灰葡萄孢HMG家族基因的全基因组鉴定与表达规律分析

doi:10.3864/j.issn.0578-1752.2025.04.007

摘要/Abstract

摘要：

【目的】高迁移率族蛋白（high mobility group protein，HMG）是广泛存在于真核生物中的一种重要蛋白质，在调控真菌的生长发育及对胁迫的响应过程中发挥关键作用。本研究旨在通过对灰葡萄孢（Botrytis cinerea）中HMG家族成员的全基因组鉴定，分析其在病菌生长发育、侵染及对胁迫的响应等过程中的表达特征，为深入探讨该家族基因在灰葡萄孢生长发育及致病机理中的功能提供理论依据。【方法】利用Pfam和HMMER工具的Hmmer search功能，在灰葡萄孢的蛋白数据库中筛选HMG家族蛋白基因，并使用在线SMART软件进行验证，以最终确定灰葡萄孢HMG家族成员。通过使用ProtParam、TBtools、MEME、MEGA、MCScanX等工具，对灰葡萄孢HMG基因家族成员的理化性质、染色体定位、基因结构、系统进化关系及基因间的共线性进行分析。同时，基于灰葡萄孢在分生孢子发育及侵染过程中的转录组数据，利用TBtools软件分析HMG家族基因在这两个过程中的表达规律。此外，通过实时定量PCR（qPCR）技术，观察灰葡萄孢HMG家族基因在NaCl、KCl、H₂0₂等胁迫下的表达变化规律。【结果】在灰葡萄孢基因组中鉴定出9个HMG家族成员，这些成员的编码氨基酸数量在101—1 076个，其分子量在11.48—120.64 kDa。这些HMG家族成员可进一步分为HMGA和HMGB亚家族，并均具有保守的HMG结构域。同时，它们在6条染色体上分布，与禾谷镰孢（Fusarium graminearum）和尖镰孢（Fusarium oxysporum）之间显示出基因共线性。通过表达规律分析发现，HMG家族基因在灰葡萄孢分生孢子发育和侵染过程中表达量呈现明显变化。其中，Bcin01g08840、Bcin07g04610、Bcin11g04340和Bcin11g03320在灰葡萄孢分生孢子发育阶段表现出持续高表达水平，而Bcin07g04610、Bcin11g04340、Bcin11g05790和Bcin01g08840在灰葡萄孢侵染时表现出明显的表达下调。qPCR分析发现，该家族基因在NaCl和KCl胁迫处理后也呈现明显的下调趋势。【结论】灰葡萄孢中包含9个HMG家族成员，该家族成员可被划分为HMGA和HMGB亚家族，分布在6条染色体上，在病菌的分生孢子发育、侵染及胁迫响应过程中具有不同的表达模式，推测该家族基因在灰葡萄孢生长发育、致病性及胁迫响应中发挥重要作用。

关键词: 灰葡萄孢, HMG家族基因, 全基因组, 基因表达, 生物信息学, 胁迫

Abstract:

【Objective】High mobility group protein (HMG), as a widespread eukaryotic protein, plays an important role in the regulation of fungal growth and development. This study aims to identify the HMG family members of Botrytis cinerea through the genome-wide identification, and analyze their expression rules during the growth and development, infection and response to stress, so as to lay a foundation for further investigation of the function of this family gene in the growth and development and pathogenic mechanism of B. cinerea.【Method】HMMER software was used to screen out possible HMG gene IDs in B. cinerea protein database, and the online tools Pfam and SMART were used to verify the possible HMG family members. Using ProtParam, TBtools, MEME, MEGA, MCScanX and other tools, the physicochemical characteristics, chromosome localization, gene structure, phylogenetic tree and collinearity of B. cinerea HMG gene family members were analyzed. Based on transcriptome sequencing data of B. cinerea during conidial development and infection, the expression of HMG family genes in B. cinerea during conidial development and infection was analyzed by using TBtools software. In addition, the expression of HMG family genes in B. cinerea under NaCl, KCl, H₂O₂ and other stresses was observed by real-time quantitative PCR (qPCR).【Result】Nine HMG family members were identified in B. cinerea, the number of encoded amino acids ranged from 101 to 1076, and the molecular weight ranged from 11.48 to 120.64 kDa. They could be divided into HMGA and HMGB subfamilies, which had conserved HMG domain, distributed on six chromosomes, and had gene collinearity with Fusarium graminearum and Fusarium oxysporum. The expression pattern analysis showed that the expression levels of this family gene showed obvious changes during conidial development and B. cinerea infection. Among them, Bcin01g08840, Bcin07g04610, Bcin11g04340 and Bcin11g03320 continued to be highly expressed during conidial development. The expression levels of Bcin07g04610, Bcin11g04340, Bcin11g05790 and Bcin01g08840 were significantly down-regulated during B. cinerea infection. qPCR analysis showed that the gene expression of this family was significantly down-regulated after NaCl and KCl stress treatment.【Conclusion】B. cinerea contains nine HMG family members, which can be divided into HMGA and HMGB subfamilies, the members distribute on six chromosomes, and have different expression patterns in the process of conidial development, infection and stress response of the pathogen. It is speculated that the family genes play an important role in the growth and development, pathogenicity and stress response of B. cinerea.

Key words: Botrytis cinerea, HMG family gene, genome-wide, gene expression, bioinformatics, stress

张天雨, 李白, 藏金萍, 曹宏哲, 董金皋, 邢继红, 张康. 灰葡萄孢HMG家族基因的全基因组鉴定与表达规律分析[J]. 中国农业科学, 2025, 58(4): 704-718.

ZHANG TianYu, LI Bai, ZANG JinPing, CAO HongZhe, DONG JinGao, XING JiHong, ZHANG Kang. Genome-Wide Identification and Expression Analysis of HMG Family Genes in Botrytis cinerea[J]. Scientia Agricultura Sinica, 2025, 58(4): 704-718.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2025.04.007

https://www.chinaagrisci.com/CN/Y2025/V58/I4/704

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基因名称 Gene name	引物序列 Primer sequence (5′→3′)
Bcin07g04610	F: GAATGGGAAGGCAAGCACAC	R: CGCCTCTATTGACTCGCCAT
Bcin09g02870	F: GCGCGGTGATTGCTATTGAG	R: TCCTGCATCTCAGAATCCGC
Bcin11g03320	F: AACAAGGCTGTCAATGCACG	R: CGTTGCTCAGGCGACATAGA
Bcin05g01760	F: TCTACATGCAAACCGCTCGT	R: CTACGAGTTGAGCATCGGCA
Bcin02g06030	F: CCGCATACCATCTACCCCAC	R: GCTCCTGATACCTCTTCGCC
Bcin11g05790	F: CTGTGGTGATAGTTGGCCGT	R: CTGCATGGGTCTCTGTTGGT
Bcin01g08840	F: ACAGGGCTACAGGGAAGGAT	R: CGGCGATGCTGTTTTGAGTC
Bcin11g04340	F: TCCCCAGCAATCTTTCACCC	R: TGGAAGGTGTTGATTGGGCT
Bcin11g05240	F: GCTCGCCATCCTCCAATACA	R: GCAGAAAGTCCACGCTTTGG
β-tubulin	F: ACATGCTCTGCCATTTTCCG	R: TTGTTAGGGATCCACTCAACGAAG

基因名称 Gene name	起始位点 Initiation site	终止位点 Termination site	CDS (bp)	氨基酸数目 Number of amino acids (aa)	分子量 Molecular weight (Da)	pI
Bcin01g08840	3070697	3074891	1629	542	59264	8.46
Bcin02g06030	2131709	2133995	2100	699	78297	8.98
Bcin05g01760	667383	669885	1026	341	36349	8.39
Bcin07g04610	1655881	1659887	3231	1076	120642	6.18
Bcin09g02870	1026663	1029821	2403	800	89042	9.39
Bcin11g03320	1138331	1139915	1008	335	37277	10.16
Bcin11g05240	1867672	1869358	306	101	11476	9.22
Bcin11g05790	2042942	2046139	1617	538	61800	6.49
Bcin11g04340	1606589	1608013	675	224	24949	7.76