Genome-wide Identification and Tissue Expression Analysis of the KNOX Gene Family in Altingia chinensis

doi:10.3969/j.issn.1009-7791.2025.01.001

Subtropical Plant Science ›› 2025, Vol. 54 ›› Issue (1): 1-10.DOI: 10.3969/j.issn.1009-7791.2025.01.001

• Research articles • Next Articles

Genome-wide Identification and Tissue Expression Analysis of the KNOX Gene Family in Altingia chinensis

WANG An-bang^1,2, YE Xing-zhuang^1,3, ZHAO Jin-tao⁴, CHEN Zhi-yun⁵, WENG Hui-ying¹, LIN Mao¹, ZHANG Guo-fang^1*

(1. College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian China; 2.College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian China; 3. Fujian Institute of Subtropical Botany, Xiamen 361006, Fujian China; 4.College of Juncao Science and Ecology (College of Carbon Neutrality), Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian China; 5.Weimin National Forest Farm of Shaowu, Nanping 354000, Fujian China)

Received:2024-12-24 Accepted:2025-02-09 Online:2025-02-28 Published:2025-05-22
Contact: ZHANG Guo-fang

蕈树KNOX基因家族鉴定及组织表达分析

王安邦^1,2，叶兴状^1,3，赵金涛⁴，陈志云⁵，翁慧莹¹，林茂¹，张国防^1*

(1. 福建农林大学林学院，福建福州 350002；2. 福建农林大学生命科学学院，福建福州 350002；3. 福建省亚热带植物研究所，福建厦门 361006；4. 福建农林大学菌草与生态学院(碳中和学院)，福建福州 350002；5. 福建省邵武卫闽国有林场，福建南平354000)

通讯作者: 张国防
基金资助:
福建农林大学林学学科创新团队支持计划(72202200205)；福建省林业科研项目(2023FKJ05)

Abstract

Abstract: The KNOX gene family has important regulatory functions in leaf-shape growth and development in plants. This paper aims to analyze the KNOX gene family of Altingia chinensis and explore its tissue expression pattern. We used bioinformatics methods to identify and study AcKNOXs at the whole genome level of A. chinensis, and analyzed the gene location, gene structure, phyloevolutionary relationships, gene collinearity and the transcriptome expression. We identified 11 AcKNOXs from 8 chromosomes in the A. chinensis genome. Among them, AcKNOX6 and AcKNOX9 lack ELK and Homeobox KN domains, AcKNOX7 lacks ELK domain, the others have four conserved domains: KNOX 1, KNOX 2, ELK and Homeobox KN. 11 AcKNOXs are classified into Class Ⅰ (AcKNOX1, AcKNOX2, AcKNOX5, AcKNOX8, AcKNOX10, AcKNOX11), Class Ⅱ (AcKNOX3, AcKNOX4, AcKNOX7) and Class M (AcKNOX6, AcKNOX9). The AcKNOXs protein contains 144 to 444 amino acids. They were all located in the nucleus and are all acidic, unstable and hydrophilic. Through the expression pattern analysis, we found that AcKNOXs genes have tissue specificity. The majority of the members of the same subfamily showed the similar expression pattern. The main amplification mode of 11 AcKNOXs were segmental duplication, no tandem repeats were found. There were four pairs of genes with collinearity, AcKNOX3/AcKNOX4, KNOX2/AcKNOX8, AcKNOX6/AcKNOX9, and AcKNOX5/AcKNOX10, respectively. The results of this research provide the study of KNOX gene family with scientific basis, which help to do in-depth study on the genomic characteristics.

Key words: Altingia chinensis, KNOX gene family, bioinformatics, issue expression

摘要： KNOX基因家族在植物叶形生长发育方面具有重要调节功能。为鉴定并分析蕈树Altingia chinensis 的KNOX基因家族，探寻其组织表达模式，借助生物信息学方法，在蕈树全基因组水平鉴定KNOX基因家族，并对其基因位置、基因结构、系统进化关系、基因共线性以及转录组表达进行分析。从蕈树基因组中8条染色体上得到11个AcKNOXs，其中AcKNOX6和AcKNOX9无ELK和Homeobox KN结构域，AcKNOX7无ELK结构域，其余均有完整结构域。蕈树AcKNOXs分为Class Ⅰ (AcKNOX1、AcKNOX2、AcKNOX5、AcKNOX8、AcKNOX10、AcKNOX11)、Class Ⅱ (AcKNOX3、AcKNOX4、AcKNOX7)和Class M (AcKNOX6、AcKNOX9)三类。AcKNOXs蛋白包含144～444个氨基酸，亚细胞定位均位于细胞核，均为酸性不稳定亲水蛋白。表达模式分析表明，AcKNOXs基因存在组织特异性，但同一亚家族大部分成员的表达模式相似。鉴定的11个AcKNOX成员扩增方式为片段复制，无串联重复。AcKNOX3/AcKNOX4、KNOX2/AcKNOX8、AcKNOX6/AcKNOX9、AcKNOX5/AcKNOX10共4对基因间存在共线性关系。该研究结果为进一步研究蕈树KNOX基因家族基因组特性提供科学依据。

关键词: 蕈树, KNOX基因家族, 生物信息学, 系统发育分析, 表达分析

CLC Number:

S792

WANG An-bang, YE Xing-zhuang, ZHAO Jin-tao, CHEN Zhi-yun, WENG Hui-ying, LIN Mao, ZHANG Guo-fang. Genome-wide Identification and Tissue Expression Analysis of the KNOX Gene Family in Altingia chinensis[J]. Subtropical Plant Science, 2025, 54(1): 1-10.

王安邦, 叶兴状, 赵金涛, 陈志云, 翁慧莹, 林茂, 张国防. 蕈树KNOX基因家族鉴定及组织表达分析[J]. 亚热带植物科学, 2025, 54(1): 1-10.

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Genome-wide Identification and Tissue Expression Analysis of the KNOX Gene Family in Altingia chinensis

蕈树KNOX基因家族鉴定及组织表达分析

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