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AutoSeqMan:batch assembly of contigs for Sanger sequences 认领 引用 被引量：5
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作者 Jie-Qiong Jin Yan-Bo Sun 《Zoological Research》 SCIE CSCD 2018年第2期123-126,共4页
With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan （in the LaserGene package） is an excellent program with an easy-t... With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan （in the LaserGene package） is an excellent program with an easy-to-use graphical user interface （GUI） employed to assemble Sanger sequences into contigs. However, with increasing data size, larger sample sets and more sequenced loci make contig assemble complicated due to the considerable number of manual operations required to run SeqMan. Here, we present the ＇autoSeqMan＇ software program, which can automatedly assemble contigs using SeqMan scripting language. There are two main modules available, namely, ＇Classification＇ and ＇Assembly＇. Classification first undertakes preprocessing work, whereas Assembly generates a SeqMan script to consecutively assemble contigs for the classified files. Through comparison with manual operation, we showed that autoSeqMan saved substantial time in the preprocessing and assembly of Sanger sequences. We hope this tool will be useful for those with large sample sets to analyze, but with little programming experience. It is freely available at https：//github.com/ Sun-Yanbo/autoSeqMan. 展开更多
关键词 Batch processing Sanger sequences Contig assembly SeqMan
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Construction of Oryza sativa genome contigs by fingerprint strategy 认领 引用 被引量：1
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作者 TAO QUANZHOU YUEMIN QIAN +7 位作者 HAIYING ZHAO SHULIANG YU LONGFANG QIU BOQIAN WU JIA ZHU DI YU XIAOHUI LIU GUOFAN HONG(Shanghai Institute of Biochemistry, Chinese Acad 《Cell Research》 SCIE CAS 1995年第2期263-271,共9页
We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa, Guang Lu Ai 4.An entire representative (sixfold coverage of rice chromosomes) and genetically stable BAC library of rice ... We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa, Guang Lu Ai 4.An entire representative (sixfold coverage of rice chromosomes) and genetically stable BAC library of rice genome constructed in this lab has been systematically analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. And all the images thus obtained were subject to image-processing, which consisted of preliminary location of bands, cooperative tracking of lanesby correlation of adjacent bands, a precise densitometric pass, alignment at the marker bands with the standard,optional interactive editing, and normalization of the accepted bands. The contigs were generated based on the Computer Software specially designed for genome map ping. The number of contigs with 600 kb in length on average was 464; of contigs with 1000 kb in length on average was 107; of contigs with 1500 kb in length on average was 23. Therefore, all the contigs we have obtained amounted up to 420 megabases in length. Considering the size of rice genome (430 megabased), the contigs generated in this lab have covered nearly 98% of the rice genome. We are now in the process of mapping the contigs to chromosomes. 展开更多
关键词 Contig genome indica oryza sativa BAC
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Telomere-to-telomere genome assembly and 3D chromatin architecture of Centella asiatica insight into evolution and genetic basis of triterpenoid saponin biosynthesis 认领 引用 被引量：2
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作者 Wan-ling Song Bao-zheng Chen +6 位作者 Lei Feng Geng Chen Si-mei He Bing Hao Guang-hui Zhang Yang Dong Sheng-chao Yang 《Horticulture Research》 SCIE CSCD 2025年第5期247-262,共16页
Centella asiatica is renowned for its medicinal properties,particularly due to its triterpenoid saponins,such as asiaticoside and madecassoside,which are in excess demand for the cosmetic industry.However,comprehensiv... Centella asiatica is renowned for its medicinal properties,particularly due to its triterpenoid saponins,such as asiaticoside and madecassoside,which are in excess demand for the cosmetic industry.However,comprehensive genomic resources for this species are lacking,which impedes the understanding of its biosynthetic pathways.Here,we report a telomere-to-telomere(T2T)C.asiatica genome.The genome size is 438.12 Mb with a contig N50 length of 54.12 Mb.The genome comprises 258.87 Mb of repetitive sequences and 25200 protein-coding genes.Comparative genomic analyses revealed C.asiatica as an early-diverging genus within the Apiaceae family with a single whole-genome duplication(WGD,Apiaceae-ω)event following the ancientγ-triplication,contrasting with Apiaceae species that exhibit two WGD events(Apiaceae-αand Apiaceae-ω).We further constructed 3D chromatin structures,A/B compartments,and topologically associated domains(TADs)in C.asiatica leaves,elucidating the influence of chromatin organization on expression WGD-derived genes.Additionally,gene family and functional characterization analysis highlight the key role of CasiOSC03 inα-amyrin production while also revealing significant expansion and high expression of CYP716,CYP714,and UGT73 families involved in asiaticoside biosynthesis compared to other Apiaceae species.Notably,a unique and large UGT73 gene cluster,located within the same TAD,is potentially pivotal for enhancing triterpenoid saponin.Weighted gene coexpression network analysis(WGCNA)further highlighted the pathways modulated in response to methyl jasmonate(MeJA),offering insights into the regulatory networks governing saponin biosynthesis.This work not only provides a valuable genomic resource for C.asiatica but also sheds light on the molecular mechanisms driving the biosynthesis of pharmacologically important metabolites. 展开更多
关键词 contig n length D chromatin architecture centella asiatica genomic resources triterpenoid saponinssuch telomere telomere genome assembly repetitive sequences triterpenoid saponin biosynthesis
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The telomere-to-telomere genome of Pucai(蒲菜)(Typha angustifolia L.):a distinctive semiaquatic vegetable with lignin and chlorophyll as quality characteristics 认领 引用
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作者 Ya-Peng Li Li-Yao Su +5 位作者 Ting Huang Hui Liu Shan-Shan Tan Yuan-Jie Deng Ya-Hui Wang Ai-Sheng Xiong 《Horticulture Research》 SCIE CSCD 2025年第7期1-14,共14页
Pucai(graphic)(Typha angustifolia L.),within the Typha spp.,is a distinctive semiaquatic vegetable.Lignin and chlorophyll are two crucial traits and quality indicators for Pucai.In this study,we assembled a 207.00-Mb ... Pucai(graphic)(Typha angustifolia L.),within the Typha spp.,is a distinctive semiaquatic vegetable.Lignin and chlorophyll are two crucial traits and quality indicators for Pucai.In this study,we assembled a 207.00-Mb high-quality gapless genome of Pucai,telomere-to-telomere(T2T)level with a contig N50 length of 13.73 Mb.The most abundant type of repetitive sequence,comprising 16.98%of the genome,is the long terminal repeat retrotransposons(LTR-RT).A total of 30 telomeres and 15 centromeric regions were predicted.Gene families related to lignin,chlorophyll biosynthesis,and disease resistance were greatly expanded,which played important roles in the adaptation of Pucai to wetlands.The slow evolution of Pucai was indicated by theσwhole-genome duplication(WGD)-associated Ks peaks from different Poales and the low activity of recent LTR-RT in Pucai.Meanwhile,we found a unique WGD event in Typhaceae.A statistical analysis and annotation of genomic variations were conducted in interspecies and intraspecies of Typha.Based on the T2T genome,we constructed lignin and chlorophyll metabolic pathways of Pucai.Subsequently,the candidate structural genes and transcription factors that regulate lignin and chlorophyll biosynthesis were identified.The T2T genomic resources will provide molecular information for lignin and chlorophyll accumulation and help to understand genome evolution in Pucai. 展开更多
关键词 lignin chlorophyll contig n Typha angustifolia long terminal repeat retrotransposons ltr rt centromeric regions pucai graphic typha angustifolia telomere telomere genome
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关于基因重组中OLC算法的改进研究 认领 引用 被引量：1
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作者 买阿丽 杨雯雯 《郑州大学学报（理学版）》 CAS 北大核心 2016年第2期34-39,46,共6页
针对基因组组装问题,从数据预处理,利用KMP算法在O(m+n)的时间上快速确定某两个碱基片段的最大重复度,将读长序列依据Overlap图连成Contigs链以及Contigs N50的确定4个环节,改进现有的OLC拼接技术,并给出优化后的模型和算法,较好地解决... 针对基因组组装问题,从数据预处理,利用KMP算法在O(m+n)的时间上快速确定某两个碱基片段的最大重复度,将读长序列依据Overlap图连成Contigs链以及Contigs N50的确定4个环节,改进现有的OLC拼接技术,并给出优化后的模型和算法,较好地解决了基因组组装问题. 展开更多
关键词 基因重组 KMP算法 Overlap图 Contigs链 Contigs N50
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Chromosomal reference genome of Merremia boisiana:unveiling the secrets of the tropical rainforest's killer plant 认领 引用
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作者 Guilian Guo Pedro García-Caparros +6 位作者 Junyu Zhang Ji Zhang Yongping Li Shuang He Jia-yu Xue Fei Chen Wenquan Wang 《Tropical Plants》 CSCD 2025年第1期325-336,共12页
Merremia boisiana,a captivating species endemic to tropical rainforest habitats,belongs to the esteemed Convolvulaceae family.Renowned for its dazzling golden flowers and exceptional growth rate.This plant rapidly exp... Merremia boisiana,a captivating species endemic to tropical rainforest habitats,belongs to the esteemed Convolvulaceae family.Renowned for its dazzling golden flowers and exceptional growth rate.This plant rapidly expands,covering other vegetation,suppressing the growth of native species,and altering light availability and nutrient distribution within the forest,thereby impacting ecological balance.Here,we report the first high-quality M.boisiana genome assembly,comprising 510 Mb with a contig N50 of 21 Mb and an assembly completeness of 98.7%.This assembly includes the identification of 15 chromosomes and the annotation of 37,389 protein-coding genes,with a high annotation rate of 99.2%.By integrating genomic data from other Convolvulaceae species,we analyzed the karyotype evolution of M.boisiana and uncovered the fundamental ploidy level of the Convolvulaceae family.Based on existing research,we identified 110 highly expressed genes involved in the biosynthesis of SA,IAA,JA,and ABA,all of which play essential roles in plant growth.The EPS1 transcription factor,involved in SA synthesis,along with YUC11 and TIR2,which participate in auxin biosynthesis,and OPR2,associated with ABA biosynthesis,collectively contribute to the enhanced root growth of M.boisiana through mechanisms such as gene expansion,gene dosage,and root-specific expression.This study not only sheds light on the genetic complexity of M.boisiana but also provides a promising direction for improving stress resistance in sweet potatoes and advancing ecological research.Our findings promote the sustainable utilization of this species while broadening our understanding of tropical plant genomics. 展开更多
关键词 Merremia boisiana plant growth native speciesand contig n karyotype evolution tropical rainforest merremia boisianaa chromosomal reference genome
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Genome of plant watercress(Nasturtium officinale R.Br.)illuminates genomic basis for marine-incursions adaptation in the Mediterranean area 认领 引用
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作者 Chao Yan Suchong Deng +6 位作者 Zhidong Li Aimei Bai Xiaoqing Ma Fei Chen Jiajun Ran Ying Li Xilin Hou 《Vegetable Research》 2025年第1期189-198,共10页
Watercress(Nasturtium officinale R.Br.),an herbaceous plant in the cruciferous family,has a long history of use as a vegetable.In this report,we present a high-quality assembly of the watercress genome,based primarily... Watercress(Nasturtium officinale R.Br.),an herbaceous plant in the cruciferous family,has a long history of use as a vegetable.In this report,we present a high-quality assembly of the watercress genome,based primarily on PacBio and Hi-C sequencing data.The assembled genome of watercress was 337.51 Mb in size,with a contig N50 length of 3.26 Mb and a scaffold N50 length of 5.85 Mb.Approximately 49.15%(165.88 Mb)of the assembled genome was annotated as repetitive sequences,with long terminal repeats(LTRs)being the most abundant,representing 41.96% of the genome.About 96.6% of the assembly was anchored onto 16 pseudo-chromosomes using Hi-C data.Analyses of the syntenic relationships within and between species collectively indicated that watercress underwent an additional whole-genome duplication(WGD)event after divergence from Arabidopsis.The time of the watercressspecific WGD was estimated to be around 4.7 to 12.6 million years ago(Mya),which coincided with the Zanclean flood about 5.33 Mya.After the WGD,a total of 14,353 homologous gene pairs,including 22,476 genes were retained,accounting for 57.71% of all genes in the watercress genome.From the perspective of the watercress genome,we found that watercress might adapt to various abiotic stresses caused by the Zanclean flood through two mechanisms:one is enhancing tolerance to various abiotic stresses,and the other is escaping various abiotic stresses by floating growth.The watercress genome and transcriptome presented here provide useful information for subsequent molecular breeding and understanding how watercress adapted to an aquatic environment. 展开更多
关键词 herbaceous plant genome assembled genome Nasturtium officinale contig n watercress marine incursions adaptation repetitive sequenceswith
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Chromosomal-level genome and multi-omics dataset of Pueraria lobata var.thomsonii provide new insights into legume family and the isoflavone and puerarin biosynthesis pathways 认领 引用 被引量：5
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作者 Xiaohong Shang Xinxin Yi +10 位作者 Liang Xiao Yansheng Zhang Ding Huang Zhengbao Xia Kunpeng Ou Ruhong Ming Wendan Zeng Dongqing Wu Sheng Cao Liuyin Lu Huabing Yan 《Horticulture Research》 SCIE CSCD 2022年第1期377-386,共10页
Pueraria lobata var.thomsonii(hereinafter abbreviated as Podalirius thomsonii),amember of the legume family,is one of the important traditional Chinese herbal medicines,and its puerarin extract is widely used in the h... Pueraria lobata var.thomsonii(hereinafter abbreviated as Podalirius thomsonii),amember of the legume family,is one of the important traditional Chinese herbal medicines,and its puerarin extract is widely used in the health and pharmaceutical industry.Here,we assembled a high-quality genome of P.thomsonii using long-read single-molecule sequencing and Hi-C technologies.The genome assembly is ~1.37 Gb in size and consists of 5145 contigs with a contig N50 of 593.70 kb,further clustered into 11 pseudochromosomes.Genome structural annotation resulted in∼869.33 Mb(~62.70% of the genome)repeat regions and 45270 protein-coding genes.Genome evolution analysis revealed that P.thomsonii is most closely related to soybean and underwent two ancient whole-genome duplication events;one was in the common ancestor shared by legume species and the other occurred independently at around 7.2million years ago,after its speciation.A total of 2373 gene familieswere found to be unique in P.thomsonii compared with five other legume species.Genes andmetabolites related to puerarin content in tuberous tissueswere characterized.A total of 572 genes that were upregulated in the puerarin biosynthesis pathway were identified,and 235 candidate genes were further enriched by omics data.Furthermore,we identified six 8-C-glucosyltransferase(8-C-GT)candidate genes significantly involved in puerarin metabolism.Our study filled a key genomic gap in the legume family,and provided valuable multi-omic resources for the genetic improvement of P.thomsonii. 展开更多
关键词 contigs puerarin extract pueraria lobata legume family multi omics podalirius thomsonii amember chromosomal level genome genome assembly
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家蚕cDNA文库构建及大规模EST测序 认领 引用 被引量：12
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作者 程道军 夏庆友 +2 位作者 周泽扬 鲁成 向仲怀 《蚕业科学》 CAS 2003年第4期335-339,共5页
EST(expressedsequencetag,表达序列标签 )测序分析技术广泛应用于基因功能和表达模式的分析研究。以家蚕品种“大造”为材料 ,采用非均一化的Oligo dT引物定向克隆技术构建了 13个组织的cDNA文库 ,进行了cDNA克隆 5′端测序 ,共获得 84... EST(expressedsequencetag,表达序列标签 )测序分析技术广泛应用于基因功能和表达模式的分析研究。以家蚕品种“大造”为材料 ,采用非均一化的Oligo dT引物定向克隆技术构建了 13个组织的cDNA文库 ,进行了cDNA克隆 5′端测序 ,共获得 84 791万条EST序列 ,初步拼接得到 2 76 93个非重复序列 ,其中包括 10 4 33个Contigs,172 6 0个Singletons。 展开更多
关键词 家蚕 cDNA文库 构建 EST 测序 表达序列标签 基因功能 表达模式 克隆 非重复序列 Contigs Singletons 组织 器官
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Haplotype-resolved genome assembly of poplar line NL895 provides a valuable tree genomic resource 认领 引用 被引量：1
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作者 Jie Luo Yan Wang +3 位作者 Zihui Li Ziwei Wang Xu Cao Nian Wang 《Forestry Research》 2024年第1期269-280,共12页
Poplar line NL895 can potentially become a model plant for poplar study as it is a widely cultivated elite line.However,the lack of genome resources hindered the use of NL895 as the major plant material in poplar.In t... Poplar line NL895 can potentially become a model plant for poplar study as it is a widely cultivated elite line.However,the lack of genome resources hindered the use of NL895 as the major plant material in poplar.In this study,we provided a high-quality genome assembly for poplar line NL895 with PacBio single molecule real-time(SMRT)sequencing and High-throughput chromosome conformation capture(Hi-C)technology.The raw assembly of NL895 for the diploid genome included 606 contigs with a total size of~815 Mb,and the monoploid genome included 246 contigs with a total size of~412 Mb.The haplotype-resolved chromosomes in the diploid genomes were also generated.All the monoploid,diploid,and haplotype-resolved genomes showed more than 97%completeness and they can largely improve the mapping efficiency in RNA-Seq analysis.By comprehensively comparing the two haplotype genomes we found the heterozygosity of NL895 is much higher than other poplar lines.We also found that NL895 harbors more genomic variants and more gene diversity.The haplotype-specific genes showed higher variable gene expression patterns.These characters would be attributed to the high heterosis of poplar line NL895.The allele-specific expression(ASE)was also investigated and lots of alleles showed biased expressions in different tissues or environmental conditions.Taken together,the genome sequence for NL895 is a valuable tree genomic resource and it would greatly facilitate studies in poplar. 展开更多
关键词 contigs haplotype resolved genome assembly model plant plant material poplar line nl genome resources raw assembly diploid genome
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A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes 认领 引用 被引量：4
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作者 Onkar Nath Stephen J.Fletcher +5 位作者 Alice Hayward Lindsay M.Shaw Ardashir Kharabian Masouleh Agnelo Furtado Robert J.Henry Neena Mitter 《Horticulture Research》 SCIE CSCD 2022年第1期3206-3215,共10页
Avocado(Persea americana)is a member of themagnoliids,an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious.Here,we report a chromosome-level genome assembly for... Avocado(Persea americana)is a member of themagnoliids,an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious.Here,we report a chromosome-level genome assembly for the commercial avocado cultivar Hass,which represents 80% of theworld’s avocado consumption.The DNA contigs produced fromPacific Biosciences HiFi readswere further assembled using a previously published version of the genome supported by a genetic map.The total assembly was 913 Mb with a contig N50 of 84 Mb.Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8% of benchmarked single-copy genes from embryophytes.Annotation of protein coding sequences identified 48915 avocado genes of which 39207 could be ascribed functions.The genome contained 62.6% repeat elements.Specific biosynthetic pathways of interest in the genome were investigated.The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes.Endoglucanase genes were high in number,consistent with avocado using cellulase for fruit ripening.The avocado genome appeared to have a limited number of translocations between homeologous chromosomes,despite having undergone multiple genome duplication events.Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family,as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots.This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality. 展开更多
关键词 haplotype repeat elements dna contigs chromosome level genome translocations avocado Persea americana endoglucanase genes
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Chromosome-scale reference genome of broccoli(Brassica oleracea var.italica Plenck)provides insights into glucosinolate biosynthesis 认领 引用 被引量：6
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作者 Qiuyun Wu Shuxiang Mao +8 位作者 Huiping Huang Juan Liu Xuan Chen Linghui Hou Yuxiao Tian Jiahui Zhang Junwei Wang Yunsheng Wang Ke Huang 《Horticulture Research》 SCIE CSCD 2024年第5期51-66,共16页
Broccoli(Brassica oleracea var.italica Plenck)is an important vegetable crop,as it is rich in health-beneficial glucosinolates(GSLs).However,the genetic basis of the GSL diversity in Brassicaceae remains unclear.Here ... Broccoli(Brassica oleracea var.italica Plenck)is an important vegetable crop,as it is rich in health-beneficial glucosinolates(GSLs).However,the genetic basis of the GSL diversity in Brassicaceae remains unclear.Here we report a chromosome-level genome assembly of broccoli generated using PacBio HiFi reads and Hi-C technology.The final genome assembly is 613.79 Mb in size,with a contig N50 of 14.70 Mb.The GSL profile and content analysis of different B.oleracea varieties,combined with a phylogenetic tree analysis,sequence alignment,and the construction of a 3D model of the methylthioalkylmalate synthase 1(MAM1)protein,revealed that the gene copy number and amino acid sequence variation both contributed to the diversity of GSL biosynthesis in B.oleracea.The overexpression of BoMAM1(BolI0108790)in broccoli resulted in high accumulation and a high ratio of C4-GSLs,demonstrating that BoMAM1 is the key enzyme in C4-GSL biosynthesis.These results provide valuable insights for future genetic studies and nutritive component applications of Brassica crops. 展开更多
关键词 phylogenetic tree content analysis chromosome level genome contig n glucosinolate biosynthesis pacbio hifi reads broccoli brassica oleracea genome assembly
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The gap-free genome and multi-omics analysis of Citrus reticulata‘Chachi’reveal the dynamics of fruit flavonoid biosynthesis 认领 引用 被引量：3
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作者 Congyi Zhu Congjun You +8 位作者 Pingzhi Wu Yongjing Huang Ruimin Zhang Zhengyan Fan Chao Yu Jinli Gong Xiaoli Hu Jiwu Zeng Xuepeng Sun 《Horticulture Research》 SCIE CSCD 2024年第8期195-207,共13页
Citrus reticulata‘Chachi’(CRC)has long been recognized for its nutritional benefits,health-promoting properties,and pharmacological potential.Despite its importance,the bioactive components of CRC and their biosynth... Citrus reticulata‘Chachi’(CRC)has long been recognized for its nutritional benefits,health-promoting properties,and pharmacological potential.Despite its importance,the bioactive components of CRC and their biosynthetic pathways have remained largely unexplored.In this study,we introduce a gap-free genome assembly for CRC,which has a size of 312.97 Mb and a contig N50 size of 32.18 Mb.We identified key structural genes,transcription factors,and metabolites crucial to flavonoid biosynthesis through genomic,transcriptomic,and metabolomic analyses.Our analyses reveal that 409 flavonoid metabolites,accounting for 83.30%of the total identified,are highly concentrated in the early stage of fruit development.This concentration decreases as the fruit develops,with a notable decline in compounds such as hesperetin,naringin,and most polymethoxyflavones observed in later fruit development stages.Additionally,we have examined the expression of 21 structural genes within the flavonoid biosynthetic pathway,and found a significant reduction in the expression levels of key genes including 4CL,CHS,CHI,FLS,F3H,and 4OMT during fruit development,aligning with the trend of flavonoid metabolite accumulation.In conclusion,this study offers deep insights into the genomic evolution,biosynthesis processes,and the nutritional and medicinal properties of CRC,which lay a solid foundation for further gene function studies and germplasm improvement in citrus. 展开更多
关键词 gap free genome citrus reticulata chachi crc contig n biosynthetic pathways multi omics analysis flavonoid biosynthesis Chachi citrus reticulata
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Genome assembly and resequencing shed light on evolution,population selection,and sex identification in Vernicia montana 认领 引用 被引量：2
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作者 Wenying Li Xiang Dong +7 位作者 Xingtan Zhang Jie Cao Meilan Liu Xu Zhou Hongxu Long Heping Cao Hai Lin Lin Zhang 《Horticulture Research》 SCIE CSCD 2024年第7期207-221,共15页
Vernicia montana is a dioecious plant widely cultivated for high-quality tung oil production and ornamental purposes in the Euphor-biaceae family.The lack of genomic information has severely hindered molecular breedin... Vernicia montana is a dioecious plant widely cultivated for high-quality tung oil production and ornamental purposes in the Euphor-biaceae family.The lack of genomic information has severely hindered molecular breeding for genetic improvement and early sex identification in V.montana.Here,we present a chromosome-level reference genome of a male V.montana with a total size of 1.29 Gb and a contig N50 of 3.69 Mb.Genome analysis revealed that different repeat lineages drove the expansion of genome size.The model of chromosome evolution in the Euphorbiaceae family suggests that polyploidization-induced genomic structural variation reshaped the chromosome structure,giving rise to the diverse modern chromosomes.Based on whole-genome resequencing data and analyses of selective sweep and genetic diversity,several genes associated with stress resistance and flavonoid synthesis such as CYP450 genes and members of the LRR–RLK family,were identified and presumed to have been selected during the evolutionary process.Genome-wide association studies were conducted and a putative sex-linked insertion and deletion(InDel)(Chr 2:102799917-102799933 bp)was identified and developed as a polymorphic molecular marker capable of effectively detecting the gender of V.montana.This InDel is located in the second intron of VmBASS4,suggesting a possible role of VmBASS4 in sex determination in V.montana.This study sheds light on the genome evolution and sex identification of V.montana,which will facilitate research on the development of agronomically important traits and genomics-assisted breeding. 展开更多
关键词 evolution contig n genomic information repeat lineages resequencing dioecious plant molecular breeding vernicia montana
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高通量测序中拼接问题的研究现状 认领 引用 被引量：2
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作者 徐鹏昊 《山东农业工程学院学报》 2016年第1期42-44,共3页
近年来,随着第二代测序技术的普及和第三代测序技术的逐步发展,高通量测序技术在实际研究中的应用越来越广泛。高速率、高性价比是其主要优点。相对于传统的桑格(Sanger)法测序来言,高通量测序得到的片段长度较为短小,故如何拼接得到完... 近年来,随着第二代测序技术的普及和第三代测序技术的逐步发展,高通量测序技术在实际研究中的应用越来越广泛。高速率、高性价比是其主要优点。相对于传统的桑格(Sanger)法测序来言,高通量测序得到的片段长度较为短小,故如何拼接得到完整的序列一直是炙手可热的研究方向。本文总结了现阶段高通量测序中拼接问题的研究结果,针对现在流行的各种算法进行了简单介绍。 展开更多
关键词 高通量测序 reads拼接 contigs组装 OLC De brujin图
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The YAC Contig Construction for Human X Chromosome Xp21. 3—11. 3 认领 引用
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作者 缪为民 《High Technology Letters》 EI CAS 1997年第2期94-99,共6页
The YAC contig construction has been done for the Human X chromosome short armXp21.3—p11.3, a region which contains several genetic disease gene loci and is of highlybiomedical importance. Using known probes(OTC, DXS... The YAC contig construction has been done for the Human X chromosome short armXp21.3—p11.3, a region which contains several genetic disease gene loci and is of highlybiomedical importance. Using known probes(OTC, DXS166, DMDcDNA) and STS markersof this region, YAC screenings are performed by both YAC colony in situ hybridization andPCR methods. Totally 55 YACs are obtained from the YAC libraries of CEPH, ICRF andthe Institute. The size determination, the analysis of 26 pairs of microsatelite STS, the single copy probe hybridization and the Alu-PCR fingerprinting are performed for these YACs.The mapping of these YACs is performed, and finally, 6 YAC contigs in Xp21.3—11.3 are obtained, covering about 15 Mb. This work will greatly facilitate the positional cloning of disease genes or the genome sequencing in this important region. 展开更多
关键词 Human genome X chromosome YAC contig STS map
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Construction of the Primary Physical Map of Rice Chromosome 12 认领 引用
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作者 Fu Bin-Ying Zhu Ying-Guo Li Zhi-Kang 《Wuhan University Journal of Natural Sciences》 EI CAS 2000年第2期238-244,共7页
A primary physical map of rice chromosome 12 was constructed using marker-based chromosome landing and chromosome walking. A BAC library from IR64 was screened using 84 RFLP markers, 4 STS markers and 6 microsatellite... A primary physical map of rice chromosome 12 was constructed using marker-based chromosome landing and chromosome walking. A BAC library from IR64 was screened using 84 RFLP markers, 4 STS markers and 6 microsatellite markers on chromosome 12 by colony hybridization and polymerase chain reaction (PCR) amplification. A total of 59 contigs consisting of 419 BAC clones including 5 single-clones were physically aligned on rice chromosome 12 with the largest BAC contig covering 855 kb. The whole physical map had a size of ～16 Mb and covered about 52% of rice chromosome 12. This physical map will be certainly helpful for map-based gene cloning of agronomically and biological important genes and understanding the genome structure of the chromosome. 展开更多
关键词 chromosome landing chromosome walking BAC contigs physical map
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Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project 认领 引用 被引量：3
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作者 Tae-Ho Park Beom-Seok Park +4 位作者 Jin-A Kim Joon Ki Hong Mina Jin Young-Joo Seol Jeong-Hwan Mun 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2011年第1期47-53,共7页
As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expec... As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa. 展开更多
关键词 Brassica rapa Chinese cabbage Fosmid library Genome sequencing Physical contig
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Investigation of genome structure of a cinnamyl alcohol dehydrogenase locus in a basal angiosperm hardwood species, Liriodendron tulipifera L., reveals low synteny 认领 引用 被引量：1
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作者 Yi XU Scott E. SCHLARBAUM Haiying LIANG 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第5期396-405,共10页
Basal angiosperms contain a wide diversity of floral and growth forms and gave rise to the largest recent angiosperm lineages.As none of the basal angiosperm genomes has been sequenced,examining large bacterial artifi... Basal angiosperms contain a wide diversity of floral and growth forms and gave rise to the largest recent angiosperm lineages.As none of the basal angiosperm genomes has been sequenced,examining large bacterial artificial chromosome（BAC） inserts remains the main approach to providing a first glimpse of the structure and organization of their genomes.In this study,we sequenced a 126.9-kbp BAC contig harboring a cinnamyl alcohol dehydrogenase gene（LtuCAD1） in a basal angiosperm species,Liriodendron tulipifera L.,an important timber tree species with significant ecological and economic values.A key enzyme in lignin biosynthesis,CAD catalyzes the final step in the synthesis of monolignols.We carried out phylogenetic analyses of seven full-length CAD family genes（LtuCAD1-7） obtained from a comprehensive Liriodendron expressed sequence tag dataset.The phylogenetic tree suggests that LtuCAD1 is the primary CAD gene involved in lignifications as it is the only Liriodendron CAD grouped with the bona fide CADs class.As well as the LtuCAD1,the BAC contig contained fragmented sequences for one integrase,eight hypothetical proteins,two gag-pol polyproteins,one RNase H family protein,and one chromatin binding protein.Comparative analysis with other angiosperm species suggests that the genomic segment in this BAC has undergone frequent arrangement.This study is our initial step in identifying and understanding lignin biosynthesis genes from basal angiosperm species.Such knowledge can help bridge the information gap between hardwood（angiosperm） and softwood（gymnosperm） species and benefit potential breeding and biotechnology application for enhanced production of biomass and digestibility in L.tulipifera. 展开更多
关键词 BAC contig cinnamyl alcohol dehydrogenase（CAD） gene order lignin biosynthesis synteny.
Bacterial artificial chromosome library construction of root-knot nematode resistant pepper genotype HDA149 and identification of clones linked to Me3 resistant locus 认领 引用
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作者 GUO Xiao YANG Xiao-hui +5 位作者 YANG Yu MAO Zhen-chuan LIU Feng MA Wei-qing XIE Bing-yan LI Guang-cun 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2017年第1期57-64,共8页
Pepper （Capsicum annuum. L.） is a widely cultivated vegetable crop worldwide and has the second largest planting area and the first largest vegetable output and value in China. Pepper root-knot nematode （Meloidogyn... Pepper （Capsicum annuum. L.） is a widely cultivated vegetable crop worldwide and has the second largest planting area and the first largest vegetable output and value in China. Pepper root-knot nematode （Meloidogyne spp.） is one of the most serious pests of pepper, which caused huge losses every year. Previous studies showed that the Me3 gene is resistant to a wide range of Meloidogyne species, including M. arenaria, M. javanica, and M. incognita. HDA149, a double haploid pepper genotype, harboring the root-knot nematode resistance gene Me3, was used to construct bacterial artificial chro- mosome library （BAC） via the vector of CopyControFM pCC1 in this study. The library consists of 210 200 BAC clones and is equivalent to 5.3 pepper genomes. The average insert size is 95 kb, and most of them are 90-120 kb; but the empty clones are less than 3%. In order to screen the BAC library easily, 550 super pools with 384 BAC clones of each pool were further developed in this study. Specific primers from Me3 gene locus were used for BAC library screening, and more than 20 positive BAC clones were obtained. Then the selected positive BAC clones were analyzed by restriction enzyme digestion, BAC-end sequencing, marker development, and new positive BAC clones exploration, respectively. Finally, the contig with total length of about 300 kb linked to the Me3 locus was constructed based on chromosome walking strategy, which made a solid foundation for the cloning of the important root-knot nematode resistance gene Me3. 展开更多
关键词 pepper bacterial artificial chromosome library.（BAC） root-knot nematode Me3 gene contig
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