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GenomeSyn-Ⅱ:a comparative genomics framework integrating synteny visualization 认领 引用
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作者 Zu-Wen Zhou Hong-Yun Zhao +6 位作者 Yi-Bo Chai Ru-Peng Zhao Yong-Qing Qian Yuan-Yuan Zhong Yan-Han Shao Ling-Ling Chen Jia-Ming Song 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2026年第7期1332-1335,共4页
The rapid advance of pangenome research has enabled comparative genomics to provide critical insights into the molecular basis of gene evolution,species divergence,and phenotypic variation by identifying syntenic rela... The rapid advance of pangenome research has enabled comparative genomics to provide critical insights into the molecular basis of gene evolution,species divergence,and phenotypic variation by identifying syntenic relationships among multiple genomes(Wei et al.,2024;Xie et al.,2024;Qian et al.,2025).Analyses of synteny and structural variations across different varieties or species have become a major research focus in recent years,driven by advances in pangenome construction strategies and the rapid growth of high‑quality genome assemblies(Yim et al.,2022;Sun et al.,2025). 展开更多
关键词 genomesyn pangenome research identifying syntenic relationships multiple genomes wei synteny structural variations across different varieties species pangenome gene evolution comparative genomics synteny
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Gap-free genome of Durio zibethinus cv.Chuongbo 认领 引用
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作者 Shenghao Wang Junyu Zhang +3 位作者 Guilian Guo Zhidong Li Fei Chen Wenquan Wang 《Tropical Plants》 CSCD 2026年第1期112-120,共9页
Durian(Durio zibethinus L.)is a tropical fruit of substantial nutritional and economic value from the family Malvaceae.Several genome assemblies for durian have been reported previously,but these assemblies contain ga... Durian(Durio zibethinus L.)is a tropical fruit of substantial nutritional and economic value from the family Malvaceae.Several genome assemblies for durian have been reported previously,but these assemblies contain gaps that have restricted their completeness and hindered their practical utility for downstream research.Here,we present the first gap-free genome assembly of Durio zibethinus cv.Chuongbo by integrating PacBio HiFi,Oxford Nanopore,and Hi-C sequencing data.The assembled genome is 824.78 Mb across 28 chromosomes,with a scaffold N50 of 30.88 Mb and 44,024 protein-coding genes.Comparative genomic analyses dated the divergence between D.zibethinus cv.Chuongbo and Herrania umbratica to 35 million years ago,and between two durian cultivars to 2 million years ago.D.zibethinus cv.Chuongbo exhibits substantial gene family expansion and a high abundance of species-specific genes,reflecting key genomic innovations underlying its unique biological traits.Additionally,comparative analysis of the TERT gene family across 27 Malvaceae species uncovered strong evolutionary constraints that maintain a predominant single-copy configuration,with two copies identified in several Gossypium taxa.This high-quality,gap-free genome provides a foundational resource for elucidating genome architecture,gene evolution,and the molecular basis of unique traits in durian and related Malvaceae species. 展开更多
关键词 gap free genome assembled genome durio zibethinus pacbio hifioxford nanoporeand durian durio zibethinus durio zibethinus cv chuongbo tropical fruit genome assemblies
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Mitochondrial genome variation sheds light on the structural plasticity and nuclear mitochondrial segments dynamics in Malus species 认领 引用
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作者 Jinrong Li Shuangyang Wu Sen Wang 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第4期950-954,共5页
The genus Malus,a cornerstone of global temperate fruit production,has experienced a complex reticulate evolutionary history that complicates organellar genome dynamics and germplasm utilization.To elucidate the genom... The genus Malus,a cornerstone of global temperate fruit production,has experienced a complex reticulate evolutionary history that complicates organellar genome dynamics and germplasm utilization.To elucidate the genomic plasticity shaped by evolutionary processes and domestication,we assembled and analyzed mitochondrial genomes from 17 Malus species.Although these mitogenomes exhibit high sequence conservation,their diversity arises from large-scale structural variations,including recombination-mediated rearrangements,lineage-specific inversions,and rep eat-driven deletions. 展开更多
关键词 assembled analyzed mitochondrial genomes genomic plasticity organellar genome dynamics reticulate evolution Malus species mitochondrial genome structural plasticity nuclear mitochondrial segments
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Exploring the evolutionary landscape of mitochondrial genomes in the sunflower family(Asteraceae) 认领 引用
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作者 Zhixi Fu Penghao Yang +2 位作者 Jiazhen Wu Guojin Zhang Yanlei Feng 《Plant Diversity》 SCIE CAS CSCD 2026年第2期278-288,共11页
Asteraceae,the largest family of flowering plants,comprises more than 26,000 species worldwide,many of which serve as crops,medicinal herbs,and ornamentals.While substantial genomic resources are available for nuclear... Asteraceae,the largest family of flowering plants,comprises more than 26,000 species worldwide,many of which serve as crops,medicinal herbs,and ornamentals.While substantial genomic resources are available for nuclear and chloroplast genomes,mitochondrial genomes(mitogenomes)in this family remain poorly explored,limiting an integrated understanding of its genomic evolution.Here,we assembled 38 complete mitogenomes representing 12 subfamilies and 22 tribes.Our analyses revealed substantial size variation,with notably larger mitogenomes in early-diverging lineages.We also observed extensive structural rearrangements across subfamilies and tribes.Although the gene content is largely conserved,we identified notable mutations,horizontal gene transfer events,and losses of RNA editing sites.We reconstructed a comprehensive mitochondrial phylogeny of Asteraceae,which revealed both congruent and conflicting relationships with phylogenies based on plastid and nuclear markers.Furthermore,our fragment analysis of total mitochondrial DNA demonstrated that the differential retention of ancestral sequences significantly influences mitogenome size variation in Asteraceae.This study provides a systematic mitogenomic resource,offering novel insights into the evolutionary dynamics of this major plant family. 展开更多
关键词 Asteraceae Mitochondrial genome Phylogeny Genome size variation Horizontal gene transfer
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Chromosome-level genome assembly of the endangered Magnolia sinostellata:Insights into genome evolution,cold stress resistance,and terpenoid biosynthesis 认领 引用
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作者 Huijuan Zhou Fan Wu +12 位作者 Hengzhao Liu Jiayu Ma Huiling Yan Renna Li Lu Fan Fangbing Ding Yuwei Linghu Bin Xie Xiaoai Fang Shu Yang Ming Yue Peng Zhao Yaling Wang 《Journal of Systematics and Evolution》 SCIE CSCD 2026年第2期260-282,共23页
The genus Magnolia belongs to Magnoliaceae,an early diverging lineage of the Magnoliales,and is cultivated globally for its high ornamental and commercial values.As a large genus in the family Magnoliaceae,Magnolia sp... The genus Magnolia belongs to Magnoliaceae,an early diverging lineage of the Magnoliales,and is cultivated globally for its high ornamental and commercial values.As a large genus in the family Magnoliaceae,Magnolia species are regarded as highly valuable in phylogenetic and conservation biological studies.However,the whole genome data of Magnolia is still relatively insufficient.Here,we present a high-quality,chromosome-level genome sequence of Magnolia sinostellata(1.86 Gb)with a scaffold N50 of 85.33 Mb.The 19 M.sinostellata genome chromosomes revealed 11 main duplications representing the subgenome.Comparative genomics analysis revealed that the variance in the number of abiotic stress resistance genes among Magnoliid species are related to different environmental adaptations.Most of the genes related to MAPK signaling and stress resistance pathways in the investigated M.sinostellata species are expanded,compared to the other species.Furthermore,the comparative genomics analysis of three Magnolia assemblies,M.sinostellata,Magnolia biondii,and Magnolia sieboldii revealed that large inversions were enriched in terpenoid metabolic pathways,stress resistance and flavonoid biosynthesis,and DNA replication proteins.Using transcriptome sequencing data,we analyzed the expression levels of genes related to terpenoid biosynthesis(terpene synthase)and ICE-CBF-COR gene models related to cold tolerance in various tissues and the buds under different temperature conditions.The high-quality assembly of M.sinostellata and the ICE-CBF-COR bioinformatic analysis cascade provide valuable resources for studying the phylogeny and evolution of Magnoliaceae and angiosperms,while the candidate genes will provide foundational support for molecular breeding in Magnolia species. 展开更多
关键词 chromosome duplication chromosome-scale genome assembly comparative genome ICE-CBF-COR signaling pathway Magnolia sinostellata terpenoid biosynthesis
Pan-genome-wide identification and co-expression analysis of rapeseed SBT genes reveals that BnaSBT1.4 negatively regulates the salt-stress response 认领 引用
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作者 Shengting Li Xiaodong Li +8 位作者 Boyu Meng Daifei Song Yuanyi Mao Lin Liu Wei Chang Yonghai Fan Mingchao Qian Shahid Ullah Khan Kun Lu 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第5期1245-1249,共5页
Subtilases(SBTs)play important roles in plant development and resistance to environmental stresses.However,a systematic pan-genome characterization and functional analysis of the SBT family in polyploid crops had not ... Subtilases(SBTs)play important roles in plant development and resistance to environmental stresses.However,a systematic pan-genome characterization and functional analysis of the SBT family in polyploid crops had not been performed.In this study,we performed a pan-genome analysis of 17 rapeseed genomes and identified 1844 SBT family members,which were divided into 82 orthologous gene groups(OGGs)and classified into six subfamilies.Analysis of gene duplication analysis and gene expression patterns reveled that SBT subfamily 1A contains many core OGGs.The expression levels of the subfamily 1 OGG member Bna SBT.CR04 increased under salt-stress treatment. 展开更多
关键词 gene duplication analysis rapeseed genomes rapeseed sbt genes salt stress response gene expression patterns co expression analysis pan genome analysis orthologous gene groups oggs
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Chromosome-scale genome assembly of the endangered aquatic plant Ottelia songmingensis elucidates genomic features and conservation implications 认领 引用
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作者 Zhi-Zhong Li Zhi-Hao Qian +1 位作者 Wei Li Jin-Ming Chen 《Journal of Systematics and Evolution》 SCIE CSCD 2026年第3期485-498,共14页
Aquatic angiosperms represent an important but underexplored lineage for understanding genome evolution,particularly in species with exceptionally large genomes.Here,we present a chromosome-scale genome assembly of th... Aquatic angiosperms represent an important but underexplored lineage for understanding genome evolution,particularly in species with exceptionally large genomes.Here,we present a chromosome-scale genome assembly of the endangered aquatic monocot Ottelia songmingensis(~10.8 Gb),providing a valuable genomic resource for studying genome gigantism and conservation.Using ONT and Hi-C technologies,we anchored 87.7%of the assembly to 11 pseudochromosomes and predicted 35362 protein-coding genes.Comparative genomics revealed two whole-genome duplication events,including a more recent duplication and an ancestral triplication shared within Alismatidae.Repetitive elements constitute 94.3%of the genome,with long terminal repeat retrotransposons alone accounting for over 90%.A recent burst of LTR activity(~6 Mya)combined with a low solo-to-intact ratio(0.61)suggests inefficient transposon removal as a driver of genome expansion.Whole-genome bisulfite sequencing showed globally high DNA methylation levels(CG~85%,CHG~78%),particularly enriched in transposable element-rich regions,highlighting the role of epigenetic regulation in stabilizing large genomes.Population resequencing further indicated extremely low nucleotide diversity(π=5.31×10⁻⁴)and a long-term decline in effective population size since the Middle Pleistocene.Together,these resources provide a genomic foundation for exploring the evolutionary forces underlying genome gigantism and for guiding conservation genomics in endangered aquatic plants. 展开更多
关键词 endangered monocots genome stability ottelia songmingensis whole-genome duplication.
Using mixed kernel support vector machine to improve the predictive accuracy of genome selection 认领 引用 被引量：2
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作者 Jinbu Wang Wencheng Zong +6 位作者 Liangyu Shi Mianyan Li Jia Li Deming Ren Fuping Zhao Lixian Wang Ligang Wang 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2026年第2期775-787,共13页
The advantages of genome selection(GS) in animal and plant breeding are self-evident.Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects acc... The advantages of genome selection(GS) in animal and plant breeding are self-evident.Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects accurately.Machine learning models have demonstrated remarkable potential in addressing these challenges.In this study,we introduced the concept of mixed kernel functions to explore the performance of support vector machine regression(SVR) in GS.Six single kernel functions(SVR_L,SVR_C,SVR_G,SVR_P,SVR_S,SVR_L) and four mixed kernel functions(SVR_GS,SVR_GP,SVR_LS,SVR_LP) were used to predict genome breeding values.The prediction accuracy,mean squared error(MSE) and mean absolute error(MAE) were used as evaluation indicators to compare with two traditional parametric models(GBLUP,BayesB) and two popular machine learning models(RF,KcRR).The results indicate that in most cases,the performance of the mixed kernel function model significantly outperforms that of GBLUP,BayesB and single kernel function.For instance,for T1 in the pig dataset,the predictive accuracy of SVR_GS is improved by 10% compared to GBLUP,and by approximately 4.4 and 18.6% compared to SVR_G and SVR_S respectively.For E1 in the wheat dataset,SVR_GS achieves 13.3% higher prediction accuracy than GBLUP.Among single kernel functions,the Laplacian and Gaussian kernel functions yield similar results,with the Gaussian kernel function performing better.The mixed kernel function notably reduces the MSE and MAE when compared to all single kernel functions.Furthermore,regarding runtime,SVR_GS and SVR_GP mixed kernel functions run approximately three times faster than GBLUP in the pig dataset,with only a slight increase in runtime compared to the single kernel function model.In summary,the mixed kernel function model of SVR demonstrates speed and accuracy competitiveness,and the model such as SVR_GS has important application potential for GS. 展开更多
关键词 genome selection machine learning support vector machine kernel function mixed kernel function
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Chromosome-level genome assembly and population genomics analysis of Camellia rubituberculata provide insights into adaptation to karst habitats 认领 引用 被引量：2
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作者 Chao Yan Ming-tai An +4 位作者 Ming Tang Xin-xiang Bai Xu Xiao Zhao-hui Ran Zhi Li 《Plant Diversity》 SCIE CAS CSCD 2026年第2期246-261,共16页
Karst flora confined to isolated‘habitat islands'evolve specialized adaptations and unique traits,serving as ideal models for investigating adaptive evolution and species diversification mechanisms.Camellia rubit... Karst flora confined to isolated‘habitat islands'evolve specialized adaptations and unique traits,serving as ideal models for investigating adaptive evolution and species diversification mechanisms.Camellia rubituberculata,endemic to the karst habitats of Guizhou,China,can serve as a model for adaptive evolution and diversity in karst-endemic woody species.However,the lack of a chromosome-level genome for this species has limited in-depth studies on its adaptations to karst and posed a barrier to its genetic improvement.In this study,a chromosome-level genome assembly of C.rubituberculata was generated,with 15 pseudo-chromosomes and a genome size of 2.50 Gb(scaffold N50=168.34 Mb,55,302 protein-coding genes).Comparative genomics revealed two whole-genome duplications(WGDs),namely,an ancient γ-event(~120 Mya)and a subsequent genus-wide event(~86 Mya),after which gene families linked to karst adaptation(e.g.,photosynthesis)were significantly expanded.Selective sweep analysis showed that selected genes were associated with phytohormone transmission and metabolism.Genes functionally annotated as involved in stress responses—including SAUR,BSK,NCL,CDPK,and NDPK—participate in calcium homeostasis and ion transport pathways under karstspecific stresses.MYB transcription factors,which are crucial in plant responses to stresses,including drought,may be key for adaptation to the high salinity and drought stress in karst environments.The divergent selection in wild and cultivated groups highlight key adaptations in plant hormone transduction and calcium transport.By elucidating karst adaptation in C.rubituberculata,this work establishes essential genomic resources for advancing genetic evolution research and molecular breeding across Camellia species. 展开更多
关键词 Camellia rubituberculata Endemic species Genome assembly Karst adaptation Population genetics
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Complete genome assembly of the Xian rice variety IR64 as a valuable source in genomics and breeding research 认领 引用 被引量：1
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作者 Min Li Tingting Sheng +13 位作者 Linjun Yu Shuyue Zheng Shijiao Li Shuran Zhou Fengcai Wu Fan Zhang Chaopu Zhang Erbao Liu Yingyao Shi Xue Mi Xueru Zhang Zhikang Li Yanru Cui Wensheng Wang 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2026年第3期551-554,共4页
IR64 is an elite Xian/indica variety developed by International Rice Research Institute(IRRl)in 1985,which has been the most widely grown variety and core breeding parent in South/Southeast Asia(Mackill and Khush,2018... IR64 is an elite Xian/indica variety developed by International Rice Research Institute(IRRl)in 1985,which has been the most widely grown variety and core breeding parent in South/Southeast Asia(Mackill and Khush,2018).IR64 has been utilized to develop stress-tolerant(such as drought-adapted and submergenceresistant)near-isogenic lines,underscoring its great potential in agricultural genomics(Tanaka et al.,2020). 展开更多
关键词 Xian rice IR core breeding parent breeding research agricultural genomics tanaka genomics genome assembly stress tolerance
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A telomere-to-telomere genome assembly of radish(Raphanus sativus L.)provides insights into QTL mapping of bolting traits 认领 引用 被引量：1
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作者 Feng Yang Sihan Peng +13 位作者 Shuai Yuan Maolin Ran Xiaomei Li Yuejian Li Bin Liu Ming Li Chuibao Kong Xiao Yang Guohui Pan Xiaoping Yong Ke Ran Na Kuang Dawei Zhang Honghui Lin 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2026年第2期305-320,共16页
Radish(Raphanus sativus L.)is an important cruciferous root vegetable,with bolting regulated by multiple genes.However,the genetic mechanisms underlying bolting regulation remain unclear.Here,the genome of the cultiva... Radish(Raphanus sativus L.)is an important cruciferous root vegetable,with bolting regulated by multiple genes.However,the genetic mechanisms underlying bolting regulation remain unclear.Here,the genome of the cultivar C60213 is assembled into a high-quality,gap-free telomere-to-telomere structure,spanning nine chromosomes and totaling 472.71 Mb,using a combination of Oxford Nanopore,PacBio,and Hi-C sequencing technologies.It identifies 49,768 protein-coding genes,97.38%of which are functionally annotated.Repetitive sequences constitute 59.72%of the genome,primarily comprising long terminal repeats.A high-density genetic linkage map is constructed using an F2 population derived from a cross between early-and late-bolting radishes,identifying seven major quantitative trait loci associated with bolting and flowering.RNA-seq and quantitative real-time PCR analysis reveal that the RsMIPS3 gene is found to be associated with bolting,with its expression decreasing during this process.Notably,RsMIPS3 overexpression in Arabidopsis delays bolting,confirming its role in regulating bolting time.These findings advance radish genome research and provide a valuable target for breeding late-bolting varieties. 展开更多
关键词 Raphanus sativus L. Telomere-to-telomere Genome QTL Late-bolting RsMIPS3
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Chromosome-level genome of Iris domestica reveals genes involved in isoflavonoid biosynthesis 认领 引用 被引量：1
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作者 Beibei Su Da Sun +7 位作者 Deyu Zhang Ping Li Xiaojie Zhao Shuo Huang Yumeng Wu Yunfan Ji Kang Zhang Dazhuang Huang 《The Crop Journal》 SCIE CSCD 2026年第1期289-295,共7页
Iris domestica,a perennial herb of the Iridaceae family,is widely recognized for its rich isoflavone content and broad therapeutic properties.To elucidate the biosynthetic pathway of these medicinally significant comp... Iris domestica,a perennial herb of the Iridaceae family,is widely recognized for its rich isoflavone content and broad therapeutic properties.To elucidate the biosynthetic pathway of these medicinally significant compounds,we constructed a haplotype-resolved genome assembly of this species.Transcriptomic and metabolomic analyses revealed tissue-specific accumulation of isoflavone,particularly in rhizomes and roots.Functional characterization identified two candidate isoflavone synthase genes,among which IdIFS was confirmed to promote the biosynthesis of key compounds tectorigenin and irisflorentin.The high-quality genome assembly presented here provides a foundational resource for further research into the evolution,secondary metabolite,and environmental adaptation of I.domestica. 展开更多
关键词 Iris domestica Genome assembly Multi-omics Isoflavonoid biosynthesis Isoflavone synthase
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High-resolution mapping through whole-genome resequencing identifies two novel QTLs controlling oil content in peanut 认领 引用 被引量：1
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作者 Nian Liu Huaiyong Luo +9 位作者 Li Huang Xiaojing Zhou Weigang Chen Bei Wu Jianbin Guo Dongxin Huai Yuning Chen Yong Lei Boshou Liao Huifang Jiang 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2026年第4期1373-1383,共11页
Increasing the oil content is a key objective in peanut breeding programs.Accurate identification of quantitative trait loci(QTLs)with linked markers for oil content can facilitate marker-assisted selection for high-o... Increasing the oil content is a key objective in peanut breeding programs.Accurate identification of quantitative trait loci(QTLs)with linked markers for oil content can facilitate marker-assisted selection for high-oil breeding.In this study,a highdensity bin map was constructed by resequencing a recombinant inbred line(RIL)population(ZH16×J11)consisting of 295 lines.The bin map contained 4,212 loci and had a total length of 1,162.3 c M.Ten QTLs for oil content were identified in six linkage groups.Notably,two of these QTLs,qOCB03.1 and qOCB06.1,were consistently detected in a minimum of three environments and explained up to 13.62%of the phenotypic variation.They have not been reported in previous studies and thus are novel QTLs.The combination of favorable alleles from qOCB03.1 and qOCB06 in the RIL population could increase oil content across multiple environments from 1.50 to 2.46%.Two insertions/deletions(In Dels)markers linked to qOCB03.1 and qOCB06.1 were developed,and their association with oil content was validated in another RIL population(ZH10×ICG12625)with diverse phenotypes.In addition,the high-resolution map allowed for the precise positioning of qOCB03.1 and qOCB06.1 within a 1.77 Mb interval on chromosome B03 and a 1.51 Mb interval on chromosome B06,respectively.The annotation of genomic variants,analysis of transcriptome sequencing,and evaluation of the allelic effects in 292 peanut varieties revealed two candidate genes associated with oil content for each of the two QTLs.The candidate genes identified in this study can enable the map-based cloning of key genes controlling oil content in peanut.Furthermore,these novel and stable QTLs and their tightly linked markers are valuable for marker-assisted breeding for greater oil content in peanut. 展开更多
关键词 peanut oil content QTL mapping whole genome resequencing
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Chromosome-level genome assembly and genome-wide analysis of the NAC gene family of Artocarpus heterophyllus 认领 引用
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作者 Yutong Chen Chengcai Xia +3 位作者 Zhaoyu Liu Lanying Wang Zhiqiang Xia Xudong Yu 《Tropical Plants》 CSCD 2026年第1期86-99,共14页
Artocarpus heterophyllus Lam.(jackfruit)is a unique tropical economic plant renowned for its massive fruit as well as substantial nutritional and medicinal values.Notably,red-fleshed jackfruit has garnered significant... Artocarpus heterophyllus Lam.(jackfruit)is a unique tropical economic plant renowned for its massive fruit as well as substantial nutritional and medicinal values.Notably,red-fleshed jackfruit has garnered significant research interest due to its distinctive nutrient profile and specialized fruit development.However,its genetic diversity and genetic mechanisms remain to be further explored.Herein,we generated a chromosome-level genome assembly of redfleshed jackfruit,which was anchored to 28 pseudochromosomes,with a total size of 1.03 Gb.The assembly was constructed from 60 scaffolds with a scaffold N50 length of 39.36 Mb,and 45,366 protein-coding genes were predicted.Comparative genomic analysis revealed that jackfruit diverged from the common ancestor of the genus Morus approximately 44.85 million years ago,and that multiple gene families underwent significant expansion during this period.Notably,we identified 110 NAC family genes from the A.heterophyllus genome.As a well characterized family of transcription factors involved in plant development and stress responses,these NAC genes represent important candidate genes potentially associated with fruit development and stress tolerance in jackfruit.This study substantially enhances our understanding of the evolution and genetics of jackfruit and its gene families,and provides key candidate genes for deciphering the molecular mechanisms underlying important traits such as fruit development and stress tolerance in jackfruit. 展开更多
关键词 genetic diversity genome wide analysis red fleshed jackfruit nac gene family artocarpus heterophyllus lam jackfruit chromosome level genome assembly tropical economic plant Artocarpus heterophyllus
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Whole genome analysis of a Non-O1,Non-O139 Vibrio cholerae isolate from a bacteremia case in Ho Chi Minh City 认领 引用
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作者 Tuan-Loc Le Ngoc-Lan Nguyen +1 位作者 Duc-Khai Luong Hieu Vu-Quang 《Asian Pacific Journal of Tropical Medicine》 SCIE CAS 2026年第2期94-96,I0062-I0065,共3页
Non-O1on-O139 Vibrio(V.)cholerae(NOVC)has emerged as a potential pathogen in patients with compromised health conditions[1].We report the whole genome sequencing(WGS)of a rare NOVC sepsis isolate(GenBank Accession:GCF... Non-O1on-O139 Vibrio(V.)cholerae(NOVC)has emerged as a potential pathogen in patients with compromised health conditions[1].We report the whole genome sequencing(WGS)of a rare NOVC sepsis isolate(GenBank Accession:GCF_051906115.1)from an 89-year-old male admitted to the Intensive Care Unit(ICU)with septic shock(lactate 6.61 mmol/L)digestive illness. 展开更多
关键词 septic shock intensive care bacteremia intensive care unit whole genome sequencing wgs Whole genome analysis non O non O Vibrio cholerae sepsis
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A haplotype-resolved genome assembly for Centella asiatica provides insights into its genome evolution and ursane-type triterpene accumulation 认领 引用
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作者 Chao Wang Yingchen Hao +4 位作者 Zhonghui Zhang Xumin Ou Zifei Guo Shouchuang Wang Jun Yang 《The Crop Journal》 SCIE CSCD 2026年第3期959-971,共13页
Centella asiatica is a medicinal plant containing various ursane-type saponins that serve as a model system for studying triterpenoid accumulation.We assembled a haplotype-resolved genome for C.asiatica,and it showed ... Centella asiatica is a medicinal plant containing various ursane-type saponins that serve as a model system for studying triterpenoid accumulation.We assembled a haplotype-resolved genome for C.asiatica,and it showed allelic imbalance between haplotypes.The genome underwent one whole-genome duplication event followed by chromosomal fusion resulting in the current karyotype.We also constructed the metabolic regulatory network of triterpenoid saponins and found that triterpenoid biosynthesis was accompanied by gene duplication.These findings may assist in mining genes for the metabolism of C.asiatica and improving the understanding of the genetic basis for the diversity of triterpenoid biosynthesis. 展开更多
关键词 Centella asiatica Haplotype-resolved genome Allelic imbalance Duplication Ursane-type triterpenes Glycosyltransferase
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Advancing Rice Resilience to Heat Stress:Insights from CRISPR/Cas9 Genome Editing 认领 引用
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作者 Zakirullah KHAN Rahmatullah JAN +3 位作者 Saleem ASIF Hayati Aulia MAHARANI Muhammad FAROOQ Kyung-Min KIM 《Rice science》 SCIE CAS CSCD 2026年第3期340-350,共11页
Heat stress during reproductive stages remains one of the most critical constraints on rice yield and grain quality, yet progress in developing heat-resilient cultivars is slowed by the complex, polygenic nature of th... Heat stress during reproductive stages remains one of the most critical constraints on rice yield and grain quality, yet progress in developing heat-resilient cultivars is slowed by the complex, polygenic nature of thermotolerance and lengthy breeding cycles. Despite incremental gains through conventional breeding, high temperatures above 35 ℃ continue to cause severe spikelet sterility, yield losses, and quality deterioration. The emergence of CRISPR/Cas genome-editing offers a precise and efficient platform to dissect heat-stress mechanisms, and accelerate the development of heat-tolerant rice. CRISPR/Cas9 studies have validated and edited key genes involved in calcium signaling, hormone pathways, reproductive processes, photosynthesis, reactive oxygen species homeostasis, and transcriptional regulation, such as OsCNGC14/16, OsNCED1, OsSPL7, and OsHSP60-3b. Beyond stress resilience, genome editing has improved major yield components, including grain size, panicle architecture, and spikelet number, through targets such as GS3, GW3, Gn1a, and Os SPL16, achieving 28%–40% increases in grain weight and 15%–25% improvements in panicle traits, alongside enhanced grain quality attributes. Remaining challenges, including off-target effects, genotype dependence, limited field validation, and regulatory constraints, are being addressed through high-fidelity Cas variants, optimized sg RNA design, DNA-free editing, and integration with genomic selection and speed breeding. This review synthesizes advances in heat-stress biology and CRISPR/Cas applications in rice, and highlights future opportunities in base and prime editing, transcriptional reprogramming, multiplex genome engineering, and field deployment. 展开更多
关键词 rice genome editing CRISPR Cas9 heat stress thermotolerance
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Whole genome sequencing analysis reveals strong reproductive isolation between two hybridizing Rhododendron species in subgenus Tsutsusi 认领 引用
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作者 Xiaoling Tian Ningning Zhang +5 位作者 Xiaohua Li Zhong Zhang Heng Shu Chunying Zhang Yongpeng Ma Yupeng Geng 《Plant Diversity》 SCIE CAS CSCD 2026年第1期212-215,共4页
Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces... Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces may balance the dynamic consequences of hybridization:fusion by hybridization-mediated gene flow,and separation by reproductive isolation(RI)(Ma et al.,2010a,b;Chang et al.,2022). 展开更多
关键词 Reproductive isolation Natural hybridization Rhododendron Mutation load Whole genome sequence
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Application of an endogenous pGhaGloA promoter in the CRISPR/Cas12a system for efficient genome editing to create glandless cotton germplasm 认领 引用
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作者 Chenyu Li Zumuremu Tuerxun +10 位作者 Yang Yang Xiaorong Li Fengjiao Hui Juan Li Zhigang Liu Guo Chen Darun Cai Hui Zhang Xunji Chen Shuangxia Jin Bo Li 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2026年第5期1836-1845,共10页
An efficient genome editing tool,the CRISPR/Cas12a system,has been used in research on plant functional genomics and the improvement of agronomic traits.In this study,the CRISPR/Cas12a system was optimized by using th... An efficient genome editing tool,the CRISPR/Cas12a system,has been used in research on plant functional genomics and the improvement of agronomic traits.In this study,the CRISPR/Cas12a system was optimized by using the endogenous pGhaGloA promoter in cotton.With this system,crRNAs were driven by the Pol Ⅱ pGhaGloA promoter to construct the pGhRBE3-pGhaGloA-GhPGF vector and carry out genetic transformation.The vector worked efficiently in all positive transgenic plants and the editing efficiencies at the crRNA1 and crRNA2 target sites were up to 93.37 and 88.24%,respectively.This system had significantly higher editing efficiency than the pGhRBE3 system with a Pol Ⅲ promoter-Ubi 6.7promoter,indicating that the Pol Ⅱ promoter is more suitable for expressing multiple sgRNAs or crRNAs than the Pol Ⅲpromoter in cotton.The vector mainly generated the editing type of fragment deletion,and the deletion sizes were in the range of 3-12 bp with the editing sites spanning the 14th to 29th bases downstream of the protospacer adjacent motif(PAM).All the targeted mutation loci were stably inherited from the T0 to T2 generations,and three transgene-free lines with target site mutations in the GhPGF gene were obtained.These glandless and gossypol-free(or low content) cotton germplasms will play a key role in healthy cottonseed oil/cake production.Therefore,the CRISPR/Cas12a system driven by the pGhαGloA promoter can efficiently edit target genes in cotton,so it can provide a powerful tool for cotton functional genomics and genetic improvement. 展开更多
关键词 cotton genome editing CRISPR/Cas12a PolⅡpromoter glandless cotton gossypol-free
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The Camellia impressinervis genome provides novel insights into the flower coloration and flavor metabolism of Jinhua tea 认领 引用
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作者 Peilan Zhang Weihong Sun +21 位作者 Siyu Chen Yuanming Zhu Yuqing Lin Shuying Chen Xinyu Xu Dexing Chen Qiongyi Zhang Lin Ni Wei Huang Xiaoxing Zou FangSong Lian Guoyong Han Linying Wang Chengyuan Zhou Mengyao Zeng Yu-Yun Hsiao Shao-Ting Lin Wen-Yu Su Wen-Chieh Tsai Siren Lan Zhongjian Liu Shuangquan Zou 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第4期965-968,共4页
Camellia impressineruis(Jnhua tea),often called the'Queen of Camellia'or'Flora Panda',is a group of yellow-flowering camellias with notable ornamental,breeding,and medicinal value(Huang et al.,2022).De... Camellia impressineruis(Jnhua tea),often called the'Queen of Camellia'or'Flora Panda',is a group of yellow-flowering camellias with notable ornamental,breeding,and medicinal value(Huang et al.,2022).Despite this inherent value,the molecular regulatory mechanisms that produce its golden flower coloration and characteristic tea flavor remain poorly understood.Here,we present a high-quality,chromosomescale genome assembly of C.impressineruis to understand the molecular basis of yellow flower formation and flavor development,providing valuable scientific resources for future research on Jinhua tea. 展开更多
关键词 genome Camellia impressinervis yellow flower flower coloration camellia impressineruis jnhua flavor metabolism molecular regulatory mechanisms Jinhua tea
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