文章摘要
陈 琼,顾志峰,王爱民,战 欣,石耀华.马氏珠母贝转录组数据的重新组装.渔业科学进展,2014,35(6):97-102
马氏珠母贝转录组数据的重新组装
Data Reassembling Reveals More Information of Transcriptome for Pinctada fucata martensii Dunker
投稿时间:2013-12-25  修订日期:2014-05-02
DOI:10.11758/yykxjz.20140614
中文关键词: 马氏珠母贝  外套膜  珍珠囊  转录组  454焦磷酸测序
英文关键词: Pinctada fucata martensii  Mantle  Pearl sac  Transcriptom  454 Pyrosequencing
基金项目:国家自然科学基金(41366003)和国家重点基础研究发展计划(973计划) (2010CB126405)共同资助
作者单位
陈 琼 海南大学海洋学院 热带生物资源教育部重点实验室 海南省热带水生生物技术重点实验室 海口 570228 
顾志峰 海南大学海洋学院 热带生物资源教育部重点实验室 海南省热带水生生物技术重点实验室 海口 570228 
王爱民 海南大学海洋学院 热带生物资源教育部重点实验室 海南省热带水生生物技术重点实验室 海口 570228 
战 欣 海南大学海洋学院 热带生物资源教育部重点实验室 海南省热带水生生物技术重点实验室 海口 570228 
石耀华 海南大学海洋学院 热带生物资源教育部重点实验室 海南省热带水生生物技术重点实验室 海口 570228 
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中文摘要:
      对本实验室和其他学者已经发表的马氏珠母贝外套膜和珍珠囊的454焦磷酸测序转录组数据以及NCBI中的EST数据进行了重组装、同源序列比对和GO注释分析。重组装获得了30266个contig,平均长度522 bp,其中最长的contig为4144 bp;NR数据库BLAST分析获取了2310个相似性contig (E≤105),其中1902个在模式动物(人、小鼠、海胆、线虫、斑马鱼、果蝇或者太平洋牡蛎和珠母贝)中可以查找到同源序列。基因注释(GO)结果表明,注释到生物学过程的3846个contig可分为23个亚类,其中代谢过程蛋白、细胞过程蛋白和生物学调控蛋白为contig数量最多的3个亚类;注释到分子功能的4601个contig共分为11个亚类,其中结合蛋白的contig数量最多,其次是具有催化活性的蛋白和结构分子活性蛋白;注释到细胞成分的2992个contig分为17个亚类,其中细胞和细胞组成部分的contig数量最多,其次分别是细胞器和大分子复合体contig数量。本研究结果有助于开展外套膜和珍珠囊特异性表达基因的大规模筛选。
英文摘要:
      The pearl oyster, Pinctada fucata martensii, was an ideal animal for studies of biomineralization. The mantle and pearl sac were the two important tissues involved in biomineralization of the shell and pearls. In this study we reassembled the transcriptome data of 454 pyrosequencing of the mantle and pearl sac. The sources of the data included studies in our own laboratory, reports from other researchers, and ESTs from NCBI. We conducted BLAST and Gene Ontology analysis, and analyzed the contig reassembling with CLC Genomics Workbench 5. The reassembling generated 30266 contigs with an average length of 522 bp, and the largest length of 4144 bp. The Blast analysis against non-redundant (NR) database revealed 2310 contigs with the E-values smaller than 105, among which 1902 contigs had homologous sequences in at least one of the following model animals of Homo sapiens, Mus musculus, Strongylocentrotus purpuratus, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, or Crassostrea gigas and Pinctada. The GO annotation showed that 3846 contigs could be characterized into 23 subcategories of biological processes, of which the top three subcategories with most contigs were metabolic process, cellular process and biological regulation; 4601 contigs could be characterized into 11 subcategories of molecular functions, of which the top three with most contigs were binding, catalytic activity, and structural molecular activity; 2992 contigs could be characterized into 17 subcategories of cellular components, of which the top three were cell part, organelle, and macromolecular complex. These results suggested that there were a great number of transcriptome contigs of P. fucata martensii. Our study will be helpful in the large-scale screening of specially-expressed genes in the mantle and pearl sac of P. fucata martensii.
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