Latest Cover

Online Office

Contact Us

Issue:ISSN 1000-7083
          CN 51-1193/Q
Director:Sichuan Association for Science and Technology
Sponsored by:Sichuan Society of Zoologists; Chengdu Giant Panda Breeding Research Foundation; Sichuan Association of Wildlife Conservation; Sichuan University
Address:College of Life Sciences, Sichuan University, No.29, Wangjiang Road, Chengdu, Sichuan Province, 610064, China
Fax:+86-28-85410485 &
Your Position :Home->Past Journals Catalog->2018 Vol.37 No.2

Whole Genome Sequencing and Analysis of Medicinal Periplaneta americana
Author of the article:JIN Jiazheng1, LI Wujiao2, MOU Biqin3, SHEN Yongmei3, GENG Funeng2, YUE Bisong1, FAN Zhenxin1,3*
Author's Workplace:1. Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China;
2. Sichuan Key Laboratory of Medicinal American Cockroach, Xichang, Sichuan Province 615000, China;
3. Sichuan Medicinal Animals Engineering Research Center, Xichang, Sichuan Province 615000, China
Key Words:Periplaneta americana; whole genome sequencing; genome assembly; genome annotation
Abstract: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
陈佳松, 陈峰, 彭锐, 等. 2017. 基于转录组测序分析美洲大蠊提取物促进小鼠创面愈合的分子机制[J]. 四川动物, 36(4):398-403.
郭美仙, 刘晓波, 刘光明, 等. 2017. 美洲大蠊提取物对H22腹水瘤小鼠肿瘤微环境的影响[J]. 大理学院学报,2(10):5-9.
李娇, 郭美仙, 张冰清, 等. 2017. 美洲大蠊提取物CⅡ-3对肝癌H22荷瘤小鼠作用研究[J]. 中华肿瘤防治杂志,24(11):739-744.
马俊, 曾远生, 刘炜. 2015. 美洲大蠊提取物对力竭运动大鼠心血管氧化损伤的保护作用[J]. 中国应用生理学杂志, 31(5):404-406.
谭巧云, 满红霞, 那凯歌, 等. 2016. 美洲大蠊提取物对口腔溃疡大鼠模型的作用[J]. 中国临床药理学杂志, 32(11):1014-1016.
夏超, 王佳佳, 李芳群, 等. 2016. 美洲大蠊水提取物对免疫性肝纤维化大鼠的保护作用[J]. 安徽医科大学学报, 51(2):199-204.
肖小芹, 汪世平, 徐绍锐, 等. 2007. 美洲大蠊提取物抗炎, 镇痛作用的实验研究[J]. 中国病原生物学杂志, 2(2):140-143.
张蕊, 袁发璐, 李婷, 等. 2017. 美洲大蠊提取物对人肝癌HepG2细胞的作用机制研究[J]. 中国现代医学杂志, 27(12):1-8.
Ahmed A, Minha K, Namood-e-Sahar, et al. 2010. In silico identification of potential American cockroach (Periplaneta americana) allergens[J]. Iranian Journal of Public Health, 39(3):109-115.
Birney E, Clamp M, Durbin R. 2004. GeneWise and genomewise[J]. Genome Research, 14(5):988-995.
Chen XG, Jiang XT, Gu JB, et al. 2015. Genome sequence of the Asian tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution[J]. Proceedings of the National Academy of Sciences of the United States of America, 112(44):E5907. DOI:10.1073/pnas.1516410112.
Consortium THG, Kanchon KD, James RW, et al. 2012. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species[J]. Nature, 487(7405):94-98.
Geoffrey MA, Patrick PA, Joanna EA, et al. 2014. Genome sequence of the tsetse fly (Glossina morsitans):vector of African trypanosomiasis[J]. Science, 344(6182):380-386.
Haas BJ, Delcher AL, Mount SM, et al. 2003. Improving the arabidopsis genome annotation using maximal transcript a lignment assemblies[J]. Nucleic Acids Research, 31(19):5654-5666.
Haas BJ, Salzberg SL, Zhu W, et al. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments[J]. Genome Biolology, 9(1):R7.
Hunter S, Apweiler R, Attwood TK, et al. 2008. InterPro:the integrative protein signature database[J]. Nucleic Acids Research, 37(suppl_1):D211-D215.
Keeling CI, Yuen MM, Liao NY, et al. 2013. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest[J]. Genome Biology, 14(3):R27.
Kim IW, Lee JH, Subramaniyam S, et al. 2016. De novo transcriptome analysis and detection of antimicrobial peptides of the American cockroach Periplaneta americana (Linnaeus)[J]. PLoS ONE, 11(5):e0155304. DOI:10.1371/journal.pone.0155304.
Korf I. 2004. Gene finding in novel genomes[J]. BMC Bioinformatics, 5(1):59.
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2[J]. Nature Methods, 9(4):357-359.
Lewis SE, Searle S, Harris N, et al. 2002. Apollo:a sequence annotation editor[J]. Genome Biolology, 3(12):research0082.1-82.14.
Luo R, Liu B, Xie Y, et al. 2012. SOAPdenovo2:an empirically improved memory-efficient short-read de novo assembler[J]. Giga Science, 1(1):18.
Marçais G, Kingsford C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers[J]. Bioinformatics, 27(6):764-770.
Sahlin K, Vezzi F, Nystedt B, et al. 2014. BESST-efficient scaffolding of large fragmented assemblies[J]. BMC Bioinformatics, 15(1):281.
Simão FA, Waterhouse RM, Ioannidis P, et al. 2015. BUSCO:assessing genome assembly and annotation completeness with single-copy orthologs[J]. Bioinformatics, 31(19):3210-3212.
Stanke M, Diekhans M, Baertsch R, et al. 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding[J]. Bioinformatics, 24(5):637-644.
Tahir HM, Mustafa R, Khan AA, et al. 2017. Toxicity and resistance of American cockroach, Periplaneta americana L.(Blattodea:Blattidae) against malathion[J]. African Entomology, 25(2):361-366.
Terrapon N, Li C, Robertson HM, et al. 2014. Molecular traces of alternative social organization in a termite genome[J]. Nature Communications, 5(6183):3636.
Wang X, Fang X, Yang P, et al. 2014. The locust genome provides insight into swarm formation and long-distance flight[J]. Nature Communications, 5(5):2957.
Weisenfeld NI, Yin S, Sharpe T, et al. 2014. Comprehensive variation discovery in single human genomes[J]. Nature Genetic, 46(12):1350-1355.
Yun JE, Hwang JS, Lee DG. 2017. The antifungal activity of the peptide, periplanetasin-2, derived from American cockroach Periplaneta americana[J]. Biochemical Journal, 474(17):3027-3043.
Zhao Y, Yang A, Tu P, et al. 2017. Anti-tumor effects of the American cockroach, Periplaneta americana[J]. Chinese Medicine, 12(1):26. DOI:10.1186/s13020-017-0149-6.
CopyRight©2018 Editorial Office of Sichuan Journal of Zoology