基于比较基因组学方法的世界范围的犬布鲁氏菌系统发育群研究 <sup>*</sup>

doi:10.13523/j.cb.1907053

中国生物工程杂志

2020, Vol. 40

Issue (3): 38-47 DOI: 10.13523/j.cb.1907053

研究报告

基于比较基因组学方法的世界范围的犬布鲁氏菌系统发育群研究 ^*

姜吉喆^1,^**,潘航^2,^**,乐敏^2,^***(

),章乐^1,^***(

)

1 四川大学计算机(软件)学院成都 610065
2 浙江大学动物科学学院动物预防医学研究所浙江省动物预防医学重点实验室杭州 310058

The Study of Worldwide Brucella canis of Phylogenetic Groups by Comparative Genomics-based Approaches

JIANG Ji-zhe^1,^**,PAN Hang^2,^**,YUE Min^2,^***(

),ZHANG Le^1,^***(

)

1 School of Computer Science (Software), Sichuan University, Chengdu 610065, China
2 Institute of Animal Preventive Medicine, College of Animal Science, Zhejiang University, Hangzhou 310058, China

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摘要：

犬布鲁氏菌病是一种世界范围内导致家畜流产和人波状热的人畜共患病, 最近随着相关宿主动物如犬类饲养数量的增多,家庭儿童的感染案例报道屡见不鲜,所以研究犬布鲁氏菌具有重要公共卫生意义.使用了全球的91个菌株,利用贝叶斯方法对菌株分群,基于core-SNPs和分子钟模型构建进化树进行种群结构和时空分布分析,使用COG功能聚类进行功能差异研究.发现的4个系统发育群(PG)与它们的地理来源显著相关,PG1~3中,存在亚洲到非洲及欧美间的传播;PG4定殖于北美,且耐药基因逐渐缺失.功能基因在4个PG中的存在/缺失谱不同,PG3功能最完整,其他PG各具独特的功能基因缺失,特别是PG2大多缺失ABC型转运系统组分.掌握犬布鲁氏菌在全球的分布和传播,理解其基因组变异有助于开发新的诊断和疫苗靶点,以对抗由犬布鲁氏菌引起的人类流行病.

关键词： 犬布鲁氏菌; SNP; 比较基因组学; 系统发育群(PG); 分支长度优化算法

Abstract:

Canine brucellosis is a zoonotic disease that causes livestock abortion and human Malta fever worldwide. Recently, with the increase in the number of related host animals such as dogs, infection reports of family children are not uncommon, so study Brucella canis has important public health implications. Using 91 strains around the world, Bayesian method was used to cluster the strains, and based on the core-SNPs and molecular clock model, the evolutionary tree was constructed for population structure and spatiotemporal distribution analysis, and COG function clustering was used to study the functional differences. The four phylogenetic groups (PG) found were significantly associated with their geographic origin. Among PG1-3, there was transmission from Asia to Africa, Europe and America. PG4 was colonized in North America, and its drug resistance genes were gradually missing. Functional gene has different presence/absence profiles in 4 PGs, PG3 is the most complete, and other PGs have unique functional gene absence, especially PG2 mostly lacks ABC-type transport system components. Understanding the global distribution and spread of Brucella canis and its genomic variation will help develop new diagnostic and vaccine targets to combat the epidemic caused by Brucella canis.

Key words: Brucella canis SNP Comparative genomics PG Branch length optimization algorithm

收稿日期: 2019-07-30 出版日期: 2020-04-18

ZTFLH:

TP3-05

基金资助: * 国家自然科学基金(6137213);科技部重大专项(2018ZX10201002)

通讯作者: 乐敏,章乐 E-mail: myue@zju.edu.cn;zhangle06@scu.edu.cn

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引用本文:

姜吉喆, 潘航, 乐敏, 章乐. 基于比较基因组学方法的世界范围的犬布鲁氏菌系统发育群研究 ^*[J]. 中国生物工程杂志, 2020, 40(3): 38-47.

JIANG Ji-zhe, PAN Hang, YUE Min, ZHANG Le. The Study of Worldwide Brucella canis of Phylogenetic Groups by Comparative Genomics-based Approaches. China Biotechnology, 2020, 40(3): 38-47.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.1907053 或 https://manu60.magtech.com.cn/biotech/CN/Y2020/V40/I3/38

图1 core-SNPs进化树构建流程

图2 分支拓扑关系

图3 基于core-SNPs的进化树

表1 PG中不同位置对应的菌株数量

图4 有关时空分布的最大似然进化树

图5 4个PG中的功能缺失

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