Current research on genomic analysis of “Candidatus Liberibacter spp.”
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摘要:
柑橘黄龙病(Citrus Huanglongbing, HLB)是柑橘生产上最具毁灭性的病害，严重威胁着世界柑橘产业的发展。该病害由难培养细菌——候选韧皮部杆菌(Candidatus Liberibacter spp.)所引起，通过带病苗木和媒介昆虫进行传播蔓延。近年来，随着DNA测序技术和生物信息学的发展，基因组学被广泛应用于柑橘黄龙病的研究，并为克服黄龙病菌难培养所造成的研究瓶颈提供了新的方法和思路。柑橘黄龙病菌基因组学的研究，不仅有助于探究黄龙病菌与寄主植物的互作关系，而且可为抗病栽培和病害早期检测提供重要的理论基础。本文结合当前柑橘黄龙病的研究概况、病原全基因组的测序策略及基因组的特征描述，重点综述基因组学在黄龙病致病机理、病原遗传多样性与分子检测等方面的研究进展。
Abstract:Citrus Huanglongbing (HLB), the highly destructive disease which has been threatening citrus production worldwide, is caused by the yet unculturable bacteria, “Candidatus Liberibacter spp.”. HLB can be spread with insect vector and contaminated seedlings. In recent years, with the rapid development of DNA sequencing technology and bioinformatics, genomic analysis had become widely used for HLB research, and had provided the new strategies to overcome the research bottleneck caused by difficulties in bacterial culture. The genomic analysis of “Candidatus Liberibacter spp.” not only helps to explore the interaction between “Candidatus Liberibacter spp.” and host plant, but also provides an important theoretical basis for resistance cultivation and early detection of HLB. This review summarizes the research progress in citrus HLB and describes the current sequencing strategy and genomic characterization of “Candidatus Liberibacter spp.”, with an emphasis on the research progress in genomic analysis of pathogenic mechanism, genetic diversity and molecular detection of “Candidatus Liberibacter spp.”.
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表 1 柑橘黄龙病菌基因组的基本信息1)
Table 1 Basic information of sequenced Candidatus Liberibacter genomes
编号2)
No.年份
Year菌株
Strain寄主
Host来源地区
Original region基因组大小/Mb
Genome size基因组完整性 genome GC含量/%
GC content预测基因数3)
Number of predicted genes测序深度
Coverage1 2009 psy62[18] 柑橘木虱 美国佛罗里达州 1.23 完整 36.5 1 186 16 x 2 2013 Gxpsy[19] 柑橘木虱 中国广西 1.27 完整 36.5 1 141 50~80 x 3 2014 A4[20] 柑橘 中国广东 1.21 完整 36.4 1 122 138 x 4 2014 HHCA[21] 柠檬 美国加州 1.15 不完整 36.5 1 131 6 x 5 2014 Ishi-1[22] 未确定 日本 1.19 完整 36.3 1 078 300 x 6 2015 FL17[23] 未确定 美国佛罗里达州 1.23 不完整 36.5 1 116 50 x 7 2015 YCPsy[24] 柑橘木虱 中国广东 1.23 不完整 36.5 1 125 1 120 x 8 2015 SGCA5[25] 橘树 美国加州 1.20 不完整 36.4 1 114 12 x 9 2017 TX2351[26] 柑橘木虱 美国德克萨斯州 1.25 不完整 36.5 1 184 7 x 10 2017 JXGC[27] 未确定 中国江西 1.23 完整 36.4 1 120 95 x 11 2018 AHCA1[28] 柑橘木虱 美国加州 1.23 完整 36.6 1 112 69 x 12 2018 SGCA1[28] 橘树 美国加州 0.23 不完整 36.3 506 1 x 13 2018 TX1712[29] 橙 美国德克萨斯州 1.20 不完整 36.4 NF 10 x 14 2018 SGpsy[28] 柑橘木虱 美国加州 0.77 不完整 36.3 NF 2 x 15 2018 YNJS7C[30] 未确定 中国云南 1.26 不完整 36.6 1 158 15 x 16 2013 PW_SP[31] 长春花 巴西圣保罗 1.18 不完整 31.1 1 006 18.6 x 17 2014 São Paulo[32] 长春花 巴西圣保罗 1.20 完整 31.1 1 028 > 100 x 18 2015 PTSAPSY[33] 南非木虱 南非比勒陀利亚 1.19 完整 34.5 1 103 60~80 x 1) 信息收集时间为2019−04−11；2) 1~15为亚洲种，16、17为美洲种，18为非洲种；3) NF表示NCBI基因组数据库未提供
1) Information was collected at 11th, April 2019; 2) 1−15:“Candidatus Liberibacter asiaticus”, 16, 17:“Candidatus Liberibacter americanus”, 18:“Candidatus Liberibacter africanus”, 3) NF represents none information found in NCBI genome database
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