烟草拮抗链霉菌FT05W基因组测序与几丁质酶家族基因鉴定

doi:10.16409/j.cnki.2095-039x.2019.03.016

摘要/Abstract

摘要： 链霉菌FT05W是一株对烟草黑胫病等土传真菌病害具有良好拮抗作用的生防放线菌。本研究利用Miseq PE300高通量测序平台对链霉菌FT05W基因组进行序列测定，共获得6914188个reads，通过SPAdes软件对序列进行拼接共得1836个contigs，其基因组全长为7699129 bp，GC比为71%，其中编码基因序列长度为6037181 bp，预测出7434个蛋白编码基因（GenBank登录号：NZ_QGMR00000000），预测编码7323个蛋白。获得的基因注释信息为今后深入开展其在烟草上的生物防治机理研究奠定了重要的基础，有助于推动烟草生防链霉菌功能基因的挖掘与利用，为烟草生防链霉菌FT05W的进一步开发与应用提供理论依据。利用MEGA 6.06构建链霉菌FT05W的几丁质酶家族基因系统发育树，共鉴定出7个几丁质酶家族基因，其中6个为18家族几丁质酶基因，1个为19家族基因。

关键词: 烟草生防菌, 链霉菌, 基因组测序, 几丁质酶家族基因

Abstract: Streptomyces sp. FT05W was a biocontrol strain with antagonism to tobacco soil-borne fungal pathogens. In this study, we used Miseq PE300 next-generation sequencing platform to perform the genome sequencing, and obtained 6914188 reads. The SPAdes software was used to splice a total of 1836 contigs with a total genome length of 7699129 bp and a GC ratio of 71%. Length of the coding gene sequence was 6037181 bp, and 7434 protein-coding genes were predicted, which are predicted to encode 7233 proteins. Subsequently, through the comparison and analysis of databases such as GO, COG, KEGG, NR and TCDB, the genome prediction and basic function annotations were completed. The obtained gene annotation information lays an important foundation for further research on its biological control mechanism in tobacco. The results will help to promote the excavation and utilization of Streptomyces sp. functional genes and provide a theoretical basis for further development and application of Streptomyces sp. FT05W. Finally, the chitinase family gene phylogenetic tree of Streptomyces sp. FT05W was constructed using MEGA 6.06. A total of seven chitinase gene families were identified. Six were family18 chitinase genes and one was family 19 gene.

Key words: tobacco biocontrol strain, Streptomyces sp., genome sequencing, chitinase family gene

中图分类号:

S476

覃可, 桑维钧, 陈孝玉龙, 李昊熙, 杨茂发. 烟草拮抗链霉菌FT05W基因组测序与几丁质酶家族基因鉴定[J]. 中国生物防治学报, 2019, 35(3): 463-473.

QIN Ke, SANG Weijun, CHEN Xiaoyulong, LI Haoxi, YANG Maofa. Genome Sequencing and Identification of Chitinase Family Genes of Streptomyces sp. FT05W, an Antagonist of Tobacco Pathogens[J]. journal1, 2019, 35(3): 463-473.

参考文献

[1] Chen X, Pizzatti C, Bonaldi M, et al. Biological control of lettuce drop and host plant colonization by rhizospheric and endophytic Streptomycetes[J]. Frontiers in Microbiology, 2016, 7(714):1-21.
[2] Chen X, Bonaldi M, Erlacher A, et al. Biocontrol of two Streptomyces spp. strains against lettuce basal drop caused by Sclerotinia sclerotiorum[J]. Phytopathology, 2016, 106(6):S7-S26.
[3] Bonaldi M, Kunova A, Saracchi M, et al. Streptomycetes as biological control agents against basal drop[J]. Acta Horticulturae, 2014, 1044(40):313-318.
[4] Kunova A, Bonaldi M, Saracchi M, et al. Selection of Streptomyces against soil borne fungal pathogens by a standardized dual culture assay and evaluation of their effects on seed germination and plant growth[J]. BMC Microbiology, 2016, 16(272), 1-11.
[5] Sardi P, Saracchi M, Quaroni S, et al. Isolation of endophytic Streptomyces strains from surface-sterilized roots[J]. Applied and Environmental Microbiology, 1992, 58(8):2691-2693.
[6] Xie C C, Jia H Y, Chen Y H. Regulation of chitinase genes expression in bacteria[J]. Hereditas, 2011, 33(10):1029-1038.
[7] Grover A. Plant chitinases:genetic diversity and physiological roles[J]. Critical Reviews in Plant Sciences, 2012, 31(1):57-73.
[8] Li P, Yan P, Sang X, et al. Transgenic indica rice expressing a bitter melon (Momordica charantia) class I chitinase gene (McCHIT1) confers enhanced resistance to Magnaporthe grisea and Rhizoctonia solani[J]. European Journal of Plant Pathology, 2009, 125(4):533-543.
[9] Kovács G, László S, Géraldine J, et al. Expression of a rice chitinase gene in transgenic banana (‘Gros Michel’, AAA genome group) confers resistance to black leaf streak disease[J]. Transgenic Research, 2013, 22(1):117-130.
[10] Chater K F, Biró S, Lee K J, et al. The complex extracellular biology of Streptomyces:review article[J]. Fems Microbiology Reviews, 2010, 34(2):171-198.
[11] 陈中义, 张杰, 黄大昉. 植物病害生防芽孢杆菌抗菌机制与遗传改良研究[J]. 植物病理学报, 2003, 33(2):97-103.
[12] Shen T, Wang C, Yang H, et al. Identification, solid-state fermentation and biocontrol effects of Streptomyces hygroscopicus, B04 on strawberry root rot[J]. Applied Soil Ecology, 2016, 103:36-43.
[13] 陈捷. 木霉菌诱导植物抗病性研究新进展[J]. 中国生物防治学报, 2015, 31(5):733-741.
[14] Ge B, Liu Y, Liu B, et al. Draft genome sequence of Streptomyces ahygroscopicus subsp. wuyiensis ck-15, isolated from soil in Fujian province, China[J]. Genome Announcements, 2015, 3(5):1-2.
[15] Saito A, Fujii T, Miyashita K. Distribution and evolution of chitinase genes in Streptomyces species:involvement of gene-duplication and domain-deletion[J]. Antonie van Leeuwenhoek, 2003, 84(1):7-15.
[16] Pawel B, Chian K, Paul S L. Not a peripheral iissue:secretion in Plant-microbe interactions[J]. Current Opinion in Plant Biology, 2010, 13(4):378-387.
[17] Kim Y C, Leveau J, Mcspadden Gardener B B, et al. The multifactorial basis for plant health promotion by plant-associated bacteria[J]. Applied and Environmental Microbiology, 2011, 77(5):1548-1555.
[18] Augustine S K, Bhavsar S P, Kapadnis B P. A non-polyene antifun-gal antibiotic from Streptomyces albidoflavus PU 23[J]. Journal of Biosciences, 2005, 30(2):201-211.
[19] Eltarabily K A. Rhizosphere-competent isolates of Streptomycete and non-Streptomycete actinomycetes capable of producing cell-wall-degrading enzymes to control Pythium aphanidermatum damping-off disease of cucumber[J]. Canadian Journal of Botany, 2006, 84(2):211-222.
[20] Bankevich A, Nurk S, Antipov D, et al. SPAdes:A new genome assembly algorithm and its applications to single-cell sequencing[J]. Journal of Computational Biology, 2012, 19(5):455-477.
[21] Seemann T. Prokka:rapid prokaryotic genome annotation[J]. Bioinformatics, 2014, 30(14):2068-2069.
[22] Bland C, Ramsey T L, Sabree F, et al. Crisper recognition tool (CRT):a tool for automatic detection of clustered regularly interspaced palindromic repeats[J]. BMC Bioinformatics. 2007, 8(209):1-8.
[23] Tatusov R L, Fedorova N D, Jackson J D, et al. The KOG database:an updated version includes eukaryotes[J]. BMC Bioin-formatics. 2003, 4(1):41.
[24] Https://web.expasy.org/docs/swiss-prot_guideline.html[DB/OL].
[25] Blake J A, Dolan M, Drabkin H, et al. Gene ontology annotations and resources[J]. Nucleic Acids Research, 2013, 41(1):530-535.
[26] Ogata H, Goto S, Sato K, et al. KEGG:kyoto encyclopedia of genes and genomes[J]. Nucleic Acids Research, 1999, 27(1):29-34.
[27] Ohno T, Armand S, Hata T, et al. A modular family 19 chitinase found in the prokaryotic organism Streptomyces griseus HUT 6037[J]. Journal of bacteriology, 1996, 178(17):5065-5070.
[28] Redenbach M, Kieser H M, Denapaite D, et al. A set of ordered cosmids and a detailed genetic and physical map for the 8Mb Streptomyces coelicolor A3(2) chromosome[J]. Molecular Microbiology, 1996, 21(1):77-96.
[29] Https://www.ncbi.nlm.nih.gov/genbank/[DB/OL].
[30] Joshi M V, Bignell D R D, Johnson E G, et al. The AraC/XylS regulator TxtR modulates thaxtomin biosynthesis and virulence in Streptomyces scabies[J]. Molecular Microbiology, 2007, 66(3):633-642.
[31] 张克诚, 李研学, 贾恩宽, 等. 拮抗链霉菌S-5对棉花病害的防治作用[J]. 中国农学通报, 2002, 18(2):26-29.
[32] 曹理想, 周世宁. 植物内生放线菌研究[J]. 微生物学通报, 2004, 31(4):93-96.
[33] 刘宇, 刘建华, 刘伟成, 等. 利迪链霉菌A02诱导番茄抗灰霉病作用机制研究-对植株防御酶系的影响[J]. 华北农学报, 2007, 22(2):152-155.
[34] Xue L, Gu M Y, Xu W L, et al. Antagonistic Streptomyces enhances defense-related responses in cotton for biocontrol of wilt caused by phytotoxin of Verticillium dahliae[J]. Phytoparasitica, 2016, 44(2):225-237.
[35] Viaene T, Langendries S, Beirinckx S, et al. Streptomyces as a plant's best friend?[J]. FEMS Microbiology Ecology, 2016, 92(8):1-10.
[36] Jiang X, Liu W, Ji Y, et al. Expression of CPY107Z13 in Streptomyces lividans TK54 catalyzes the oxidation of avermectin to 4″-oxo-avermectin[J]. Applied Microbiology and Biotechnology, 2012, 93(5):1957-1963.
[37] Kawase T, Yokokawa S, Saito A, et al. Comparison of enzymatic and antifungal properties between family 18 and 19 chitinases from Streptomyces coelicolor A3(2)[J]. Journal of the Agricultural Chemical Society of Japan, 2006, 70(4):988-998.
[38] Watanabe T, Kanai R, Kawase T. et al. Family 19 chitinases of Streptomyces species:characterization and distribution[J]. Microbiology, 1999, 145(12):3353-3363.
[39] Tsujibo H, Okamoto T, Hatano N, et al. Family 19 Chitinases from Streptomyces thermoviolaceus OPC520:molecular cloning and characterization[J]. Bioscience Biotechnology and Biochemistry, 2000, 64(11):2445-2453.
[40] Tsujibo H, Kubota T, Yamamoto M, et al. Characterization of chitinase genes from an alkaliphilic actinomycete, Nocardiopsis prasina OPC-131[J]. Appllied Environmental Microbiology, 2003, 69(2):894-900.
[41] Okazaki K, Yamashita Y, Noda M, et al. Molecular cloning and expression of the gene encoding family 19 chitinase from Streptomyces sp. J-13-3[J]. Bioscience, Biotechnology and Biochemistry, 2004, 68(2):341-351.
[42] Yamashita Y, Okazaki K. Purification and antifungal activity of recombinant chitinase from escherichia coli carrying the family 19 chitinase gene of Streptomyces sp. J-13-3[J]. Journal of the Agricultural Chemical Society of Japan, 2004, 68(10):2193-2196.