重要双壳贝类细胞遗传图谱构建及基因组特征分析
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摘要
双壳类在全球水产养殖业中占有重要地位,多数有经济价值的养殖贝类如扇贝、牡蛎都属于双壳纲。本研究针对重要双壳类长牡蛎(Crassostrea gigas)和栉孔扇贝(Chlamys farreri)开展了分子细胞遗传学和基因组学的研究,为促进基因资源发掘和良种选育奠定基础。
1.长牡蛎染色体鉴别及染色体图谱构建
本研究利用荧光原位杂交技术(fluorescence in situ hybridization, FISH)将18个BAC克隆及18S-28S rDNA分别定位在长牡蛎的10条染色体上,实现了长牡蛎全部染色体的区分鉴定,构建了染色体图谱。依据FISH结果,将染色体从大到小排列,分别命名为1号到10号染色体。其中2个克隆需要使用Cot-1DNA封阻后才能产生清晰的阳性信号。一个克隆定位在两条染色体上,其余17个克隆有单一的染色体定位。染色体的准确鉴别在长牡蛎非整倍体鉴定、多倍体染色体丢失等研究中有重要作用。
定位的BAC克隆中,8个克隆的全长序列已测序获得,与GenBank中长牡蛎数据库Blast比对,结果表明这8个克隆包含Ⅰ型TGF-β受体、金属硫蛋白等近50种基因；利用Tandem Repeats Finder (TFR)软件在序列中查找到199个微卫星,其中一个微卫星已知位于4号连锁群,根据FISH结果可以将4号连锁群与6号染色体关联。其余10个BAC克隆经双末端测序共获得14条高质量序列。将18个BAC克隆的序列与长牡蛎基因组序列拼接版本oyster_v9进行BlastN比对,结果14个BAC克隆与30条scaffold关联。
2.长牡蛎染色体图谱与遗传连锁图谱的整合
从长牡蛎10个遗传连锁群上挑选50个微卫星标记,在BAC文库中进行PCR筛选,有33个微卫星标记得以成功筛选。22个克隆利用荧光原位杂交技术定位在10条染色体上,其中19个克隆的定位需要使用Cot-1DNA进行封阻。结合本研究开发的染色体特异性探针,将10个连锁群分别与10条染色体整合,并确定了8条连锁群的方向,验证了遗传图谱中的标记位置。将微卫星序列与长牡蛎基因组序列拼接版本oyster_v9BlastN比对,19个微卫星标记均与一条scaffold关联。这些微卫星标记在遗传图谱、染色体图谱和基因组序列图谱中的位置都已获得,可作为锚定标记实现各个图谱的整合,对牡蛎基因组研究具有重要意义。
3.栉孔扇贝转录组测序分析
本研究对栉孔扇贝的胚胎、幼虫及多个成体组织进行了454转录组测序文库的构建,经测序共获得1,033,636条高质量序列,等级拼接共获得26,165条contig,聚类获得24,437条isotig,进一步分组到20,056个isogroups。对序列进行同源比对注释后共9,328(47%isogroups)条获得注释信息。对注释序列进行GO分类及KEGG代谢通路分析,发现了大量与生长、生殖和压力/免疫等相关的功能基因。与虾夷扇贝的转录组比较,结果显示两种扇贝的GO注释结构类似。两个物种序列互相比对获得1,709个直系同源序列,进行Ka/Ks分析后发现了38个可能的快速进化基因。对两种扇贝转录组分别预测了单核苷酸多态性(Single Nucleotide Polymorphism, SNP)和微卫星,栉孔扇贝中预测获得46,527个高质量SNP和352个微卫星序列,虾夷扇贝中获得20,633个高质量SNP和213个微卫星序列。本研究为功能基因研究和SNP和微卫星标记的开发提供了丰富的资源。
Bivalves, including oysters and scallops, are among the most economically importantclasses in global aquaculture. This study focuses on molecular cytogenetics and genomiccharacterization in economically important species pacific oyster (Crassostrea gigas) andZhikong scallop (Chlamys farreri). It will greatly promote the excavation of gene resources andbreeding.
1. Identification of all chromosomes in pacific oyter (Crassostrea gigas)
Eighteen bacterial artificial chromosomes (BACs) and18S-28S rDNA gene are mapped onmitotic chromosome spreads in C.gigas with fluorescence in situ hybridization (FISH). Thecombination of probes enables precise identification of all ten chromosome pairs. Based on FISHresults, chromosomes are aligned vertically, and numbered by size.Two out of eighteen BACscan only be unambiguously mapped with the aid of Cot-1DNA. Each BAC is mapped to aunique chromosomal location except one that was mapped on two sites of differentchromosomes.Precise identification and naming system of chromosomes in C.gigas will play animportant role in studies like aneuploidyidentifications and genome instability of polyploidy.
Of all mapped BACs, eight were fully sequenced. After Blast search against C.gigasdatabases, approximately50genes are identified including transforming growth factorbetareceptor type-1and metallothionein. Tandem Repeats Finder (TFR) software is used fordiscovery of199microsatellite, one out of which was discovered and has been used for linkageanalysis in previous study. Combining FISH result and linkage information of this marker,linkage group4is assigned to chromosome6. BACs end sequencing of the other10clones generates14high quality sequences. BAC sequences are compared with genome assemblyversion oyster_v9using BlastN.14BACs are anchored in30assembled scaffolds.
2. Assignment of pacific oyster (Crassostrea gigas) linkage groups to specific chromosomes
Assignment of linkage groups to specific chromosomes as a necessary part of the genomeproject has been carried out in this study for C.gigas. Microsatellite markers are selected from10linkage groups and screened in a BAC library.22BACs that are positive for mappedmicrosatellite markers (including the BAC containing a mapped microsatellite maker mentionedabove) are successfully used for chromosomal assignment with FISH. Referring to chromosomalidentification and naming system developed above,10linkage groups are assigned to10chromosomes respectively. Orientations of8linkage groups are also assigned at the same time.Comparison between linkage groups and chromosome allows examination and revision ofmarker orders and distances.19out of22BACs can only be unambiguously mapped with the aidof Cot-1DNA.19microsatellite sequences are anchored to genome assembly version oyster_v9using BlastN. Microsatellite markers which are anchored in genetic maps, chromosomes andgenome assembly, enable integration of these maps.
3. Transcriptome sequencing of Zhikong scallop (Chlamys farreri)
Genetic breeding programs have been initiatedfor genetic improvement of scallop species,and research effort has been devoted to identify genes or genetic loci responsible foreconomically important traits such as rapid growth and disease resistance.In this study, denovotranscriptome sequencing is performed by next generation sequencing technology454GSFLX. In a single sequencing run,1,033,636reads were produced and then assembled into26,165contigs.These contigs were then clustered into24,437isotigs and further grouped into20,056isogroups. About47%of the isogroups showed significant matches to known proteinsbased onsequence similarity. Transcripts putatively involved in growth, reproduction andstress/immune-response were identified through Gene ontology (GO) and KEGG pathwayanalyses. Transcriptome comparison with P. yessoensis revealed similar patterns of GOrepresentation. Moreover,38putativefast-evolving genes were identified from1,709orthologousgene pairs between the two scallop species.45,527single nucleotide polymorphisms (SNPs) and 352simple sequence repeats (SSRs) were detected in C. farreri, and20,633SNPs and213SSRswere detected in P. yessoensis.
1.长牡蛎染色体鉴别及染色体图谱构建
本研究利用荧光原位杂交技术(fluorescence in situ hybridization, FISH)将18个BAC克隆及18S-28S rDNA分别定位在长牡蛎的10条染色体上,实现了长牡蛎全部染色体的区分鉴定,构建了染色体图谱。依据FISH结果,将染色体从大到小排列,分别命名为1号到10号染色体。其中2个克隆需要使用Cot-1DNA封阻后才能产生清晰的阳性信号。一个克隆定位在两条染色体上,其余17个克隆有单一的染色体定位。染色体的准确鉴别在长牡蛎非整倍体鉴定、多倍体染色体丢失等研究中有重要作用。
定位的BAC克隆中,8个克隆的全长序列已测序获得,与GenBank中长牡蛎数据库Blast比对,结果表明这8个克隆包含Ⅰ型TGF-β受体、金属硫蛋白等近50种基因；利用Tandem Repeats Finder (TFR)软件在序列中查找到199个微卫星,其中一个微卫星已知位于4号连锁群,根据FISH结果可以将4号连锁群与6号染色体关联。其余10个BAC克隆经双末端测序共获得14条高质量序列。将18个BAC克隆的序列与长牡蛎基因组序列拼接版本oyster_v9进行BlastN比对,结果14个BAC克隆与30条scaffold关联。
2.长牡蛎染色体图谱与遗传连锁图谱的整合
从长牡蛎10个遗传连锁群上挑选50个微卫星标记,在BAC文库中进行PCR筛选,有33个微卫星标记得以成功筛选。22个克隆利用荧光原位杂交技术定位在10条染色体上,其中19个克隆的定位需要使用Cot-1DNA进行封阻。结合本研究开发的染色体特异性探针,将10个连锁群分别与10条染色体整合,并确定了8条连锁群的方向,验证了遗传图谱中的标记位置。将微卫星序列与长牡蛎基因组序列拼接版本oyster_v9BlastN比对,19个微卫星标记均与一条scaffold关联。这些微卫星标记在遗传图谱、染色体图谱和基因组序列图谱中的位置都已获得,可作为锚定标记实现各个图谱的整合,对牡蛎基因组研究具有重要意义。
3.栉孔扇贝转录组测序分析
本研究对栉孔扇贝的胚胎、幼虫及多个成体组织进行了454转录组测序文库的构建,经测序共获得1,033,636条高质量序列,等级拼接共获得26,165条contig,聚类获得24,437条isotig,进一步分组到20,056个isogroups。对序列进行同源比对注释后共9,328(47%isogroups)条获得注释信息。对注释序列进行GO分类及KEGG代谢通路分析,发现了大量与生长、生殖和压力/免疫等相关的功能基因。与虾夷扇贝的转录组比较,结果显示两种扇贝的GO注释结构类似。两个物种序列互相比对获得1,709个直系同源序列,进行Ka/Ks分析后发现了38个可能的快速进化基因。对两种扇贝转录组分别预测了单核苷酸多态性(Single Nucleotide Polymorphism, SNP)和微卫星,栉孔扇贝中预测获得46,527个高质量SNP和352个微卫星序列,虾夷扇贝中获得20,633个高质量SNP和213个微卫星序列。本研究为功能基因研究和SNP和微卫星标记的开发提供了丰富的资源。
Bivalves, including oysters and scallops, are among the most economically importantclasses in global aquaculture. This study focuses on molecular cytogenetics and genomiccharacterization in economically important species pacific oyster (Crassostrea gigas) andZhikong scallop (Chlamys farreri). It will greatly promote the excavation of gene resources andbreeding.
1. Identification of all chromosomes in pacific oyter (Crassostrea gigas)
Eighteen bacterial artificial chromosomes (BACs) and18S-28S rDNA gene are mapped onmitotic chromosome spreads in C.gigas with fluorescence in situ hybridization (FISH). Thecombination of probes enables precise identification of all ten chromosome pairs. Based on FISHresults, chromosomes are aligned vertically, and numbered by size.Two out of eighteen BACscan only be unambiguously mapped with the aid of Cot-1DNA. Each BAC is mapped to aunique chromosomal location except one that was mapped on two sites of differentchromosomes.Precise identification and naming system of chromosomes in C.gigas will play animportant role in studies like aneuploidyidentifications and genome instability of polyploidy.
Of all mapped BACs, eight were fully sequenced. After Blast search against C.gigasdatabases, approximately50genes are identified including transforming growth factorbetareceptor type-1and metallothionein. Tandem Repeats Finder (TFR) software is used fordiscovery of199microsatellite, one out of which was discovered and has been used for linkageanalysis in previous study. Combining FISH result and linkage information of this marker,linkage group4is assigned to chromosome6. BACs end sequencing of the other10clones generates14high quality sequences. BAC sequences are compared with genome assemblyversion oyster_v9using BlastN.14BACs are anchored in30assembled scaffolds.
2. Assignment of pacific oyster (Crassostrea gigas) linkage groups to specific chromosomes
Assignment of linkage groups to specific chromosomes as a necessary part of the genomeproject has been carried out in this study for C.gigas. Microsatellite markers are selected from10linkage groups and screened in a BAC library.22BACs that are positive for mappedmicrosatellite markers (including the BAC containing a mapped microsatellite maker mentionedabove) are successfully used for chromosomal assignment with FISH. Referring to chromosomalidentification and naming system developed above,10linkage groups are assigned to10chromosomes respectively. Orientations of8linkage groups are also assigned at the same time.Comparison between linkage groups and chromosome allows examination and revision ofmarker orders and distances.19out of22BACs can only be unambiguously mapped with the aidof Cot-1DNA.19microsatellite sequences are anchored to genome assembly version oyster_v9using BlastN. Microsatellite markers which are anchored in genetic maps, chromosomes andgenome assembly, enable integration of these maps.
3. Transcriptome sequencing of Zhikong scallop (Chlamys farreri)
Genetic breeding programs have been initiatedfor genetic improvement of scallop species,and research effort has been devoted to identify genes or genetic loci responsible foreconomically important traits such as rapid growth and disease resistance.In this study, denovotranscriptome sequencing is performed by next generation sequencing technology454GSFLX. In a single sequencing run,1,033,636reads were produced and then assembled into26,165contigs.These contigs were then clustered into24,437isotigs and further grouped into20,056isogroups. About47%of the isogroups showed significant matches to known proteinsbased onsequence similarity. Transcripts putatively involved in growth, reproduction andstress/immune-response were identified through Gene ontology (GO) and KEGG pathwayanalyses. Transcriptome comparison with P. yessoensis revealed similar patterns of GOrepresentation. Moreover,38putativefast-evolving genes were identified from1,709orthologousgene pairs between the two scallop species.45,527single nucleotide polymorphisms (SNPs) and 352simple sequence repeats (SSRs) were detected in C. farreri, and20,633SNPs and213SSRswere detected in P. yessoensis.
引文
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