柑橘黄龙病菌亚洲种的泛基因组分析

doi:10.16420/j.issn.0513-353x.2023-0171

摘要/Abstract

摘要：

利用34个柑橘黄龙病菌亚洲种“Candidatus Liberibacter asiaticus”（CLas）基因组进行泛基因组（Pan-genome）构建，并对其进化和拷贝数变异（Copy number variations，CNV）等方面进行了深入分析。结果表明此泛基因组共含有36 593个基因，1 188个基因簇，其中核心基因簇有872个、可变基因簇271个和个体特有基因簇45个。对所有基因簇进行选择压力分析，发现159个基因簇经历了适应性进化。结合GO注释数据，本研究中挖掘出CLas中两个基因可能与致病性或治疗耐药性相关。对所有的基因簇进行拷贝数进行统计，同时深入分析其中8个基因簇，结果发现其中5个基因簇与CLas的致病性或抗性有关，因此推测拷贝数增加的基因可能与抗药性相关。

关键词: 柑橘, 黄龙病菌, 泛基因组, 适应性进化, 拷贝数变异

Abstract:

In this work，a pan-genome from 34 genomes of Candidatus Liberibacter asiaticus（CLas）was constructed and the extensive analyses of evolution and copy number variations were completed. The CLas pan-genome was composed of 36 593 genes and 1 188 gene clusters，including 872 core gene clusters，271 accessory gene clusters，and 45 strain-specific gene clusters. An examination for selection pressures of all gene clusters showed that 159 of them underwent adaptive evolution. Two genes associated with pathogenicity or treatment resistance in CLas were mined in combination with GO annotation data. An in-depth analysis of copy number variations in eight genes revealed that five genes were connected to pathogenicity or resistance of CLas. This result revealed that CLas develops resistance to antiseptics by increasing the copy number of relevant genes.

Key words: citrus, Huanglongbing, pan-genome, adaptive evolution, copy number variation

熊志伟, 李智龙, 尹晖, 高玉霞. 柑橘黄龙病菌亚洲种的泛基因组分析[J]. 园艺学报, 2024, 51(4): 737-747.

XIONG Zhiwei, LI Zhilong, YIN Hui, GAO Yuxia. Pan-Genome Analysis of Candidatus Liberibacter asiaticus Causing Huanglongbing of Citrus[J]. Acta Horticulturae Sinica, 2024, 51(4): 737-747.

图/表 5

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株名 Strain	GenBank数据库号 Accession number	组装程度 Assembly level	大小/Mb Size	基因数量 Gene count	样品来源 Country
9PA	GCA_013778575.1	重叠群Contig	1.23	1 224	巴西圣保罗Sao Paulo，Brazil
CHUC	GCA_009756785.1	重叠群Contig	1.21	1 095	中国China
YCPsy	GCA_001296945.1	重叠群Contig	1.23	1 113	中国广东 Guangdong，China
gxpsy	GCA_000346595.1	基因组Genome	1.27	1 191	中国广西 Guangxi，China
A4	GCA_000590865.3	基因组Genome	1.23	1 123	中国广东 Guangdong，China
JXGC	GCA_002216815.1	基因组Genome	1.23	1 118	中国江西 Jiangxi，China
JXGZ-1	GCF_009764765.1	重叠群Contig	1.22	1 095	中国江西 Jiangxi，China
YNXP-1	GCF_009764755.1	重叠群Contig	1.21	1 094	中国云南 Yunnan，China
YNJS7C	GCA_003615235.1	重叠群Contig	1.26	1 158	中国云南 Yunnan，China
CoFLP	GCA_014107775.1	基因组Genome	1.23	1 104	哥伦比亚迪布利亚 MunicipioDibulla，Colombia
ReuSP1	GCA_022220845.1	基因组Genome	1.23	1 099	法国留尼汪La Reunion，France
Ishi-1	GCA_000829355.1	基因组Genome	1.20	1 127	日本冲绳 Okinawa，Japan
Mex8	GCA_009756755.1	重叠群Contig	1.24	1 131	墨西哥莫西卡利 Mexicali，Mexico
PA19	GCF_013309695.2	重叠群Contig	1.22	1 106	巴基斯坦 Pakistan
PA20	GCF_016758155.2	重叠群Contig	1.23	1 109	巴基斯坦Pakistan
TaiYZ2	GCA_014217975.1	基因组Genome	1.23	1 123	泰国宋卡 Songkhla，Thailand
psy62	GCA_000023765.2	基因组Genome	1.23	1 162	美国 USA
AHCA1	GCA_003143875.1	染色体Chromosome	1.23	1 112	美国加利福尼亚 California，USA
A-SBCA19	GCA_014892655.1	重叠群Contig	1.19	1 115	美国加利福尼亚 California，USA
AHCA17	GCF_009859045.1	支架Scaffold	1.21	1 097	美国加利福尼亚 California，USA
SGCA5	GCA_001430705.1	重叠群Contig	1.20	1 100	美国加利福尼亚 California，USA
CRCFL16	GCA_009756805.1	重叠群Contig	1.21	1 091	美国弗罗里达 Florida，USA
MFL16	GCA_009756815.1	重叠群Contig	1.20	1 081	美国弗罗里达 Florida，USA
JRPAMB1	GCA_013462975.1	基因组Genome	1.24	1 128	美国弗罗里达 Florida，USA
HHCA16	GCA_009756845.1	重叠群Contig	1.21	1 101	美国哈先达岗 Hacienda Heights，USA
HHCA	GCF_000724755.1	重叠群Contig	1.15	1 199	美国洛杉矶 Los Angeles，USA
SGCA16	GCA_009756855.1	重叠群Contig	1.21	1 098	美国圣盖博 San Gabriel，USA
TX2351	GCA_001969535.1	重叠群Contig	1.25	1 184	美国德克萨斯 Texas，USA
DUR2TX1	GCA_009756725.1	重叠群Contig	1.21	1 117	美国德克萨斯 Texas，USA
GFR3TX3	GCA_009756735.1	重叠群Contig	1.21	1 092	美国德克萨斯 Texas，USA
DUR1TX1	GCA_009756745.1	重叠群Contig	1.21	1 091	美国德克萨斯 Texas，USA
LBR19TX2	GCA_009756885.1	重叠群Contig	1.20	1 085	美国德克萨斯 Texas，USA
LBR23TX5	GCA_009756915.1	重叠群Contig	1.20	1 089	美国德克萨斯 Texas，USA
FL17	GCA_000820625.1	重叠群Contig	1.23	1 103	美国弗罗里达 Florida，USA

株名 Strain	GenBank数据库号 Accession number	组装程度 Assembly level	大小/Mb Size	基因数量 Gene count	样品来源 Country
9PA	GCA_013778575.1	重叠群Contig	1.23	1 224	巴西圣保罗Sao Paulo，Brazil
CHUC	GCA_009756785.1	重叠群Contig	1.21	1 095	中国China
YCPsy	GCA_001296945.1	重叠群Contig	1.23	1 113	中国广东 Guangdong，China
gxpsy	GCA_000346595.1	基因组Genome	1.27	1 191	中国广西 Guangxi，China
A4	GCA_000590865.3	基因组Genome	1.23	1 123	中国广东 Guangdong，China
JXGC	GCA_002216815.1	基因组Genome	1.23	1 118	中国江西 Jiangxi，China
JXGZ-1	GCF_009764765.1	重叠群Contig	1.22	1 095	中国江西 Jiangxi，China
YNXP-1	GCF_009764755.1	重叠群Contig	1.21	1 094	中国云南 Yunnan，China
YNJS7C	GCA_003615235.1	重叠群Contig	1.26	1 158	中国云南 Yunnan，China
CoFLP	GCA_014107775.1	基因组Genome	1.23	1 104	哥伦比亚迪布利亚 MunicipioDibulla，Colombia
ReuSP1	GCA_022220845.1	基因组Genome	1.23	1 099	法国留尼汪La Reunion，France
Ishi-1	GCA_000829355.1	基因组Genome	1.20	1 127	日本冲绳 Okinawa，Japan
Mex8	GCA_009756755.1	重叠群Contig	1.24	1 131	墨西哥莫西卡利 Mexicali，Mexico
PA19	GCF_013309695.2	重叠群Contig	1.22	1 106	巴基斯坦 Pakistan
PA20	GCF_016758155.2	重叠群Contig	1.23	1 109	巴基斯坦Pakistan
TaiYZ2	GCA_014217975.1	基因组Genome	1.23	1 123	泰国宋卡 Songkhla，Thailand
psy62	GCA_000023765.2	基因组Genome	1.23	1 162	美国 USA
AHCA1	GCA_003143875.1	染色体Chromosome	1.23	1 112	美国加利福尼亚 California，USA
A-SBCA19	GCA_014892655.1	重叠群Contig	1.19	1 115	美国加利福尼亚 California，USA
AHCA17	GCF_009859045.1	支架Scaffold	1.21	1 097	美国加利福尼亚 California，USA
SGCA5	GCA_001430705.1	重叠群Contig	1.20	1 100	美国加利福尼亚 California，USA
CRCFL16	GCA_009756805.1	重叠群Contig	1.21	1 091	美国弗罗里达 Florida，USA
MFL16	GCA_009756815.1	重叠群Contig	1.20	1 081	美国弗罗里达 Florida，USA
JRPAMB1	GCA_013462975.1	基因组Genome	1.24	1 128	美国弗罗里达 Florida，USA
HHCA16	GCA_009756845.1	重叠群Contig	1.21	1 101	美国哈先达岗 Hacienda Heights，USA
HHCA	GCF_000724755.1	重叠群Contig	1.15	1 199	美国洛杉矶 Los Angeles，USA
SGCA16	GCA_009756855.1	重叠群Contig	1.21	1 098	美国圣盖博 San Gabriel，USA
TX2351	GCA_001969535.1	重叠群Contig	1.25	1 184	美国德克萨斯 Texas，USA
DUR2TX1	GCA_009756725.1	重叠群Contig	1.21	1 117	美国德克萨斯 Texas，USA
GFR3TX3	GCA_009756735.1	重叠群Contig	1.21	1 092	美国德克萨斯 Texas，USA
DUR1TX1	GCA_009756745.1	重叠群Contig	1.21	1 091	美国德克萨斯 Texas，USA
LBR19TX2	GCA_009756885.1	重叠群Contig	1.20	1 085	美国德克萨斯 Texas，USA
LBR23TX5	GCA_009756915.1	重叠群Contig	1.20	1 089	美国德克萨斯 Texas，USA
FL17	GCA_000820625.1	重叠群Contig	1.23	1 103	美国弗罗里达 Florida，USA

基因家族 Gene family	基因 Gene	功能 Function	致病/耐药相关 Associated with pathogenic/drug resistance	参考文献 Reference
1	多药物耐药蛋白 Multidrug resistance protein	参与多药物耐药过程 Mediate multidrug resistance	是 Yes	Wang et al.， 2021
2	Flp/Fap菌毛组成 Flp/Fap pilin component	毒力因子 Virulence determinant	是 Yes	Nykyri et al.， 2013
3	切除核酸酶ABC的C亚基 Excinuclease ABC subunit C	参与氧化应激反应 Involved in the oxidative stress response	是 Yes	Silva et al.,2020
4	外膜蛋白Outer membrane protein	免疫原性 Immunogenic	是 Yes	Nie et al.,2020
5	磺酸ABC转运体酶 Sulfonate ABC transporter permease	参与多药物耐药过程 Mediate multidrug resistance	是 Yes	Yu et al.,2021
6	DNA聚合酶 DNA polymerase	DNA复制 DNA replication	否 No	—
7	未知功能蛋白 Protein of unknown function	—	否 No	—
8	假定蛋白 Hypothetical protein	—	否 No	—

基因家族 Gene family	基因 Gene	功能 Function	致病/耐药相关 Associated with pathogenic/drug resistance	参考文献 Reference
1	多药物耐药蛋白 Multidrug resistance protein	参与多药物耐药过程 Mediate multidrug resistance	是 Yes	Wang et al.， 2021
2	Flp/Fap菌毛组成 Flp/Fap pilin component	毒力因子 Virulence determinant	是 Yes	Nykyri et al.， 2013
3	切除核酸酶ABC的C亚基 Excinuclease ABC subunit C	参与氧化应激反应 Involved in the oxidative stress response	是 Yes	Silva et al.,2020
4	外膜蛋白Outer membrane protein	免疫原性 Immunogenic	是 Yes	Nie et al.,2020
5	磺酸ABC转运体酶 Sulfonate ABC transporter permease	参与多药物耐药过程 Mediate multidrug resistance	是 Yes	Yu et al.,2021
6	DNA聚合酶 DNA polymerase	DNA复制 DNA replication	否 No	—
7	未知功能蛋白 Protein of unknown function	—	否 No	—
8	假定蛋白 Hypothetical protein	—	否 No	—