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A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

Horticultural Plant Journal 2024年第3期10卷 911-930页

作者： Yishan Feng Zhenyi Wang Qimeng Xiao Jia Teng Jianyu Wang Zijian Yu Jiaqi Wang Qiang Xu Yan Zhang Shaoqi Shen Shoutong Bao Yu Li Zimo Yan Yue Ding Zihan Liu Yuxian Li Tianyu Lei Min Yuan Xiu-Qing Li Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China Fredericton Research and Development Centre Agriculture and Agri-Food CanadaFrederictonNew Brunswick E3B 4Z7Canada State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.

关键词： Nyssaceae polyploidization Multigenome alignment Evolutionary rate Autotetraploidization Karyotype evolution

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Allotetraploidization event of Coptis chinensis shared by all Ranunculales

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Horticultural Plant Journal 2024年第1期10卷 288-303页

作者： Yan Zhang Weina Ge Jia Teng Yanmei Yang Jianyu Wang Zijian Yu Jiaqi Wang Qimeng Xiao Junxin Zhao Shaoqi Shen Yishan Feng Shoutong Bao Yu Li Yuxian Li Tianyu Lei Yuxin Pan Lan Zhang Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China School of Life Sciences North China University of Science and TechnologyTangshanHebei 063000China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal value.In our study,by using syntenic analysis combined with phylogenomic analysis of C.chinensis and four other representative genomes from basal and core eudicots,we confirmed that the WGD event in C.chinensis was shared by Aquilegia coerulea and Papaver somniferum L.and quickly occurred after Ranunculales diverged from other eudicots,likely a Ranunculales common tetraploidization(RCT).The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the P.somniferum genome is faster than that of the C.chinensis genome by approximately 13.7%,possibly due to Papaveraceaes having an additional special tetraploidization event(PST).After Ks correction,the RCT dated to 115—130 million years ago(MYA),which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately115.45—130.51 MYA.Moreover,we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference genomes.Notably,the event-related subgenomes in the basal genomes all showed genomic fractionation bias,suggesting a likely allopolyploid nature of the RCT,PST and T-Alpha and T-Beta events in Tetracentron sinense.In addition,we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales,and most of them were related to the RCT and PST events.We constructed a new platform for Early Eudicot Comparative Genomic Research(http://www.***.top/index.html)to store more information.In summary,our findings support the WGD of C.chinensis shared by Ranunculales,which is likely an allotetraploidization event.This present effort offered new insights into the evolution of key polyploidization events and the genes related to secondary metabolites during the diversification of ea

关键词： Coptis chinensis Ranunculales polyploidization Genomic fractionation P450 genes

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Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae:Insights into the polyploidization of Phlegmariurus

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Plant Diversity 2022年第3期44卷 262-270页

作者： Zeng-Qiang Xia Zuo-Ying Wei Hui Shen Jiang-Ping Shu Ting Wang Yu-Feng Gu Amit Jaisi Yue-Hong Yan Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of ShenzhenShenzhen518114China CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and EcologyChinese Academy of Sciences300 Fenglin RoadShanghai200032China Shanghai Chenshan Plant Science Research Center Chinese Academy of Sciences3888 Chenhua Road SongjiangShanghai201602China University of Chinese Academy of Sciences Beijing100049China College of Life and Sciences Shanghai Normal UniversityShanghai201602China Life Science and Technology College Harbin Normal UniversityHarbinHeilongjiang 150025China Drug and Cosmetics Excellence Center School of PharmacyWalailak UniversityNakhon Si Thammarat80160Thailand

Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploidization,in spore-dispersed vascular plants.However,a lack of genome sequence data limits the reliable detection of very ancient WGDs,small-scale duplications(SSDs),and recent WGDs.Here,we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites(Ks)of the transcriptomes of 13 species of lycophytes to identify,locate,and date multiple WGDs in the lycophyte family Lycopodiaceae.Additionally,we examined the genus Phlegmariurus for signs of genetic discordance,which can provide valuable insight into the underlying causes of such conflict(e.g.,hybridization,incomplete lineage sorting,or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae,with one occurring in the common ancestor of extant Phlegmariurus(Lycopodiaceae)approximately 22-23 million years ago(Mya)and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya.Interestingly,we found significant genetic discordance in the genus Phlegmariurus,indicating that the genus has a complex evolutionary history.This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.

关键词： Lycophytes Whole genome duplication polyploidization Phylogenomics Gene tree conflict

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Comparative genomic analyses reveal cis-regulatory divergence after polyploidization in cotton

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The Crop Journal 2022年第6期10卷 1545-1556页

作者： Jiaqi You Min Lin Zhenping Liu Liuling Pei Yuexuan Long Lili Tu Xianlong Zhang Maojun Wang National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070HubeiChina School of Pharmaceutical Sciences South-Central University for NationalitiesWuhan 430074HubeiChina

polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty.However,knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited.In this study,we characterized transcriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors.We identified 144,827,99,609,and 219,379 Tn5 transposase-hypersensitive sites(THSs)in Gossypium arboreum,G.raimondii,and G.hirsutum,respectively,and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression.This observation was consistent with analysis of transcription-factor binding sites(TFBS)for 262 known motifs:genes with higher TFBS conservation scores(CS)showed less change than those genes with lower TFBS CS in expression levels.TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton.We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development(fiber-related genes).Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits.

关键词： Cotton polyploidization Transcriptional regulation Fiber development

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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 changes.However,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 ignored.Here,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 stimulation.The 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 plants.The expansions showed coincident enrichments in-times around and/or after the K-Pg boundary,when global cooling was a major environmental stressor.Consequently,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 networks.Moreover,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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Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat

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Science China(Life Sciences) 2023年第4期66卷 819-834页

作者： Hongcui Pei Wan Teng Lifeng Gao Hengbin Gao Xueni Ren Yanhong Liu Jizeng Jia Yiping Tong Yonghong Wang Zefu Lu Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory of Crop Biology College of Life SciencesShandong Agricultural UniversityTai’an 271018China Institute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China The State Key Laboratory for Plant Cell and Chromosome Engineering the Innovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China

Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat(Triticum aestivum.L.,BBAADD)is hypothesized to increase its adaptability and/or plasticity.However,the molecular basis of expression divergence remains unclear.Squamosa promoter-binding protein-like(SPL)transcription factors are critical for a wide array of biological processes.In this study,we constructed expression regulatory networks by combining DAP-seq for 40 SPLs,ATACseq,and RNA-seq.Our findings indicate that a group of low-affinity SPL binding regions(SBRs)were targeted by diverse SPLs and caused different sequence preferences around the core GTAC motif.The SBRs including the low-affinity ones are evolutionarily conserved,enriched GWAS signals related to important agricultural traits.However,those SBRs are highly diversified among the cis-regulatory regions(CREs)of syntenic genes,with less than 8%SBRs coexisting in triad genes,suggesting that CRE variations are critical for subgenome differentiations.Knocking out of Ta SPL7A/B/D and Ta SPL15A/B/D subfamily further proved that both high-and low-affinity SBRs played critical roles in the differential expression of genes regulating tiller number and spike sizes.Our results have provided baseline data for downstream networks of SPLs and wheat improvements and revealed that CRE variations are critical sources for subgenome divergence in the allohexaploid wheat.

关键词： wheat(Triticum aestivum L.) squamosa promoter-binding protein-like(SPL) transcriptional regulation cis-regulatory regions polyploidization low-affinity binding sites

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polyploidization Genetic Mechanism of Sugarcane Genome

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Asian Agricultural Research 2017年第8期9卷 84-87页

作者： Jungang WANG Tingting ZHAO Benpeng YANG Guoru XIONG Shuzhen ZHANG Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences/Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture

The sugarcane genome polyploidization can reduce the pressure of gene evolution selection,promote the fixation of fine traits,and increase the biomass and economic value of sugarcane.This paper mainly introduced the origin of the sugarcane genome,the chromosome composition,the research progress of polyploidization genetic mechanism,in the hope of providing theoretical reference for sugarcane polyploidization breeding.

关键词： polyploidization Genome Genetic evolution Molecular mechanism Sugarcane

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Evolutionary genetics of wheat mitochondrial genomes

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The Crop Journal 2023年第6期11卷 1774-1781页

作者： Hui-Lin Hu Fan Zhang Pei Wang Fu-Hao Lu State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004HenanChina Henan Key Laboratory of Big Data Analysis and Processing School of Computer and Information EngineeringHenan UniversityKaifeng 475004HenanChina School of Mathematics and Statistics Henan UniversityKaifeng 475004HenanChina

The Triticum-Aegilops complex provides ideal models for the study of polyploidization,and mitochondrial genomes(mtDNA)can be used to trace cytoplasmic inheritance and energy production following polyploidization.In this study,gapless mitochondrial genomes for 19 accessions of five Triticum or Aegilops species were assembled.Comparative genomics confirmed that the BB-genome progenitor donated mtDNA to tetraploid T.turgidum(genome formula AABB),and that this mtDNA was then passed on to the hexaploid T.aestivum(AABBDD).T urartu(AA)was the paternal parent of T.timopheevii(AAGG),and an earlier Ae.tauschii(DD)was the maternal parent of Ae.cylindrica(CCDD).Genic sequences were highly conserved within species,but frequent rearrangements and nuclear or chloroplast DNA insertions occurred during speciation.Four highly variable mitochondrial genes(atp6,cob,nad6,and nad9)were established as marker genes for Triticum and Aegilops species identification.The BB/GG-specific atp6 and cob genes,which were imported from the nuclear genome,could facilitate identification of their diploid progenitors.Genic haplotypes and repeat-sequence patterns indicated that BB was much closer to GG than to Ae.speltoides(SS).These findings provide novel insights into the polyploid evolution of the Triticum/Aegilops complex from the perspective of mtDNA,advancing understanding of energy supply and adaptation in wheat species。

关键词： Wheat Mitochondrion mtDNA Comparative genomics polyploidization

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Evidence for the Role Evolutionary Increase Yield in Cotton of Transfer Cells in the in Seed and Fiber Biomass

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Molecular Plant 2010年第6期3卷 1075-1086页

作者： Deborah A. Pugh Christina E. Offler Mark J. Talbot Yong-Ling Ruan School of Environmental and Life Sciences University of Newcastle Callaghan NSW 2308 Australia Australia-China Research Centre for Crop Improvement University of Newcastle Callaghan NSW 2308 Australia CSIRO Plant Industry Canberra ACT 2601 Australia

Transfer cells （TCs） are specialized cells exhibiting invaginated wall ingrowths （Wls）, thereby amplifying their plasma membrane surface area （PMSA） and hence the capacity to transport nutrients. However, it remains unknown as to whether TCs play a role in biomass yield increase during evolution or domestication. Here, we examine this issue from a comparative evolutionary perspective. The cultivated tetraploid AD genome species of cotton and its A and D genome diploid progenitors displayed high, medium, and low seed and fiber biomass yield, respectively. In all three species, cells of the innermost layer of the seed coat juxtaposed to the filial tissues trans-differentiated to a TC morphology. Electron microscopic analyses revealed that these TCs are characterized by sequential formation of flange and reticulate Wls during the phase of rapid increase in seed biomass. Significantly, TCs from the tetraploid species developed substantially more flange and reticulate Wls and exhibited a higher degree of reticulate WI formation than their progenitors. Consequently, the estimated PMSA of TCs of the tetraploid species was about 4 and 70 times higher than that of TCs of the A and D genome progenitors, respectively, which correlates positively with seed and fiber biomass yield. Further, TCs with extensive Wls in the tetraploid species had much stronger expression of sucrose synthase, a key enzyme involved in TC Wl formation and function, than those from the A and D progenitors. The analyses provide a set of novel evidence that the development of TC Wls may play an important role in the increase of seed and fiber biomass yield through polyploidization during evolution.

关键词： Callose cell wall cellulose cotton fiber evolution polyploidization seed development sucrose synthase transfer cell.

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The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits

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Plant Communications 2023年第2期4卷 77-92页

作者： Kang Zhang Yinqing Yang Xin Zhang Lingkui Zhang Yu Fu Zhongwei Guo Shumin Chen Jian Wu James C.Schnable Keke Yi Xiaowu Wang Feng Cheng Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of AgricultureSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 10008China Department of Agronomy and Horticulture University of NebraskaLincolnNE 68588USA Key Laboratory of Plant Nutrition and Fertilizer Ministry of AgricultureInstitute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing 100081China

Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental plant.The high oil content and abundance of unsaturated fatty acids in O.violaceus seeds make it a potential high-quality oilseed crop.Here,we generated a whole-genome assembly for O.violaceus using Nanopore and Hi-C sequencing technologies.The assembled genome of O.violaceus was~1.3 Gb in size,with 12 pairs of chromosomes.Through investigation of ancestral genome evolution,we determined that the genome of O.violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype.Comparisons between the reconstructed subgenomes of O.violaceus identified indicators of subgenome dominance,indicating that subgenomes likely originated via allotetraploidy.O.violaceus was phylogenetically close to the Brassica genus,and tetraploidy in O.violaceus occurred approximately 8.57 million years ago,close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage.However,the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica,as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks.Moreover,identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O.violaceus.These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O.violaceus.

关键词： Orychophragmus violaceus eryuelan genome assembly polyploidization subgenome differentiation function innovation

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