海洋蛭弧菌DA5全基因组测序及序列分析

doi:10.11978/2018016

摘要/Abstract

摘要：

为深入挖掘和利用海洋蛭弧菌及其基因资源, 本研究利用Illumina HiSeq测序平台对一株属于嗜盐噬菌弧菌(Halobacteriovorax)的海洋蛭弧菌DA5进行了全基因组测序, 对基因组进行组装、基因预测和功能注释, 并与其他8株蛭弧菌进行了比较基因组分析。结果显示: DA5基因组大小为3.27Mb, GC含量为36.5%, 预测编码基因3175个。在DA5基因组中注释到303个基因具有直系同源蛋白簇分类, 与代谢通路相关基因1239个。比较基因组分析表明: DA5符合海洋蛭弧菌基因组的基本特征, 与其他8株蛭弧菌共有467个同源基因家族, 而DA5特有基因为266个。DA5中与细胞运动相关基因62个, 其中编码甲基受体趋化蛋白、鞭毛蛋白、鞭毛马达及其开关蛋白基因均与嗜盐噬菌弧菌BAL6_X的对应基因亲缘关系最近。对DA5全基因组序列的注释和功能分析, 为深入研究其捕食特性和作用机制, 并更有效地利用其防控海水养殖细菌病害提供了基础。

关键词: 海洋蛭弧菌, 嗜盐噬菌弧菌, 全基因组测序, 基因功能, 比较基因组分析

Abstract:

To explore and utilize marine Bdellovibrio-and-like organisms (BALO) and their genes, the whole genome of Halobacteriovorax sp. DA5 was sequenced using the Illumina HiSeq platform. Then, fragment assembly, gene prediction and functional annotation were analyzed in comparison with those of other eight BALO strains. The results showed that the genome size of strain DA5 is 3.27 Mb with GC content of 36.5%, and encodes 3175 predicted genes, including 303 genes found in the Clusters of Orthologous Groups (COG) database and 1239 genes related to metabolic pathways. Comparative genomic analysis showed that DA5 has typical characteristics identified in genomes of the marine BALOs, and there were 467 homologous gene families common in genomes of DA5 and other eight BALOs, while 266 unique genes were found only in DA5 genome. Among all the 62 genes associated with cell motility of strain DA5, members such as methyl-accepting chemotaxis protein, putative flagellin, flagellar motor proteins, and flagellar motor switch proteins were most affiliated phylogenetically with those of Halobacteriovorax sp. BAL6_X. Therefore, annotation and functional analysis of the genome sequence of DA5 provide insight into its predatory property and interaction mechanism with host, and establish the basis for DA5 as biocontrol agent against harmful bacteria occurring in marine aquaculture.

Key words: marine Bdellovibrio-and-like organisms, Halobacteriovorax, whole-genome sequencing, gene function, comparative genomic analysis

中图分类号:

Q933

陆友云, 薛明, 李志桦, 温崇庆. 海洋蛭弧菌DA5全基因组测序及序列分析[J]. 热带海洋学报, 2018, 37(6): 112-119.

Youyun LU, Ming XUE, Zhihua LI, Chongqing WEN. Whole-genome sequencing and analysis of marine Bdellovibrio-and-like organism DA5[J]. Journal of Tropical Oceanography, 2018, 37(6): 112-119.

图/表 7

表1

图1

表2

图2

图3

表3

嗜盐噬菌弧菌DA5运动相关基因"

基因名称	基因数量	编码蛋白名称	重叠群
mcp	7	Methyl-accepting chemotaxis protein	contig1、contig3、contig7、contig9
mcp	1	chemotaxis protein	contig7
fliM/fliN/fliG	3	flagellar motor switch protein	contig3、contig3、contig9
motB/motA	2	Flagellar motor protein	contig1
motA	2	transporter, MotA/TolQ/ExbB proton channel family protein	contig1
cheW	1	CheW-like protein	contig3
cheY/cheA/cheW	4	putative chemotaxis protein	contig3、contig3、contig7
cheY	2	response regulator receiver domain protein	contig1、contig8
cheX	1	chemotaxis phosphatase	contig3
cheB/cheR	2	protein-glutamate O-methyltransferase	contig3、contig9
cheR	1	putative chemotaxis protein methyltransferase	contig7
cheD	1	putative methylation of MCP proteins-related protein	contig7
aer	1	hypothetical protein	contig7
dppA	1	putative dipeptide ABC transporter, periplasmic dipeptide-binding protein DppA	contig11
MYLPF	1	Regulation of actin cytoskeleton	contig36、contig37
fliC	5	putative flagellin protein	contig8、contig1
fliC	1	flagellin N-terminal domain protein	contig12
fliP/fliQ/flhB/flhA	4	flagellar biosynthetic protein	contig3
flhF	1	hypothetical protein	contig3
fliR	1	bacterial export protein, family 1	contig3
flhG, fleN	1	ATPase MipZ	contig3
flhG, fleN	1	CobQ/CobB/MinD/ParA nucleotide binding domain protein	contig3
fliS	1	flagellar protein	contig8
fliD/flgL/flgK	3	flagellar hook-associated protein	contig8
flgI	1	flagellar P-ring protein	contig8
flgH	1	flagellar L-ring protein	contig8
fliF	1	flagellar M-ring protein	contig9
flgG/flgF/flgB/flgC	4	flagellar basal-body rod protein	contig8、contig8、contig9、contig9
fliE	1	flagellar hook-basal body complex protein	contig9
fliH	1	flagellar assembly protein	contig9
fliI	1	flagellum-specific ATP synthase	contig9
fliJ	1	flagellar FliJ protein	contig9
flgD	1	putative flagellar hook capping protein	contig9
flgE	1	flagellar hook-basal body protein	contig9
pilT	1	twitching motility protein	contig8

表3

表4

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功能类别	基因数量	比例/%
翻译、核糖体结构和生物合成	45	14.85
能量产生与转换	33	10.89
翻译后修饰、蛋白质周转和分子伴侣	30	9.90
氨基酸转运与代谢	21	6.93
无机离子转运与代谢	19	6.27
脂类转运与代谢	15	4.95
转录	15	4.95
一般功能预测	15	4.95
复制、重组和修复	14	4.62
核苷酸转运与代谢	11	3.63
细胞运动	11	3.63
碳水化合物的运输和代谢	10	3.30
信号转导机制	10	3.30
辅酶转运与代谢	8	2.64
细胞周期调控, 细胞分裂, 染色体分裂	5	1.65
细胞壁/膜/包体生物合成	5	1.65
防御机制	5	1.65
胞内运输、分泌和囊泡运输	3	0.99
次级代谢产物的生物合成、运输和分解代谢	2	0.66
细胞骨架	1	0.33
功能未知	25	8.25

菌株	基因组大小/bp	拼接水平	GC含量/%	预测基因总数	编码基因数量	tRNA数量
B. bacteriovorus HD100	3782950	chromosome	50.6	3597	3548	36
H. marinus. SJ	3435933	chromosome	36.7	3307	3254	36
H. marinus. BE01	3393238	chromosome	36.7	3257	3201	36
Halobacteriovorax sp. BSW11_IV	3650096	contig	36.9	3491	3457	30
Halobacteriovorax sp. SEQ25_V	3450786	contig	36.0	3332	3292	32
Halobacteriovorax sp. DB6_IX	2969235	contig	37.6	3218	3192	23
Halobacteriovorax sp. BAL6_X	3233679	contig	36.5	3101	3065	31
Halobacteriovorax sp. JY17	3470022	contig	36.1	3316	3263	33
Halobacteriovorax sp. DA5	3272462	contig	36.5	3175	3125	31