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| 1 | Genome sequences of horticultural plants:past,present,and future显示文摘Horticultural plants play various and critical roles for humans by providing fruits,vegetables,materials for beverages,and herbal medicines and by acting as ornamentals.They have also shaped human art,culture,and environments and thereby have influenced the lifestyles of humans.With the advent of sequencing technologies,there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade.The genomes of horticultural plants are highly diverse and complex,often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication.Here we summarize the advances in the genome sequencing of horticultural plants,the reconstruction of pan-genomes,and the development of horticultural genome databases.We also discuss past,present,and future studies related to genome sequencing,data storage,data quality,data sharing,and data visualization to provide practical guidance for genomic studies of horticultural plants.Finally,we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project. | Fei Chen Yunfeng Song Xiaojiang Li Junhao Chen Lan Mo Xingtan Zhang Zhenguo Lin Liangsheng Zhang | 2019 | Horticulture Research2019，6，1： | 16 |
| 2 | PacBio Sequencing Reveals Transposable Elements as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae显示文摘 | Jiandong Bao Meilian Chen Zhenhui Zhong Wei Tang Lianyu Lin Xingtan Zhang Haolang Jiang Deyu Zhang Chenyong Miao Haibao Tang Jisen Zhang Guodong Lu Ray Ming Justice Norvienyeku Baohua Wang Zonghua Wang | 2017 | Molecular Plant2017，10，11： | 5 |
| 3 | Genetic basis of high aroma and stress toleranee in the oolong tea cultivar genome显示文摘Tea plants(Camellia sinensis)are commercially cultivated in>60 countries,and their fresh leaves are processed into tea,which is the most widely consumed beverage in the world.Although several chromosome-level tea plant genomes have been published,they collapsed the two haplotypes and ignored a large number of allelic variations that may underlie important biological functions in this species.Here,we present a phased chromosome-scale assembly for an elite oolong tea cultivar,'Huangdan',that is well known for its high levels of aroma.Based on the two sets of haplotype genome data,we identi fi ed numerous genetic variations and a substantial proportion of allelic imbalance related to important traits,including aroma-and stress-related alleles.Comparative genomics revealed extensive structural variations as well as expansion of some gene families,such as terpene synthases(TPSs),that likely contribute to the high-aroma characteristics of the backbone parent,underlying the molecular basis for the biosynthesis of aroma-related chemicals in oolong tea.Our results uncovered the genetic basis of special features of this oolong tea cultivar,providing fundamental genomic resources to study evolution and domestication for the economically important tea crop. | Pengjie Wang Jiaxin Yu Shan Jin Shuai Chen Chuan Yue Wenling Wang Shuilian Gao Hongli Cao Yucheng Zheng Mengya Gu Xuejin Chen Yun Sun Yuqiong Guo Jiangfan Yang Xingtan Zhang Naixing Ye | 2021 | Horticulture Research2021，8，1： | 4 |
| 4 | The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids显示文摘Magnolia biondii Pamp.(Magnoliaceae,magnoliids)is a phylogenetically,economically,and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China.Determining the genome sequence of M.biondii would help resolve the phylogenetic uncertainty of magnoliids and improve the understanding of individual trait evolution within the Magnolia genus.We assembled a chromosome-level reference genome of M.biondii using~67,~175,and~154Gb of raw DNA sequences generated via Pacific Biosciences single-molecule real-time sequencing,10X Genomics Chromium,and Hi-C scaffolding strategies,respectively.The final genome assembly was~2.22Gb,with a contig N50 value of 269.11 kb and a BUSCO complete gene percentage of 91.90%.Approximately 89.17%of the genome was organized into 19 chromosomes,resulting in a scaffold N50 of 92.86Mb.The genome contained 47,547 protein-coding genes,accounting for 23.47%of the genome length,whereas 66.48%of the genome length consisted of repetitive elements.We confirmed a WGD event that occurred very close to the time of the split between the Magnoliales and Laurales.Functional enrichment of the Magnolia-specific and expanded gene families highlighted genes involved in the biosynthesis of secondary metabolites,plant–pathogen interactions,and responses to stimuli,which may improve the ecological fitness and biological adaptability of the lineage.Phylogenomic analyses revealed a sister relationship of magnoliids and Chloranthaceae,which are sister to a clade comprising monocots and eudicots.The genome sequence of M.biondii could lead to trait improvement,germplasm conservation,and evolutionary studies on the rapid radiation of early angiosperms. | Shanshan Dong Min Liu Yang Liu Fei Chen Ting Yang Lu Chen Xingtan Zhang Xing Guo Dongming Fang Linzhou Li Tian Deng Zhangxiu Yao Xiaoan Lang Yiqing Gong Ernest Wu Yaling Wang Yamei Shen Xun Gong Huan Liu Shouzhou Zhang | 2021 | Horticulture Research2021，8，1： | 4 |
| 5 | Papaya CpbHLH1/2 regulate carotenoid biosynthesis-related genes during papaya fruit ripening显示文摘The ripening of papaya is a physiological and metabolic process associated with accumulation of carotenoids,alternation of flesh color and flavor,which depending on genotype and external factors such as light and hormone.Transcription factors regulating carotenoid biosynthesis have not been analyzed during papaya fruit ripening.RNA-Seq experiments were implemented using different ripening stages of papaya fruit from two papaya varieties.Cis-elements in lycopeneβ-cyclase genes(CpCYC-B and CpLCY-B)were identified,and followed by genome-wide analysis to identify transcription factors binding to these cis-elements,resulting in the identification of CpbHLH1 and CpbHLH2,two bHLH genes.The expressions of CpbHLH1/2 were changed during fruit development,coupled with transcript increase of carotenoid biosynthesis-related genes including CpCYC-B,CpLCY-B,CpPDS2,CpZDS,CpLCY-E,and CpCHY-B.Yeast onehybrid(Y1H)and transient expression assay revealed that CpbHLH1/2 could bind to the promoters of CpCYC-B and CpLCY-B,and regulate their transcriptions.In response to strong light,the results of elevated expression of carotenoid biosynthesis-related genes and the changed expression of CpbHLH1/2 indicated that CpbHLH1/2 were involved in light-mediated mechanisms of regulating critical genes in the carotenoid biosynthesis pathway.Collectively,our findings demonstrated several TF family members participating in the regulation of carotenoid genes and proved that CpbHLH1 and CpbHLH2 individually regulated the transcription of lycopeneβ-cyclase genes(CpCYC-B and CpLCY-B).This study yielded novel findings on regulatory mechanism of carotenoid biosynthesis during papaya fruit ripening. | Dong Zhou Yanhong Shen Ping Zhou Mahpara Fatima Jishan Lin Jingjing Yue Xingtan Zhang Li-Yu Chen Ray Ming | 2019 | Horticulture Research2019，6，1： | 3 |
| 6 | Chromatin accessibility and translational Iandscapes of tea plants under chilling stress显示文摘Plants have evolved regulatory mechanisms at multiple levels to regulate gene expression in order to improve their cold adaptability.However,limited information is available regarding the stress response at the chromatin and translational levels.Here,we characterize the chromatin accessibility,transcriptional,and translational landscapes of tea plants in vivo under chilling stress for the first time.Chilling stress signi ficantly affected both the transcription and translation levels as well as the translation efficiency of tea plants.A total of 3010 genes that underwent rapid and independent translation under chilling stress were observed,and they were signi ficantly enriched in the photosynthesis-antenna protein and phenylpropanoid biosynthesis pathways.A set of genes that were signi ficantly responsive to cold at the transcription and translation levels,including four(+)-neomenthol dehydrogenases(MNDs)and two(E)-nerolidol synthases(NESs)arranged in tandem on the chromosomes,were also found.We detected potential upstream open reading frames(uORFs)on 3082 genes and found that tea plants may inhibit the overall expression of genes by enhancing the translation of uORFs under chilling stress.In addition,we identi fied distal transposase hypersensitive sites(THSs)and proximal THSs and constructed a transcriptional regulatory network for tea plants under chilling stress.We also identi fied 13 high-con fidence transcription factors(TFs)that may play a crucial role in cold regulation.These results provide valuable information regarding the potential transcriptional regulatory network in plants and help to clarify how plants exhibit flexible responses to chilling stress. | Pengjie Wang Shan Jin Xuejin Chen Liangyu Wu Yucheng Zheng Chuan Yue Yongchun Guo Xingtan Zhang Jiangfan Yang Naixing Ye | 2021 | Horticulture Research2021，8，1： | 2 |
| 7 | A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis(Podostemaceae)显示文摘The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction.The taxonomic status of Podostemaceae has always been controversial.Here,we report the first high-quality genome assembly for Cladopus chinensis of Podostemaceae,obtained by incorporating Hi-C,Illumina and PacBio sequencing.We generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding genes.The assembled genome size was close to the estimated size,and 659.42 Mb of the assembly was assigned to 29 superscaffolds(scaffold N5021.22 Mb).A total of 59.20%repetitive sequences were identified,among which long terminal repeats(LTRs)were the most abundant class(28.97%of the genome).Genome evolution analysis suggested that the divergence time of Cladopus chinensis(106 Mya)was earlier than that of Malpighiales(82 Mya)and that this taxon diverged into an independent branch of Podestemales.A recent whole-genome duplication(WGD)event occurred 4.43 million years ago.Comparative genomic analysis revealed that the expansion and contraction of oxidative phosphorylation,photosynthesis and isoflavonoid metabolism genes in Cladopus chinensis are probably related to the genomic characteristics of this growing submerged species.Transcriptome analysis revealed that upregulated genes in the shoot group compared to the root group were enriched in the NAC gene family and transcription factors associated with shoot development and defense responses,including WUSCHEL(WUS),ASYMMETRIC LEAVES(ASL),SHOOT MERISTEMLESS(STM),NAC2,NAC8,NAC29,NAC47,NAC73,NAC83 and NAC102.These findings provide new insights into the genomic diversity of unusual aquatic angiosperms and serve as a valuable reference for the taxonomic status and unusual shoot apical meristem of Podostemaceae. | Ting Xue Xuehai Zheng Duo Chen Limin Liang Nan Chen Zhen Huang Wenfang Fan Jiannan Chen Wan Cen Shuai Chen Jinmao Zhu Binghua Chen Xingtan Zhang Youqiang Chen | 2020 | Horticulture Research2020，7，1： | 1 |
| 8 | Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species,Cyclocarya paliurus显示文摘Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently.Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B.Here,we presented three C.paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly.Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids.Resequencing analysis of 45 C.paliurus individuals uncovered two bottlenecks,consistent with the known events of environmental changes,and many selectively swept genes involved in critical biological functions,including plant defense and secondary metabolite biosynthesis.We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes,in particular gibberellinrelated genes,associated with the heterodichogamy in C.paliurus species.Our study sheds light on evolutionary history of C.paliurus and provides genomic resources to study the medicinal herbs. | Yinquan Qu Xulan Shang Ziyan Zeng Yanhao Yu Guoliang Bian Wenling Wang Li Liu Li Tian Shengcheng Zhang Qian Wang Dejin Xie Xuequn Chen Zhenyang Liao Yibin Wang Jian Qin Wanxia Yang Caowen Sun Xiangxiang Fu Xingtan Zhang Shengzuo Fang | 2023 | Genomics, Proteomics & Bioinformatics2023，21，3： | 1 |
| 9 | Cloning and evolutionary analysis of tobacco MAPK gene family显示文摘 | Xingtan Zhang Tingcai Cheng Genhong Wang Yafei Yan Qingyou Xia | 2013 | Molecular Biology Reports2013，，2： | 1 |
| 10 | A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus(JUJUNCAO)provides insights into its evolution and C4 photosynthesis显示文摘JUJUNCAO(Cenchrus fungigraminus;2n=4x=28)is a Cenchrus grass with the highest biomass production among cultivated plants,and it can be used for mushroom cultivation,animal feed,and biofuel production.Here,we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated2.7 million years ago(mya).Its genome consists of two subgenomes,and subgenome A shares high collinear synteny with pearl millet.We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO.Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes,which was a further indication of asymmetric DNA methylation.The three types of centromeric repeat in the JUJUNCAO genome(CEN137,CEN148,and CEN156)may have evolved independently within each subgenome,with some introgressions of CEN156 from the B to the A subgenome.We investigated the photosynthetic characteristics of JUJUNCAO,revealing its typical C4 Kranz anatomy and high photosynthetic efficiency.NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO,which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield.Taken together,our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies,as well as genetic improvement of Cenchrus grasses. | Huakun Zheng Baiyu Wang Xiuting Hua Ruiting Gao Yuhao Wang Zixin Zhang Yixing Zhang Jing Mei Yongji Huang Yumin Huang Hui Lin Xingtan Zhang Dongmei Lin Siren Lan Zhongjian Liu Guodong Lu Zonghua Wang Ray Ming Jisen Zhang Zhanxi Lin | 2023 | Plant Communications2023，4，5： | 1 |
| 11 | A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance显示文摘The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing,Oxford Nanopore 50-kb ultra-long,and high-throughput chromatin conformation capture technologies.The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps,while a total of 633.0 Mb genomic sequences were generated.The origination analysis identified 338.5Mb genomic sequences originating from citron(53.5%),147.4Mb frommandarin(23.3%),and 147.1Mb frompummelo(23.2%).The genome included 30528 protein-coding genes,and most of the assembled sequences were found to be repetitive sequences.Several significantly expanded gene families were associated with plant-pathogen interactions,plant hormone signal transduction,and the biosynthesis of major active components,such as terpenoids and f lavor compounds.Most HLB-tolerant genes were expanded in the lemon genome,such as 2-oxoglutarate(2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1,cell wall-related genes,and lignin synthesis genes.Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon.Our results provide insight into lemon genome evolution,active component biosynthesis,and genes associated with HLB tolerance. | Yixue Bao Ziyan Zeng Wei Yao Xiao Chen Mengwei Jiang Akbar Sehrish Bo Wu Charles A.Powell Baoshan Chen Jianlong Xu Xingtan Zhang Muqing Zhang | 2023 | Horticulture Research2023，10，4： | 0 |
| 12 | Recent Advances in Assembly of Complex Plant Genomes显示文摘Over the past 20 years,tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already,ranging from those of nonvascular plants to those of flowering plants.However,complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity,highly repetitive sequences,or high ploidy characteristics of complex genomes.Herein,we summarize the challenges of and advances in complex plant genome assembly,including feasible experimental strategies,upgrades to sequencing technology,existing assembly methods,and different phasing algorithms.Moreover,we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes.Finally,we expect that the accurate,gapless,telomere-totelomere,and fully phased assembly of complex plant genomes could soon become routine. | Weilong Kong Yibin Wang Shengcheng Zhang Jiaxin Yu Xingtan Zhang | 2023 | Genomics, Proteomics & Bioinformatics2023，21，3： | 0 |
| 13 | The high-resolution three-dimensional(3D)chromatin map of the tea plant(Camellia sinensis)显示文摘Dear Editor,Tea plant(Camellia sinensis(L.)O.Kuntze)is one of the world’s most important non-alcoholic beverages,with great economic,health,and cultural value.Recently,several genomes of C.sinensis var.assamica(CSA)(Yunkang 10),C.sinensis var.sinensis(CSS)(Shuchazao,Biyun,Longjing 43,Tieguanyin,Huangdan),and ancient tea plant(DASZ)have been deciphered[1-3]. | Weilong Kong Jiaxin Yu Jingjing Yang Yanbing Zhang Xingtan Zhang | 2023 | Horticulture Research2023，10，10： | 0 |
| 14 | Genome sequencing revealed the red-flower trait candidate gene of a peach landrace显示文摘Peach(Prunus persica)is an economically important fruit crop globally and an excellent material for genomic studies.While considerable progress has been made in unveiling trait-associated genes within cultivars and wild relatives,certain novel genes controlling valuable traits in peach landraces,such as the red-flowering gene,remained unclear.In this study,we sequenced and assembled the diploid genome of the red-flower landrace‘Yingzui’(abbreviated as‘RedY’).Multi-omics profiling of red petals of‘RedY’revealed the intensified red coloration associated with anthocyanins accumulation and concurrent decline in f lavonols.This phenomenon is likely attributed to a natural variant of Flavonol Synthase(FLS)harboring a 9-bp exonic insertion.Intriguingly,the homozygous allelic configurations of this FLS variant were only observed in red-flowered peaches.Furthermore,the 9-bp sequence variation tightly associated with pink/red petal color in genome-wide association studies(GWAS)of collected peach germplasm resources.Functional analyses of the FLS variant,purified from procaryotic expression system,demonstrated its diminished enzymatic activity in f lavonols biosynthesis,impeccably aligning with the cardinal trait of red flowers.Therefore,the natural FLS variant was proposed as the best candidate gene for red-f lowering trait in peach.The pioneering unveiling of the red-flowered peach genome,coupled with the identification of the candidate gene,expanded the knowledge boundaries of the genetic basis of peach traits and provided valuable insights for future peach breeding efforts. | Ping Zhou Siru Lei Xiaodan Zhang Yinghao Wang Rui Guo Shaobin Yan Guang Jin Xingtan Zhang | 2023 | Horticulture Research2023，10，11： | 0 |
| 15 | 5mC DNA methylation modification-mediated regulation in tissue functional differentiation and important flavor substance synthesis of tea plant (Camellia sinensis L.)显示文摘In plants,5mC DNA methylation is an important and conserved epistatic mark involving genomic stability,gene transcriptional regulation,developmental regulation,abiotic stress response,metabolite synthesis,etc.However,the roles of 5mC DNA methylation modification(5mC methylation)in tea plant growth and development(in pre-harvest processing)and flavor substance synthesis in pre-and post-harvest processing are unknown.We therefore conducted a comprehensive methylation analysis of four key pre-harvest tissues(root,leaf,flower,and fruit)and two processed leaves during oolong tea post-harvest processing.We found that differential 5mC methylation among four key tissues is closely related to tissue functional differentiation and that genes expressed tissue-specifically,responsible for tissue-specific functions,maintain relatively low 5mC methylation levels relative to non-tissue-specifically expressed genes.Importantly,hypomethylation modifications of CsAlaDC and TS/GS genes in roots provided the molecular basis for the dominant synthesis of theanine in roots.In addition,integration of 5mC DNA methylationomics,metabolomics,and transcriptomics of post-harvest leaves revealed that content changes in flavor metabolites during oolong tea processing were closely associated with transcription level changes in corresponding metabolite synthesis genes,and changes in transcript levels of these important synthesis genes were strictly regulated by 5mC methylation.We further report that some key genes during processing are regulated by 5mC methylation,which can effectively explain the content changes of important aroma metabolites,includingα-farnesene,nerolidol,lipids,and taste substances such as catechins.Our results not only highlight the key roles of 5mC methylation in important flavor substance synthesis in pre-and post-harvest processing,but also provide epimutation-related gene targets for future improvement of tea quality or breeding of whole-tissue high-theanine varieties. | Weilong Kong Qiufang Zhu Qing Zhang Yiwang Zhu Jingjing Yang Kun Chai Wenlong Lei Mengwei Jiang Shengcheng Zhang Jinke Lin Xingtan Zhang | 2023 | Horticulture Research2023，10，8： | 0 |
| 16 | Haplotype-resolved and chromosome-level genome assembly of Colorado potato beetle显示文摘As the most important non-cereal food crop,potatoes are a staple food for 1.3 billion people(Stokstad,2019).However,these cultivated potatoes are challenged with multiple biotic stresses(i.e.,pathogens and pests),some of which can evade host resistance,leading to a serious dampening of potato yield.One of these pests is the Colorado potato beetle(hereafter referred to as CPB,Leptinotarsa decemlineata Say).CPB is a member of the order Coleoptera,and originated in the southwestern United States and Mexico(Alyokhin et al.,2008). | Ziqi Ye Ruirui Lu Chao Li Doudou Yang Zhuozhen Zeng Weichao Lin Jie Cheng Zhongmin Yang Li Wang Yulin Gao Sanwen Huang Xingtan Zhang Suhua Li | 2023 | Journal of Genetics and Genomics2023，50，7： | 0 |
| 17 | Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution显示文摘Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes.We sequenced the genomes of Pistacia vera cultivar(cv.)Siirt,the female parent,and P.vera cv.Bagyolu,the male parent.Two chromosome-level reference genomes of pistachio were generated,and Z and W chromosomes were assembled.The ZW chromosomes originated from an autosome following the first inversion,which occurred approximately 8.18 Mya.Three inversion events in the W chromosome led to the formation of a 12.7-Mb(22.8%of the W chromosome)non-recombining region.These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio.The W-specific genes,including defA,defA-like,DYT1,two PTEN1,and two tandem duplications of six VPS13A paralogs,are strong candidates for sex determination or differentiation.Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago,dating the domestication event close to the archeological record of pistachio domestication in Iran.We identified 390,211,and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality,grafting success,flowering time shift,and drought tolerance.These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks. | Salih Kafkas Xiaokai Ma Xingtan Zhang Hayat Topc¸u Rafael Navajas-Pérez Ching Man Wai Haibao Tang Xuming Xu Mortaza Khodaeiaminjan Murat Güney Aibibula Paizila Harun Karcı Xiaodan Zhang Jing Lin Han Lin Roberto de la Herrán Carmelo Ruiz Rejón Jerson Alexander García-Zea Francisca Robles Coral del Val Muñoz Agnes Hotz-Wagenblatt Xiangjia Jack Min HakanÖzkan Elmira Ziya Motalebipour Hatice Gozel Nergiz C¸oban Nesibe Ebru Kafkas Andrej Kilian HuaXing Huang Xuanrui Lv Kunpeng Liu Qilin Hu Ewelina Jacygrad William Palmer Richard Michelmore Ray Ming | 2023 | Plant Communications2023，4，3： | 0 |
| 18 | Evolutionary genomics of structural variation in the tea plant,Camellia sinensis显示文摘Structural variants(SVs)are a type of genetic variation that contribute substantially to phenotypic diversity and evolution.Further study of SVs will help us understand the influence of SVs associated with tea quality and stress resistance and provide new insight into tea plant breeding improvement and genetic research.However,SVs have not been thoroughly discovered in the tea plant genomes.Herein,we constructed a large-scale SV map across a population of 107 resequenced genomes,including both ancient and cultivated tea plants.A total of 44,240 highconfident SVs were identified,including 34,124 DEL(deletions),4,448 DUP(duplications),2,503 INV(inversions),544 INS(insertions)and 2,621 TRA(translocations).In total,12,400 protein-coding genes were overlapped with SVs,of which 49.5%were expressed in all five tea tissues.SVbased analysis of phylogenetic relationships and population structure in tea plants showed a consistent evolutionary history with the SNP-based results.We also identified SVs subject to artificial selection and found that genes under domestication were enriched in metabolic pathways involving theanine and purine alkaloids,biosynthesis of monoterpenoid,phenylpropanoid,fatty acid,and isoflavonoid,contributing to traits of agronomic interest in tea plants.In addition,a total of 27 terpene synthase(TPS)family genes were selected during domestication.These results indicate that these SVs could provide extensive genomic information for tea quality improvement. | Shuai Chen Jingping Fang Yibin Wang Pengjie Wang Shengcheng Zhang Zhenyang Liao Hong Lu Xingtan Zhang | 2022 | Tropical Plants2022，1，1： | 0 |
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