葡萄牙牡蛎外套膜转录组测序及壳色基因挖掘
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摘要
采用Illumina高通量测序平台对黑壳与金壳葡萄牙牡蛎(Crassostrea angulata)外套膜组织开展转录组测序研究,其中黑壳组总计产出5 857 718 092 nt数据,筛选后的干净阅读子58 004 560个;金壳组产出6 727 447 326 nt数据,干净阅读子66 614 854个。将发掘的新基因与COG、GO、KEGG、Swiss-Prot、NR数据库进行序列比对,最终得到各数据库注释的新基因数量分别为147、397、203、567、1 347个。通过对差异表达基因的序列进行生物学功能注释和聚类分析以及利用已知贝壳基质蛋白序列进行搜索,鉴定出14条可能与壳色表达有关的贝壳基质蛋白基因,其中5条下调基因可能与金壳基因表达相关。
Shell coloration is one of important traits for genetic breeding, for improving genome structure and explore new potential gene and further determine the genetic structure of golden shell gene of oyster, the transcriptome sequencing of Crassostrea angulata with black shell and golden shell mantle were performed by Illumina platform. Data were obtained from black shell and golden shell transcriptome were 5 857 718 092 nt and 6 727 447 326 nt respectively, out of which 58 004 560 and 66 614 854 clean reads were remained after screening, respectively. To compare with the database from COG, GO, KEGG, Swiss-Prot and NR, new gene numbers corresponding to each database were 147, 397, 203, 567, and 1 347 respectively. To further explore the shell color genes of oyster, functional annotation, clustering analysis and screening from the reported shell matrix proteins on the differential expression gene(DEGs), 14 genes related to shell color expression were identified out and 5 down-regulated genes out of them might be related to the expression of golden shell.
Shell coloration is one of important traits for genetic breeding, for improving genome structure and explore new potential gene and further determine the genetic structure of golden shell gene of oyster, the transcriptome sequencing of Crassostrea angulata with black shell and golden shell mantle were performed by Illumina platform. Data were obtained from black shell and golden shell transcriptome were 5 857 718 092 nt and 6 727 447 326 nt respectively, out of which 58 004 560 and 66 614 854 clean reads were remained after screening, respectively. To compare with the database from COG, GO, KEGG, Swiss-Prot and NR, new gene numbers corresponding to each database were 147, 397, 203, 567, and 1 347 respectively. To further explore the shell color genes of oyster, functional annotation, clustering analysis and screening from the reported shell matrix proteins on the differential expression gene(DEGs), 14 genes related to shell color expression were identified out and 5 down-regulated genes out of them might be related to the expression of golden shell.
引文
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[3]Clydesdale F M.Color as a factor in food choice[J].Critical Reviews in Food Science and Nutrition,1993,33(1):83–101.
[4]管云雁,何毛贤.海产经济贝类壳色多态性的研究进展[J].海洋通报,2009(1):108–114.
[5]李国江,盛红禄,宋京辉,等.海洋贝类养殖新品种——‘中科红’海湾扇贝[J].科学养鱼,2005(2):22.
[6]Hedgecock D,Perry G M L,Voigt M L.Mapping heterosis QTL in the Pacific oyster Crassostrea gigas[J].Aquaculture,2006,272:267–268.
[7]Jianlong Ge,Qi Li,Hong Yu,et al.Identification and mapping of a SCAR marker linked to a locus involved in shell pigmentation of the Pacific oyster(Crassostrea gigas)[J].Aquaculture,2014,434:249–253.
[8]巫旗生,曾志南,宁岳,等.葡萄牙牡蛎工厂化人工育苗技术[J].福建水产,2015,37(5):399–405.
[9]於俊琦,陈琛,冀德伟,等.高效生态循环养殖系统中的葡萄牙牡蛎单体养殖试验[J].科学养鱼,2013(10):41–42.
[10]王华青,张志杨,梁和平.单体葡萄牙牡蛎筏式笼养试验[J].中国水产,2014(2):70–71.
[11]巫旗生.福建沿海主要养殖牡蛎种类及其遗传多样性研究[D].长沙:湖南农业大学,2012.
[12]王桂玲,李家乐.淡水育珠蚌外套膜提取总RNA的改良方法[J].生物技术通报,2008(S1):356–361.
[13]Trapnell C,Williams B A,Pertea G,et al.Transcript assembly and quantification by RNA Seq reveals unannotated transcripts and isoform switching during cell differentiation[J].Nature Biotechnology,2010,28(5):511–515.
[14]Altschul S F,Madden T L,Schaffer A A,et al.Gapped BLAST and PSI BLAST:a new generation of protein database search programs[J].Nucleic Acids Research,1997,25(17):3389–3402.
[15]Weiss I M,Kaufmann S,Mann K,et al.Purification and characterization of perlucin and perlustrin,two new proteins from the shell of the mollusk Haliotis laevigata[J].Biochemical and Biophysical Research Communications,2000,267(1):17–21.
[16]Mann K,Weiss I M,AndréS,et al.The amino-acid sequence of the abalone(Haliotis laevigata)nacre protein perlucin:Detection of s functional C–type lectin domain with galactose/mannose sepecificity[J].The Federation of European Biochemical Societies Journal,2000,267(16):5257–5264.
[17]Kong Y M,Jing G,Yan Z G,et al.Cloning and characterization of Prisilkin–39,a novel matrix protein serving a dual role in the prismatic layer formation from the oyster Pinctada fucata[J].Journal of Biological Chemistry,2009,284(16):10841–10854.
[18]Suzuki M,Saruwatari K,Kogure T,et al.An acidic matrix protein,Pif,is a key macromolecule for nacre formation[J].Science,2009,325(5946):1388–1390.