副猪嗜血杆菌高自然转化效率菌株的筛选及全基因组测序

doi:10.11843/j.issn.0366-6964.2018.11.016

摘要/Abstract

摘要：

旨在筛选具有高自然转化效率的副猪嗜血杆菌（HPS）菌株，为自然转化机制及基因功能研究提供生物材料；对所得菌株进行全基因组测序，通过比较基因组分析，挖掘HPS自然转化发生的分子背景。本研究采用自然转化方法对75株HPS田间分离株及15株标准株进行自然感受态菌株的筛选，并测定各自然感受态菌株的转化效率。采用PacBio三代测序技术对具有高自然转化效率的HPS菌株SC1401进行全基因组测序，对测序数据进行组装、基因预测、功能注释及共线性分析。将SC1401株测序结果与NCBI发布的SH0165（CP001321）、SH03（CP009158）、KL0318（CP009237）和ZJ0906（CP005384）进行全基因组比对。结果如下：1）共筛选出11株HPS自然感受态菌株，均为野生型，其中SC1401菌株自然转化效率最高；2）全基因组测序结果显示SC1401菌株整个基因组大小为2 277 540 bp，GC含量为40.03%，共编码2 220个基因，占整个基因组序列的87.75%（序列已上传至GenBank数据库，登录号为CP015099）；3）基因组共线性分析表明SC1401与其他四株全基因组测序菌株的共线性良好；4）比较基因组分析表明，SC1401菌株含特有基因385个，远多于其他4株菌株所含有的特有基因；5株HPS含有一系列相同的与自然转化相关的基因，且除tfox基因外，各基因氨基酸序列一致性均达90%以上。本研究首次报道了一株强自然转化能力的副猪嗜血杆菌SC1401的全基因组序列，并分析了其基因组基本特征，为后续HPS自然转化机制的研究提供一定理论基础。

Abstract:

This study aimed to screen highly transformable Haemophilus parasuis (HPS)strains, which in the hope of providing biological materials for the further study of natural competence mechanism and gene function research. Based on the genome sequences of the selected strain and comparative genome analysis, we attempted to investigate the molecular genetic basis of natural transformation of HPS. In this study, 75 HPS field isolates and 15 standard strains were screened by natural transformation method, and the transformation efficiency of the natural competent strain was determined. The genome of the strain SC1401 with high natural transformation efficiency was sequenced using the third-generation sequencing technology on PacBio, and then analyzed using related software for genome assembly, gene prediction, functional annotation and synteny analysis. The sequencing result of SC1401 strain was compared with those of SH0165 strain (GenBank:CP001321), SH03 strain (GenBank:CP009158), KL0318 strain (GenBank:CP009237) and ZJ0906 strain (GenBank:CP005384). The results showed that:1) 11 HPS strains were identified as natural competent strain, which all were wild type, and SC1401 had the highest transformation efficiency among them. 2) The genome size is 2 277 540 bp with GC content of 40.03%. The total gene quantity is 2 220, accounting for 87.75% of the whole genome. This genome sequence had been submitted to GenBank database under the accession number CP015099. 3) Synteny analysis indicated that the relationship between the 5 HPS strains were close-related. 4) Comparative genomics analysis showed that SC1401 isolates contained 385 unique genes, much more than the other 4 strains. Five HPS strains contained a series of identical genes related to natural transformation, and in addition to the tfox, the homogeneity of the amino acid sequences of each gene had reached over 90%. This study is the first report of the whole genome sequence of SC1401, a highly naturally competent strain, and analyzed the basic characterization of the genome, so as to provide a theoretical basis for later research on the mechanism of natural transformation of HPS.

中图分类号:

S852.612

杨振, 谨瑾, 马小雨, 代科, 王正皓, 曹三杰, 黄小波, 伍锐, 赵勤, 文翼平. 副猪嗜血杆菌高自然转化效率菌株的筛选及全基因组测序[J]. 畜牧兽医学报, 2018, 49(11): 2442-2450.

YANG Zhen, JIN Jin, MA Xiao-yu, DAI Ke, WANG Zheng-hao, CAO San-jie, HUANG Xiao-bo, WU Rui, ZHAO Qin, WEN Yi-ping. Screening the Highly Transformable Haemophilus parasuis Strain and Whole-Genome Sequencing[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2018, 49(11): 2442-2450.

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