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药用美洲大蠊全基因组测序分析
Whole Genome Sequencing and Analysis of Medicinal Periplaneta americana
晋家正1, 李午佼2, 牟必琴3, 沈咏梅3, 耿福能2, 岳碧松1, 范振鑫1,3*
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作者单位:1. 生物资源与生态环境教育部重点实验室, 四川大学生命科学学院, 成都 610065;
2. 药用美洲大蠊四川省重点实验室, 四川西昌 615000;
3. 四川省药用动物工程技术研究中心, 四川西昌 615000
中文关键字:美洲大蠊;药用昆虫;全基因组测序;基因组装;基因注释
英文关键字:Periplaneta americana; whole genome sequencing; genome assembly; genome annotation
中文摘要:以美洲大蠊Periplaneta americana为原料生产的康复新液等药品临床疗效显著,得到了广泛应用。本文以四川好医生攀西药业有限责任公司饲养的药用美洲大蠊为材料,首次采用Illumina HiSeq 2000和PacBio SMRT测序平台开展了全基因组测序,并进行基因组组装、注释和分析。原始测序数据经过滤后得到1.4 Tb的二代测序数据和33.81 Gb的三代测序数据。组装结果表明,美洲大蠊基因组大小为3.26 Gb,这在已报道的昆虫基因组中仅次于东亚飞蝗Locusta migratoria。基因组重复序列含量为62.38%,杂合度为0.635%,表明其为复杂基因组。组装的Contig N50和scaffold N50长度分别为28.2 kb、315 kb,单拷贝基因完整性为88.1%,小片段文库测序数据平均比对率为99.8%,测序和组装质量满足后续分析要求。采用De novo预测、同源预测和基于转录本预测3种方法共注释到14 568个基因,其中92.4%的基因获得了功能注释。本研究首次完成了美洲大蠊的全基因组测序,也是大蠊属Periplaneta昆虫的第一个基因组,为美洲大蠊遗传进化分析和药用基因资源挖掘打下了重要基础。
英文摘要:In this study, the whole genomic DNA of medicinal American cockroach (Periplaneta americana) was firstly sequenced by Illumina HiSeq 2000 and PacBio SMRT platforms. In total, 1.4 Tb Illumina data and 33.81 Gb PacBio data were retained after the quality control of the raw sequence data. After genome assembly using these clean data, here we confirm that the complete genome size of P. americana is 3.26 Gb, and this is only smaller than Locusta migratoria among all of the reported genomes of insects. Specifically, the heterozygosity rate of P. americana genome is 0.635%, and 62.38% of the genome sequences are found to be repeats sequences. The lengths of Contig N50 and scaffold N50 are 28.2 kb and 315 kb, respectively. Moreover, 88.1% of the single copy orthologs are successfully detected by using BUSCO analysis, and the results of gene prediction based on De novo, homology and transcriptome showed that there are 14 568 genes in the genome of P. americana, and 92.4% of them can be functionally annotated. Our study provides the first whole genome sequence of P. americana, and also the first genomic information of the insect in Periplaneta genus, which can significantly contribute to further genome based analysis and the exploration of medicinal resources.
2018,37(2): 121-126 收稿日期:2017-11-28
DOI:10.11984/j.issn.1000-7083.20170377
分类号:Q959.229.9;R857.3
基金项目:国家中医药管理局"中成药大宗品种康复新液全程质量控制体系及优质产品标准建设(ZYY-2017-054)"项目
作者简介:范振鑫,E-mail:zxfan@scu.edu.cn
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