A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN(duplex-specific nuclease) normalization method combined with the SMART(Switching Mechanism At 5' end of...A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN(duplex-specific nuclease) normalization method combined with the SMART(Switching Mechanism At 5' end of the RNA Transcript) technique.The titer of the original cDNA library was about1.5 x 10~6 cfu.mL^(-1) and the average insertion size was about 1 kb with a high recombination rate(97%).The 5011 high-quality expressed sequence tags(ESTs) were obtained from 5393 randomly picked cDNA clones.Clustering and assembly of ESTs resulted in 2984 unique sequences,consisting of 618 contigs and2366 singlets.EST sequence annotation revealed that 2333 and 1901 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database,respectively.Functional analysis demonstrated that 1495(50.1%) unigenes were associated with 4082 Gene Ontology(GO) terms.A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups(COG) functional categories.Based on the EST dataset,22 ESTs that encoded putative receptor-like protein kinase(RLK) genes were screened.Furthermore,a total of 94 simple sequence repeats(SSRs) were discovered,of which 20 loci were successfully amplified in C.debaoensis.This study is the first EST analysis for the coralloid roots of C.debaoensis and provides a valuable genomic resource for novel gene discovery,gene expression and comparative genomics,conservation and management studies as well as applications in C.debaoensis and related cycad species.展开更多
德保苏铁 新种 Cycas debaoensis Y.C.Zhong et C.J.Chen,sp.nov. Cycas multipinnatae C.J.Chen et S.Y.Yang affinis sed frondibus 7～11,1.5～3.5 mlongis,pinnulis fasciariis,apice longe acuminatis,ovulis persaepe 4,segmentis...德保苏铁 新种 Cycas debaoensis Y.C.Zhong et C.J.Chen,sp.nov. Cycas multipinnatae C.J.Chen et S.Y.Yang affinis sed frondibus 7～11,1.5～3.5 mlongis,pinnulis fasciariis,apice longe acuminatis,ovulis persaepe 4,segmentis laminarummegasporophyllarum usque ad 50,filiformibus differt. 本种苏铁与多歧苏铁Cycas multipinnata C.J.Chen et S.Y.Yang相似。展开更多
以德保苏铁珊瑚根为材料,利用DSN(duplex-specific nuclease)均一化与SMART(switching mechanism at 5′end of RNA transcript)技术,构建均一化全长cDNA文库。经检测原始文库滴度为1.5×106 cfu·mL-1,文库重组率达97%,插入片...以德保苏铁珊瑚根为材料,利用DSN(duplex-specific nuclease)均一化与SMART(switching mechanism at 5′end of RNA transcript)技术,构建均一化全长cDNA文库。经检测原始文库滴度为1.5×106 cfu·mL-1,文库重组率达97%,插入片段平均长度为1 kb。从文库中随机挑取192个cDNA克隆测序,获得175条高质量EST序列,装备成165条unique序列,其中包括7条contigs和158条singlets,EST冗余度为5.71%。将获得的174条干净的高质量EST序列与NCBI非冗余核酸库(NT)和非冗余蛋白库(NR)数据库进行Blast比对(分值≥200,一致性≥60),其中66.1%(115)的EST序列发现了与其同源的序列,而33.9%(59)的EST序列未发现与其显著同源的序列。构建德保苏铁珊瑚根均一化全长cDNA文库为功能性标记开发和功能基因研究提供了丰富的信息平台。展开更多
基金supported by the Grant(201522)from Shenzhen Urban Management
文摘A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN(duplex-specific nuclease) normalization method combined with the SMART(Switching Mechanism At 5' end of the RNA Transcript) technique.The titer of the original cDNA library was about1.5 x 10~6 cfu.mL^(-1) and the average insertion size was about 1 kb with a high recombination rate(97%).The 5011 high-quality expressed sequence tags(ESTs) were obtained from 5393 randomly picked cDNA clones.Clustering and assembly of ESTs resulted in 2984 unique sequences,consisting of 618 contigs and2366 singlets.EST sequence annotation revealed that 2333 and 1901 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database,respectively.Functional analysis demonstrated that 1495(50.1%) unigenes were associated with 4082 Gene Ontology(GO) terms.A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups(COG) functional categories.Based on the EST dataset,22 ESTs that encoded putative receptor-like protein kinase(RLK) genes were screened.Furthermore,a total of 94 simple sequence repeats(SSRs) were discovered,of which 20 loci were successfully amplified in C.debaoensis.This study is the first EST analysis for the coralloid roots of C.debaoensis and provides a valuable genomic resource for novel gene discovery,gene expression and comparative genomics,conservation and management studies as well as applications in C.debaoensis and related cycad species.
文摘德保苏铁 新种 Cycas debaoensis Y.C.Zhong et C.J.Chen,sp.nov. Cycas multipinnatae C.J.Chen et S.Y.Yang affinis sed frondibus 7～11,1.5～3.5 mlongis,pinnulis fasciariis,apice longe acuminatis,ovulis persaepe 4,segmentis laminarummegasporophyllarum usque ad 50,filiformibus differt. 本种苏铁与多歧苏铁Cycas multipinnata C.J.Chen et S.Y.Yang相似。
文摘以德保苏铁珊瑚根为材料,利用DSN(duplex-specific nuclease)均一化与SMART(switching mechanism at 5′end of RNA transcript)技术,构建均一化全长cDNA文库。经检测原始文库滴度为1.5×106 cfu·mL-1,文库重组率达97%,插入片段平均长度为1 kb。从文库中随机挑取192个cDNA克隆测序,获得175条高质量EST序列,装备成165条unique序列,其中包括7条contigs和158条singlets,EST冗余度为5.71%。将获得的174条干净的高质量EST序列与NCBI非冗余核酸库(NT)和非冗余蛋白库(NR)数据库进行Blast比对(分值≥200,一致性≥60),其中66.1%(115)的EST序列发现了与其同源的序列,而33.9%(59)的EST序列未发现与其显著同源的序列。构建德保苏铁珊瑚根均一化全长cDNA文库为功能性标记开发和功能基因研究提供了丰富的信息平台。
