| 陈雪峰,杨国梁,王军毅,高强,宫金华,叶少群,张海鹏.2011.罗氏沼虾缅甸野生原种rDNA-ITS区序列特征.动物学杂志,46(3):19-27. |
| 罗氏沼虾缅甸野生原种rDNA-ITS区序列特征 |
| Analysis on Sequences of Ribosomal DNA Internal Transcribed Spacers of Macrobrachium rosenbergii |
| 投稿时间：2010-10-14 修订日期：2011-03-02 |
| DOI： |
| 中文关键词: 罗氏沼虾 内转录间隔区 序列特征 |
| 英文关键词:Macrobrachium rosenbergii Internal transcribed spacers (ITS) Sequence analysis |
| 基金项目:浙江省重大科技专项项目(No.2007C12059),科技部农业科技成果转化资金项目(No. 2007GB2C 200124); |
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| 中文摘要: |
| 对罗氏沼虾( Macrobrachium rosenbergii )内转录间隔区(internal transcribed spacer, ITS)全序列特征进行了分析。罗氏沼虾ITS1长度为1 070~1 150 bp,GC含量为51.4%~52.7%;5.8S长度一致为163 bp,GC含量为55.2%;ITS2长度为484~545 bp,GC含量为53.4%~54.6%。序列比对显示,ITS1存在61处SNPs,其中C/T转换为28处(占45.9%),A/G转换为23处(占37.7%),A/T颠换为1处(占1.6%),T/G颠换为3处(占4.9%),C/G颠换为4处(占6.6%),A/C颠换为2处(占3.3%);ITS2存在15处SNPs,其中C/T转换为6处(占40%),A/G转换为5处(占33.3%), A/T颠换为1处(占6.7%),T/G颠换为2处(占13.3%),C/G颠换为1处(占6.7%)。整个ITS中微卫星序列(SSR)共有20处,其中ITS1中有14处,以(AG)n类型最多;ITS2中有6处,以(GA)n类型最多。人工查找结果发现,罗氏沼虾ITS1在181、390和781位点存在3处59 bp正向重复单元。个体内差异分析表明,罗氏沼虾ITS由于SSR重复数不同,而存在个体内差异。同源性分析表明,罗氏沼虾ITS1与海南沼虾( M. hainanense )同源性最高,为50.64%,而与脊尾白虾( Exopalaemon carinicauda )同源性最低,为45.39%;5.8S与其他甲壳动物有着极高的同源性,其中与日本沼虾( M.nipponense )同源性达到100%;ITS2与日本沼虾同源性最高,为53.46%,而与克氏原螯虾( Procambarus clark )的同源性最低,为42.53%。基于ITS构建的NJ树显示,罗氏沼虾与同属的日本沼虾聚为一支,与传统分类相符。 |
| 英文摘要: |
| Internal transcribed spacers in ribosomal DNA were often used as molecular sequence in phylogenetic study. The complete sequence of internal transcribed spacers of Macrobrachium rosenbergii was isolated by PCR. The length of ITS1 was 1 070-1 150 bp with a GC content of 51.4%-52.7%, and the length of 5.8S was 163 bp with a GC content of 55.2%. Compared to ITS1, the length of ITS2 (484-545 bp) was shorter while GC content (53.4%-54.6%) was higher. By comparison of sequence from different individuals, 61 SNP loci were found in ITS1, including 28 C/T transitions (45.9%), 23 A/G transitions (37.7%), 1 A/T transversions (1.6%), 3 T/G transversions (4.9%), 4 C/G transversions (6.6%), and 2 A/C transversions (3.3%); 15 SNP loci were found in ITS2, including 6 C/T transitions (40%), 5 A/G transitions (33.3%), 1 A/T transversions (6.7%), 2 T/G transversions (13.3%), and 1 C/G transversions (6.7%). SSR loci were searched by the SSRHunter software, and the results showed that the SSR loci in ITS1 and ITS2 were 14 and 6 respectively, the type of (AG)n was rich in ITS1 and the type of (GA)n was rich in ITS2.There were three repeat units with a length of 59 bp in ITS1, and the loci were 181, 390 and 781, respectively. The results of ITS intravariances analysis demonstrated that clones from the same individual were different in length because of SSR. Furthermore, homology comparison of ITS sequence indicated that the similarity of each ITS1 was 45.39%-50.64%, and the highest occurred between M. rosenbergii and M.hainanense , while the lowest occurred between M.rosenbergii and Exopalaemon carinicauda . 5.8S showed very high similarity with other crustaceans, and the homology was 100% between M.rosenbergii and M.nipponense . The similarity of each ITS2 was 42.53%-53.46%, and the highest occurred between M.rosenbergii and M.nipponense , while the lowest occurred between M.rosenbergii and Procambarus clark . Phylogenetic tree based on the ITS was constructed by Neighbor-joining method, and the results showed that the relationship between M.rosenbergii and M.nipponense was the closest, which accorded with morphology classification. |
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