Journal of Tropical Oceanography >
Draft genome sequence and comparative genome analysis of Alliroseovarius sp. Z3
Copy editor: YAO Yantao
Received date: 2021-02-13
Revised date: 2021-04-08
Online published: 2021-04-12
Supported by
National Natural Science Foundation of China(31672658)
General Research Project of Zhejiang Education Department, China(Y201839299)
Agricultural Major Project of Ningbo, China(2017C110001)
Alliroseovarius sp. Z3 was isolated from guts of Litopenaeus vannamei. In the study, Illumina Hiseq sequencing platform was used for genome sequencing; then, the genome was assembled, annotated by software SOAPdenovo etc., and compared with other five similar type strains. Genome annotation results showed that Z3 genome consists of 3525503 bp with a guanine-cytosine (GC) content of 59.4%, and 3509 protein-coding genes. The results of 16S rRNA sequence alignment, average nucleotide identity (ANI), DNA-DNA hybridization (DDH) and collinearity analysis showed that strain Z3 had the highest 16S rRNA similarity with Aliiroseovarius crassostreae CV919-312T, at 98.20%, and had the highest DDH and ANI values with Aliiroseovarius sediminilitoris DSM 29439T, at 26.80% and 84.95%, respectively. It was considered to be a new species of Alliroseovarius, and was named Aliiroseovarius sp. Z3. Comparative genomic analysis displayed that Aliiroseovarius sp. Z3 shared 2005 core orthologous gene clusters with other five similar type strains, and Z3 had 413 specific genes that are related to carbohydrate transport and metabolism, amino acid transport and metabolism, replication, recombination and repair, etc. After functional annotations, we found that Z3 possesses a complete denitrification pathway, indicating that Z3 can utilize nitrate and nitrite in the environment. These results related to the genome features and comparative genome of strain Z3 not only enrich the gene source of Aliiroseovarius genus, but also provide a molecular basis for studying its characteristics of denitrification.
LIU Wei , GUO Haipeng , DONG Pengsheng , YAN Mengchen , ZHANG Demin . Draft genome sequence and comparative genome analysis of Alliroseovarius sp. Z3[J]. Journal of Tropical Oceanography, 2022 , 41(1) : 52 -61 . DOI: 10.11978/2021018
图3 基于最大似然法构建的别样玫瑰变色杆菌Z3 16S rRNA基因的系统发育树Fig. 3 The phylogenetic tree of Aliiroseovarius sp. Z3 16S rRNA gene based on the maximum likelihood method |
图4 基于单拷贝直系同源基因构建的系统发育树Fig. 4 The phylogenetic tree based on the single copy orthologous gene families |
表1 6株别样玫瑰变色杆菌属细菌平均核苷酸同一性的值Tab. 1 Average nucleotide identity (ANI) values of six Aliiroseovarius spp. |
Aliiroseovarius sp. Z3 | A. crassostreae CV919-312T | A. halocynthiae MA1-10T | A. marinus A6024T | A. pelagivivens GYSW-22T | A. sediminilitoris DSM 29439T | |
---|---|---|---|---|---|---|
Aliiroseovarius sp. Z3 | * | 84.51% | 84.33% | 84.87% | 84.49% | 84.95% |
A. crassostreae CV919-312T | 84.51% | * | 84.82% | 84.95% | 85.04% | 83.92% |
A. halocynthiae MA1-10T | 84.33% | 84.81% | * | 85.82% | 85.52% | 83.69% |
A. marinus A6024T | 84.87% | 84.94% | 85.83% | * | 86.50% | 83.62% |
A. pelagivivens GYSW-22T | 84.51% | 85.02% | 85.52% | 86.50% | * | 83.63% |
A. sediminilitoris DSM 29439T | 84.95% | 83.92% | 83.69% | 83.61% | 83.65% | * |
表2 别样玫瑰变色杆菌Z3与其他5株模式株DNA- DNA杂交的值Tab. 2 DNA-DNA hybridization (DDH) values between Aliiroseovarius sp. Z3 and other five Aliiroseovarius spp. |
Aliiroseovarius sp. Z3 | |
---|---|
A. crassostreae CV919-312T | 20.90% |
A. sediminilitoris DSM 29439T | 26.80% |
A. marinus A6024T | 20.60% |
A. halocynthiae MA1-10T | 20.30% |
A. pelagivivens GYSW-22T | 20.30% |
表3 Z3和与其近缘的5株别样玫瑰变色杆菌属模式株的基因组基本特征Tab. 3 Genome features summary of Z3 and other five similar type strains from Aliiroseovarius genus |
名称 | 大小/Mb | GC含量/% | 编码蛋白 | 分离来源 |
---|---|---|---|---|
Aliiroseovarius sp. Z3 | 3.53 | 59.4 | 3509 | 中国浙江宁波: 凡纳滨对虾肠道 |
A. crassostreae CV919-312T | 3.73 | 58.4 | 3693 | 美国缅因州达马里斯科塔河: 患病牡蛎 |
A. sediminilitoris DSM 29439T | 3.41 | 58.7 | 3323 | 中国南部吉野岛: 近海沉积物 |
A. marinus A6024T | 3.13 | 59.9 | 3027 | 中国山东日照: 海水 |
A. halocynthiae MA1-10T | 3.39 | 57.1 | 3349 | 南海: 海鞘 |
A. pelagivivens GYSW-22T | 3.33 | 58.1 | 3218 | 韩国巨济岛: 海水 |
图5 菌株Z3与其他5个别样玫瑰变色杆菌Aliiroseovarius crassostreae CV919-312T(a)、Aliiroseovarius sediminilitoris DSM 29439T(b)、Aliiroseovarius halocynthiae MA1-10T(c)、Aliiroseovarius marinus A6024T(d)和Aliiroseovarius pelagivivens GYSW-22T(e)的共线性分析图中数值表示基因片段大小 Fig. 5 Synteny blocks between Aliiroseovarius sp. Z3 and other five Aliiroseovarius spp., Aliiroseovarius. crassostreae CV919-312T (a), Aliiroseovarius sediminilitoris DSM 29439T (b), Aliiroseovarius. halocynthiae MA1-10T (c), Aliiroseovarius marinus A6024T (d), and Aliiroseovarius pelagivivens GYSW-22T (e). The value in the figure indicates the size of the gene fragment |
图6 6株别样玫瑰变色杆菌的直系同源基因和特异性基因簇的数量Fig. 6 The numbers of orthologous and unique gene clusters among six Aliiroseovarius spp. |
表4 基于COG数据库比对的6株别样玫瑰变色杆菌属细菌的直系同源核心基因和Z3的特异性基因Tab. 4 The number of core orthologous gene clusters of six Aliiroseovarius spp. and specific 418 genes in the genome of Aliiroseovarius sp. Z3 based on COG categories analysis |
COG分类 | 核心基因/个 | Z3的特异性基因/个 |
---|---|---|
未分类(Unassigned) | 992 | 220 |
能量产生与转换(C) | 149 | 13 |
细胞周期调控、细胞分裂、染色体分区(D) | 9 | 2 |
氨基酸转运与代谢(E) | 305 | 14 |
核苷酸转运与代谢(F) | 22 | 2 |
碳水化合物的转运与代谢(G) | 139 | 15 |
辅酶转运与代谢(H) | 97 | 6 |
脂类转运与代谢(I) | 78 | 6 |
翻译、核糖体结构和生物合成(J) | 30 | 3 |
转录(K) | 217 | 12 |
复制、重组和修复(L) | 31 | 12 |
细胞壁/膜/包体生物合成(M) | 76 | 10 |
细胞运动(N) | 2 | 0 |
翻译后修饰、蛋白质周转和分子伴侣(O) | 46 | 8 |
无机离子转运与代谢(P) | 235 | 12 |
次生代谢物的生物合成、转运和分解代谢(Q) | 48 | 2 |
功能未知(S) | 184 | 68 |
信号转导机制(T) | 110 | 4 |
细胞内运输、分泌和囊泡运输(U) | 17 | 3 |
防御机制(V) | 44 | 6 |
[1] |
刘志迎, 许海, 詹旭, 等, 2019. 蓝藻水华对太湖水柱反硝化作用的影响[J]. 环境科学, 40(3): 1261-1269.
|
[2] |
|
[3] |
|
[4] |
|
[5] |
|
[6] |
|
[7] |
|
[8] |
|
[9] |
|
[10] |
|
[11] |
|
[12] |
|
[13] |
|
[14] |
|
[15] |
|
[16] |
|
[17] |
|
[18] |
|
[19] |
|
[20] |
|
[21] |
|
[22] |
|
[23] |
|
[24] |
|
[25] |
|
[26] |
|
[27] |
|
[28] |
|
[29] |
|
[30] |
|
[31] |
|
[32] |
|
[33] |
|
[34] |
|
[35] |
|
[36] |
|
[37] |
|
[38] |
|
[39] |
|
[40] |
|
[41] |
|
[42] |
|
/
〈 |
|
〉 |