiation of the *** expansions showed coincident enrichments in-times around and/or after the K-Pg boundary,when global cooling was a major environmental ***,convergent expansions and co-retentions of AP2/ERF Ⅲ C-repeat binding factor(CBF)duplicates and their regulons in different eudicot lineages contributed to the rewiring of cold-specific regulatory ***,promoter analysis of cold-responsive AP2/ERF genes revealed an underlying cis-regulatory code(G-box:CACGTG).We propose a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF Ⅲ and IX genes that has contributed to eudicot adaptation during paleoenvironmental changes,and we suggest that TD may be a reciprocal/alternative mechanism for genetic innovation in plants that lack WGD.

关键词： polyploidization tandem duplication AP2/ERF family adaptive evolution global cooling abiotic stress

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The origin,diversification and adaptation of a major mangrove clade(Rhizophoreae) revealed by whole-genome sequencing

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National Science Review 2017年第5期4卷 721-734页

作者： Shaohua Xu Ziwen He Zhang Zhang Zixiao Guo Wuxia Guo Haomin Lyu Jianfang Li Ming Yang Zhenglin Du Yelin Huang Renchao Zhou Cairong Zhong David E.Boufford Manuel Lerdau Chung-I Wu Norman C.Duke Suhua Shi State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant ResourcesKey Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes School of Life Sciences Sun Yat-Sen University Core Genomic Facility Beijing Institute of Genomics Chinese Academy of Sciences Hainan Dongzhai Harbor National Nature Reserve Harvard University Herbaria Departments of Environmental Sciences and of Biology University of Virginia Department of Ecology and evolution University of Chicago Centre for Tropical Water and Aquatic Ecosystem Research James Cook University The International Mangrove Consortium

Mangroves invade some very marginal habitats for woody plants—at the interface between land and *** mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads and the more conventional short reads are generated from Rhizophora apiculata for the de novo assembly of its genome to a near chromosome level. The longest scaffold, N50 and N90 for the R. apiculata genome, are 13.3 Mb, 5.4 Mb and 1.0 Mb, respectively. Short reads for the genomes and transcriptomes of eight related species are also generated. We find that the ancestor of Rhizophoreae experienced a whole-genome duplication70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exome modifications of amino acid（AA） usage as well as unusual AA substitutions among closely related species. The usage and substitution of AAs, unique among plants surveyed, is correlated with the rapid evolution of proteins in mangroves. A small subset of these substitutions is associated with mangroves' highly specialized traits（vivipary and red bark） thought to be adaptive in the intertidal habitats. Despite the many adaptive features, mangroves are among the least genetically diverse plants, likely the result of continual habitat turnovers caused by repeated rises and falls of sea level in the geologically recent past. Mangrove genomes thus inform about their past evolutionary success as well as portend a possibly difficult future.

关键词： mangrove whole-genome sequencing adaptive evolution protein evolution genetic diversity sea-level changes

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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

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Signatures of functional constraint at Fgfr1a Genes in schizothoracine fishes (Pisces: Cypriniformes): The dermal skeleton variation adapted to high-altitude environments

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Integrative Zoology 2016年第2期11卷 86-97页

作者： Xinyi GUO Ling XIE Xuze ZHANG Yinfa JI Juan CHEN Bo PANG Yongtao XU Delin QI Songchang GUO Key laboratory of Adaptation and evolution of Plateau Biota Northwest Institute of Plateau BiologyCASXiningChina University of Chinese Academy of Sciences BeijingChina Qinghai University for Nationalities XiningChina Qinghai Normal University XiningChina Animal Science Department of Agriculture and Animal Husbandry College Qinghai UniversityXiningChina

Fishes harbor a huge resource of phenotypic diversity and are useful for understanding the genetic basis of morphological ***,it is difficult to transfer classical genetic mapping to most non-model *** this study,we performed a comparative sequence analysis of Fgfr1a to first interpret the evolution of this candidate scale-loss gene in 15 schizothoracine fishes with various scale *** considerable amino acid(AA)substitutions were observed,molecular evolution analysis indicates that the overall coding regions were subject to functional *** also identified extra copies of Fgfr1a in 4 scale-loss fishes and detected accelerated evolution in one AA substitution specific to these *** speculate that Fgfr1a had accumulated mutations in the ancestral lineage of scale-loss schizothoracine fishes before experiencing duplication events,which was further followed by the diversification of *** silico mutation analysis predicted deleterious effects of the mutations while no disruptive molecular mechanism was ***,our results highlight the important role of Fgfr1a gene in the adaptive evolution of schizothoracine fishes during their radiation in the Qinghai-Tibetan Plateau.

关键词： adaptive evolution Fgfr1a scale loss Schizothoracine

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Convergent adaptation of the genomes of woody plants at the land–sea interface

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National Science Review 2020年第6期7卷 978-993页

作者： Ziwen He Shaohua Xu Zhang Zhang Wuxia Guo Haomin Lyu Cairong Zhong David E.Boufford Norman C.Duke The International Mangrove Consortium Suhua Shi State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes School of Life Sciences Sun Yat-Sen University Hainan Dongzhai Harbor National Nature Reserve Administration Harvard University Herbaria Centre for Tropical Water and Aquatic Ecosystem Research James Cook University the Consortium of 26 Institutions

Sequencing multiple species that share the same ecological niche may be a new frontier for genomic *** such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method(convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with Ptrue(probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid(AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence.

关键词： convergent evolution genome mangrove adaptive evolution woody plants

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Does the diversification rate of endemic birds of China's Mainland follow abrupt,gradual shifting or constant patterns?

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Integrative Zoology 2017年第2期12卷 165-171页

作者： Youhua CHEN Department of Renewable Resources University of AlbertaEdmontonCanada

In this brief report,time-varying(including both gradual and abrupt change)and time-constant diversification models are fitted on a phylogeny of endemic birds of China's Mainland to test the diversification patterns of endemic birds in the *** results show that phylogeny of endemic birds is best quantified by a constant-rate diversification model through model *** of the study are *** particular,ignorance of non-endemic taxa and the limited sampling of endemic taxa could influence the conclusions of the study.

关键词： adaptive evolution avian endemism diversification analysis macroevolution

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Identification of genes under positive selection reveals evolutionary adaptation of Ulva mutabilis

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Acta Oceanologica Sinica 2020年第10期39卷 35-41页

作者： Jian Zhang Xiaowen Zhang Wentao Han Xiao Fan Yitao Wang Dong Xu Yan Zhang Jian Ma Chengwei Liang Naihao Ye College of Marine Science and Biological Engineering Qingdao University of Science and TechnologyQingdao 266042China Yellow Sea Fisheries Research Institute Chinese Academy of Fishery SciencesQingdao 266071China Function Laboratory for Marine Fisheries Science and Food Production Processes Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China

Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress *** are untapped resources for food,fuel,and high-value *** rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and *** now,the Ulva mutabilis genome is the only Ulva genome to have been *** obtain further insights into the evolutionary forces driving divergence in Ulva species,we analyzed 3905 single copy ortholog family from ***,Chlamydomonas reinhardtii and Volvox carteri to identify genes under positive selection(GUPS)in *** detected 63 orthologs in *** that were considered to be under positive *** analyses revealed that several adaptive modifications in photosynthesis,amino acid and protein synthesis,signal transduction and stress-related processes might explain why this alga has evolved the ability to grow very rapidly and cope with the variable coastal ecosystem environments.

关键词： green algae Ulva mutabilis positive selection adaptive evolution

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Genomes of 12 fig wasps provide insights into the adaptation of pollinators to fig syconia

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Journal of Genetics and Genomics 2021年第3期48卷 225-236页

作者： Jinhua Xiao Xianqin Wei Yi Zhou Zhaozhe Xin Yunheng Miao Hongxia Hou Jiaxing Li Dan Zhao Jing Liu Rui Chen Liming Niu Guangchang Ma Wenquan Zhen Shunmin He Jianxia Wang Xunfan Wei Weihao Dou Zhuoxiao Sui Haikuan Zhang Shilai Xing Miao Shi Dawei Huang Institute of Entomology College of Life SciencesNankai UniversityTianjin 300071China Institute of Zoology Chinese Academy of SciencesBeijing 100101China Environment and Plant Protection Institute Chinese Academy of Tropical Agricultural SciencesHaikou 571101China Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation College of Marine SciencesBeibu Gulf UniversityQinzhou 535011China Institute of Biophysics Chinese Academy of SciencesBeijing 100101China Berry Genomics Corporation Beijing 102206China

Figs and fig pollinators are one of the few classic textbook examples of obligate pollination *** specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat ***,there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig *** fig syconia,there are also non-pollinator *** non-pollinator species differ in their evolutionary and life histories from *** conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published *** pollinators colonized the figs approximately 66.9 million years ago,consistent with the origin of host *** with nonpollinators,many more genes in pollinators were subject to relaxed *** genes were absent in pollinators in response to environmental stress and immune *** had more streamlined gene repertoires in the innate immune system,chemosensory toolbox,and detoxification *** results provide genomic evidence for the differentiation between pollinators and *** data suggest that owing to the long-term adaptation to the fig,some genes related to functions no longer required are absent in pollinators.

关键词： Phylogenetics Natural selection Immunity Chemosensory adaptive evolution

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Gene duplication and functional divergence of new genes contributed to the polar acclimation of Antarctic green algae

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Marine Life Science & Technology 2023年第4期5卷 511-524页

作者： Xiaowen Zhang Wentao Han Xiao Fan Yitao Wang Dong Xu Ke Sun Wei Wang Yan Zhang Jian Ma Naihao Ye State Key Laboratory of Mariculture Biobreeding and Sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdao 266071China Laboratory for Marine Fisheries Science and Food Production Processes Laoshan LaboratoryQingdao 266200China

Psychrophilic microalgae successfully survive in the extreme and highly variable polar ecosystems,which represent the energy base of most food webs and play a fundamental role in nutrient *** success of microalgae is rooted in their adaptive *** how they have evolved to thrive in extreme polar environments will help us better understand the origin of life in polar *** isolated a psychrophilic unicellular green alga,Microglena ***,from Antarctic sea ice which has a huge ***,we predicted that gene replication may play an important role in its polar adaptive *** found that its protein-coding gene number significantly increased and the duplication time was dated between 37 and 48 million years ago,which is consistent with the formation of the circumpolar Southern *** duplicated paralogous genes were enriched in pathways related to photosynthesis,DNA repair,and fatty acid ***,there were a total of 657 Microglena-specific families,including collagen-like *** divergence in the expression patterns of the duplicated and species-specific genes reflects sub-and neo-functionalization during stress ***,key findings from this study provide new information on how gene duplication and their functional novelty contributed to polar algae adaptation to the highly variable polar environmental conditions.

关键词： Psychrophilic microalgae adaptive evolution Gene replication

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Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole-Genome Duplications and Key Morphological and Molecular Innovations

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Molecular Plant 2020年第8期13卷 1117-1133页

作者： Jing Guo Weibin Xu Yi Hu Jie Huang Yiyong Zhao Lin Zhang Chien-Hsun Huang Hong Ma Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering Institute of Biodiversity Sciences and Institute of Plant BiologySchool of Life SciencesFudan University2005 Songhu RoadShanghai 200438China Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain Guangxi Institute of BotanyGuangxi Zhuangzu Autonomous Region and Chinese Academy of SciencesGuilin 541006China Department of Biology the Huck Institutes of Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA 16802USA

The ability of climbing plants to grow upward along others to reach the canopy for photosynthesis is hypothesized as a key innovation in flowering *** members of the Cucurbitaceae,a family containing^1000 species and many important crops,are climbers and have characteristic tendrils and pepo ***,we present 127 newly sequenced transcdptomes and genomes along with other datasets for a total of 136 cucurbits representing all tribes to establish a robust Cucurbitaceae phylogeny containing eight highly resolved major *** analyzed whole-genome duplication,diversification dynamics,and ancestral morphologies,and found that after early genome duplication event(s),a burst of diversification and morphological innovations in flower,fruit,and root characters occurred under the climate optimum in the Early *** radiation during the Mid-Eocene Climatic Optimum also coincided with several morphological changes shared by 80%of *** found that the cucurbit-specific tendril identity gene TEN originated from a paleo-polyploidization event at the origin of the *** results support the hypothesis that cucurbit diversifications were probably driven by increased genetic diversity following polyploidizations and by trait morphological innovations under paleo-climate *** study provides a phylogenetic framework and new insights into morphological and genomic changes underlying the adaptive evolution of Cucurbitaceae.

关键词： Cucurbitaceae transcriptome phylogeny divergence time genome duplication diversification morphology adaptive evolution

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