茶树炭疽菌N425全基因组测序与基因功能注释

张承康; 周子文; 郭田龙; 彭成彬; 陈美霞; 刘伟

doi:10.19303/j.issn.1008-0384.2023.12.007

茶树炭疽菌N425全基因组测序与基因功能注释

doi: 10.19303/j.issn.1008-0384.2023.12.007

张承康^{1, 2,},
周子文¹,
郭田龙^{1, 2},
彭成彬¹,
陈美霞¹,
刘伟^1, ,

1.
宁德师范学院生命科学学院省级产学研合作示范基地，福建　宁德　352100
2.
福建农林大学生物农药与化学生物学教育部重点实验室，福建　福州　350002

基金项目: 国家自然科学基金项目（32001853）；生物农药与化学生物学教育部重点实验室开放课题（Keylab2020-05）；宁德师范学院科研项目（2020Y02、2022T01）

详细信息

作者简介:
张承康（1988 —），男，博士，讲师，主要从事植物病原菌致病分子机理研究，E-mail：shin_ichi@126.com

通讯作者:
刘伟（1971 — ），男，博士，研究员，主要从事植物病害防治研究，E-mail：liuwei0591@126.com

中图分类号: S436
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出版历程
- 收稿日期: 2023-08-29
- 修回日期: 2023-09-30
- 网络出版日期: 2023-12-21
- 刊出日期: 2023-12-28

Sequence and Annotation of Colletotrichum fructicola N425 Genome on Tea Plant

1.
Provincial demonstration base for industry university research cooperation, College of Life Science, Ningde Normal University, Ningde, Fujian　352100, China
2.
Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian　350002, China

摘要

摘要: 目的对茶树炭疽菌N425进行全基因组测序和基因功能注释并从中初筛出致病相关基因。方法通过Illumina HiSeq2500 PE150平台对N425菌株进行全基因组测序和组装，并利用NR、KEGG、KOG等功能基因数据库进行基因预测和功能注释。结果茶树炭疽菌N425基因组全长约56.3 Mbp，G+C含量为53.2%，共预测出10 157个蛋白编码基因和若干各类非蛋白编码序列。其中，1 356个基因在病原与宿主互作数据库（PHI）中得到注释，包括140个注释为致病力丧失的基因；720个基因在碳水化合物酶数据库（CAZy）中得到注释；302个基因被预测为次生代谢物相关基因。这些基因中有涉及cAMP-PKA、MAPK等信号通路以及降解宿主细胞壁等致病相关过程，是潜在的致病相关基因。结论本研究成功获得茶树炭疽菌N425全基因组序列和基因功能注释，并从中挖掘出潜在致病相关基因，为后续展开对茶树炭疽菌侵染茶树的致病分子机制研究奠定基础。
- 茶树炭疽病 /
- 基因组测序 /
- 基因注释 /
- 致病相关基因
Abstract: Objective Sequence and annotation of Colletotrichum fructicola N425 genomefrom a diseased tea plant were determined, and primary virulence-related genes identified. Method Whole genome of N425 was sequenced and assembled using the Illumina HiSeq2500 PE150 platform. Predicted protein structure and functional annotation of the genes were obtained using the NR, KEGG, and KOG databases. Results The genome was approximately 56.3 Mbp in length with 53.2% of G+C, 10 157 protein-coding genes, and several types of non-protein coding sequences. Of the genes, 1 356 were annotated in the PHI database that included 140 as the loss of pathogenicity, 720 in the CAZy database, and 302 related to the secondary metabolites. Some of these genes were involved in the cAMP-PKA and MAPK cascade signaling pathways as well as other pathogenic processes, such as host cell wall degradation, which could be responsible for the virulence on tea plants. Conclusion The sequence and annotation of whole C. fructicola N425 genome were successfully obtained, and probable virulence-related genes identified.
- Tea plant anthracnose /
- whole-genome sequence /
- gene annotation /
- virulence-related genes

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图 1 茶树炭疽菌N425基因长度分布

Figure 1. Distribution of C. fructicola N425 gene length

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图 2 茶树炭疽菌N425基因在不同数据库中得到注释的个数

Figure 2. Number of annotated C. fructicola N425 genes from various databases

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图 3 在CAZy数据库中得到注释的茶树炭疽菌N425基因的分类

Figure 3. Classification of C. fructicola N425 genes annotated in CAZy database

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图 4 茶树炭疽菌N425中预测为次生代谢物相关的基因簇和基因分布

Figure 4. Distributions of predicted secondary metabolites-associated gene clusters and genes in C. fructicola N425

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表 1 经PHI数据库归类为致病性丧失的前18个基因的注释信息

Table 1. Annotation on first 18 loss of pathogenicity genes classified by PHI database

基因编号 Gene No.	同源基因名称 Homologous gene name	同源基因所属病原菌 Pathogen to which homologous gene belongs	宿主 Host	基因注释 Gene annotation	参考文献 Reference
A00871	ChMK1	希金斯炭疽菌 Colletotrichum higginsianum	拟南芥 Thale cress	促分裂原活化蛋白激酶 Mitogen-activated protein kinase（MAPK）	[17]
A09504	CgAP1	胶孢炭疽菌 C. gloeosporioides	芒果 Mango	bZIP 转录因子 bZIP transcription factor	[18]
A08060	CAP20	胶孢炭疽菌 C. gloeosporioides	牛油果 Avocado	附着胞细胞壁 Appressorial wall	[19]
A03691	CAM	稻瘟病菌 Magnaporthe oryzae	小麦 Wheat	钙调蛋白 Calmodulin	[20]
A04430	MoYpt7	稻瘟病菌 M. oryzae	水稻 Rice	小GTP酶 Small GTPase	[21]
A04622	ClaSSD1	葫芦炭疽菌 C. lagenaria	黄瓜 Cucumber	细胞壁组装调控 Regulation of cell wall assembly	[22]
A09136	ChSte7	希金斯炭疽菌 C. higginsianum	拟南芥 Thale cress	促分裂原活化蛋白激酶 Mitogen-activated protein kinase kinase（MAPKK）	[23]
A01252	RAC1	稻瘟病菌 M. oryzae	水稻 Rice	RhoGTP酶 Rho GTPase	[24]
A00884	CNB	稻瘟病菌 M. oryzae	小麦 Wheat	钙调磷酸酶调节亚基 Calcineurin regulatory subunits	[20]
A03506	CLAP1	菜豆炭疽病菌 C. lindemuthianum	四季豆 String bean	铜转运ATP酶 Copper transporting ATPase	[25]
A02922	ChPMA2	希金斯炭疽菌 C. higginsianum	拟南芥 Thale cress	质膜质子泵 Plasma membrane proton pump	[26]
A09008	GPI8	禾生炭疽菌 C. graminicola	玉米 Maize	半胱氨酸蛋白酶 Cystein protease	[27]
A06226	CgPKS1	禾生炭疽菌 C. graminicola	玉米 Maize	聚酮合酶 Polyketide synthase	[28]
A02402	ACL	禾谷镰刀菌 Fusarium graminearum	小麦 Wheat	ATP柠檬酸裂解酶 ATP citrate lyase	[29]
A09126	RPK1	葫芦炭疽菌 C. lagenaria	黄瓜 Cucumber	蛋白激酶A调节亚基 Protein kinase A（PKA）regulatory subunit	[30]
A05844	FGA2	尖孢镰刀菌 F. oxysporum	西红柿 Tomato	G蛋白α亚基 G protein alpha subunit	[31]
A01313	MgRho3	稻瘟病菌 M. oryzae	水稻 Rice	RhoGTP酶 Rho GTPase	[32]
A07576	VdNoxB	大丽轮枝菌 Verticillium dahliae	棉花 Cotton	NADPH 氧化酶 NADPH oxidase	[33]

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表 2 部分CAZy基因的注释信息

Table 2. Annotation on some CAZy genes

基因编号 Gene No.	同源基因GenBank登录号 Homologous gene GenBank accession No.	同源基因所属病原菌 Pathogen to which homologous gene belongs	基因注释 Gene annotation	CAZy_家族 CAZy_family
A02429	AUT30986.1	胶孢炭疽菌 Colletotrichum gloeosporioides	果胶裂解酶2 Pectin lyase 2	PL1_4
A03941	ELA25906.1	果生炭疽菌 C. fructicola	半乳糖氧化酶前体 Galactose oxidase precursor	AA5_2
A03990	AUT30987.1	胶孢炭疽菌 C. gloeosporioides	多聚半乳糖醛酸内切酶1 Endopolygalacturonase 1	GH28
A07825	AUT30984.1	胶孢炭疽菌 C. gloeosporioides	果胶酸裂解酶B Pectate lyase B	PL1_7
A00270	AHC30245.1	胶孢炭疽菌 C. gloeosporioides	漆酶2 Laccase 2	AA1_3
A00454	AND80748.1	胶孢炭疽菌 C. gloeosporioides	内切葡聚糖酶1B Endoglucanase 1B	GH12
A07600	AAL38030.1	胶孢炭疽菌 C. gloeosporioides	角质酶 Cutinase	CE5
A06012	AFK76451.1	胶孢炭疽菌 C. gloeosporioides	漆酶 Laccase	AA1_3
A07644	AAD00894.3	胶孢炭疽菌 C. gloeosporioides	甾醇糖基转移酶 Sterol glycosyltransferase	GT1
A07350	AUT30983.1	胶孢炭疽菌 C. gloeosporioides	果胶酸裂解酶A Pectate lyase A	PL1_7
A04870	AUT30985.1	胶孢炭疽菌 C. gloeosporioides	果胶裂解酶1 Pectin lyase 1	CBM1/PL1_4
A02466	AAG32629.1	里氏木霉 Trichoderma reesei	甘露糖磷酸醇合成酶 Mannose phospho-dolichol synthase	GT2
A04591	CAP73770.1	柄孢霉 Podospora anserina	糖原合成酶 Glycogen synthase	GT3
A08316	AAL23719.1	禾生炭疽菌 C. graminicola	几丁质合成酶C Chitin synthase C	GT2
A00674	AAL23718.1	禾生炭疽菌 C. graminicola	几丁质合成酶B Chitin synthase B	GT2
A06213	AAL23717.1	禾生炭疽菌 C. graminicola	几丁质合成酶A Chitin synthase Ａ	GT2

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