Genome-wide identification, molecular evolution, and expression divergence of the hexokinase gene family in apple

doi:10.1016/S2095-3119(20)63562-6

Journal of Integrative Agriculture ›› 2021, Vol. 20 ›› Issue (8): 2112-2125.DOI: 10.1016/S2095-3119(20)63562-6

所属专题：园艺-分子生物合辑Horticulture — Genetics · Breeding

收稿日期:2020-05-18 出版日期:2021-08-01 发布日期:2021-07-20

Genome-wide identification, molecular evolution, and expression divergence of the hexokinase gene family in apple

ZHU Ling-cheng¹, SU Jing¹, JIN Yu-ru¹, ZHAO Hai-yan¹, TIAN Xiao-cheng¹, ZHANG Chen², MA Feng-wang¹, LI Ming-jun¹, MA Bai-quan¹

¹ State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, P.R.China
² Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

Received:2020-05-18 Online:2021-08-01 Published:2021-07-20
Contact: Correspondence LI Ming-jun, Tel/Fax: +86-29-87082613, E-mail: limingjun@nwsuaf.edu.cn; MA Bai-quan, Tel/Fax: +86-29-87082613, E-mail: bqma87@nwsuaf.edu.cn
About author:ZHU Ling-cheng, E-mail: zhulingcheng316@nwsuaf.edu.cn;
Supported by:
This work was supported by the National Natural Science Foundation of China (31672128) and the Training Program Foundation for the Young Talents of Northwest A&F University, China (2452020004).

摘要/Abstract

摘要：

己糖激酶（HXK）是糖酵解途径中第一个不可逆的催化酶，不仅为植物的生长和发育提供能量，而且还作为响应环境变化的信号分子。但是，HXK基因家族在苹果中的进化模式仍然未知。本研究中，在苹果（Malus×domestica）基因组GDDH13 v1.1中共鉴定出9个HXKs基因，分析了MdHXKs基因的生理和生化特性，外显子-内含子结构，保守基序和顺式元件，亚细胞定位预测结果表明MdHXKs基因主要分布在线粒体、细胞质和细胞核中。基因复制结果显示，全基因组复制（WGD）和片段复制在MdHXKs基因家族扩展中起着至关重要的作用。成对MdHXKs基因的ω值表明，该家族在苹果驯化过程中经历了强烈的纯化选择。此外，对五个亚家族进行了分类，并根据系统进化树分析确定了最近和最老的重复事件，并评估了不同HXKs亚家族之间的进化速率。此外，MdHXKs基因在四个源/库组织和五个苹果果实发育不同阶段的表达模式表明，MdHXKs基因在苹果果实发育和糖积累中起着至关重要的作用。本研究为今后阐明苹果果实发育过程中MdHXKs基因的生物学功能提供了理论基础。

Abstract:

Hexokinase (HXK) is the first irreversible catalytic enzyme in the glycolytic pathway, which not only provides energy for plant growth and development but also serves as a signaling molecule in response to environmental changes. However, the evolutionary pattern of the HXK gene family in apple remains unknown. In this study, a total of nine HXK genes were identified in the Malus×domestica genome GDDH13 v1.1. The physiological and biochemical properties, exon-intron structures, conserved motifs, and cis-elements of the MdHXK genes were determined. Predicted subcellular localization indicated that the MdHXK genes were mainly distributed in the mitochondria, cytoplasm, and nucleus. Gene duplication revealed that whole-genome duplication (WGD) and segmental duplication played vital roles in MdHXK gene family expansion. The ω values of pairwise MdHXK genes indicated that this family was subjected to strong purifying selection during apple domestication. Additionally, five subfamilies were classified, and recent/old duplication events were identified based on phylogenetic tree analysis. Different evolutionary rates were estimated among the various HXK subfamilies. Moreover, divergent expression patterns of the MdHXK genes in four source-sink tissues and at five different apple fruit developmental stages indicated that they play vital roles in apple fruit development and sugar accumulation. Our study provides a theoretical basis for future elucidation of the biological functions of the MdHXK genes during apple fruit development.

Key words: apple , hexokinase , cis-element screening , evolutionary pattern , sugar accumulation

. [J]. Journal of Integrative Agriculture, 2021, 20(8): 2112-2125.

ZHU Ling-cheng, SU Jing, JIN Yu-ru, ZHAO Hai-yan, TIAN Xiao-cheng, ZHANG Chen, MA Feng-wang, LI Ming-jun, MA Bai-quan. Genome-wide identification, molecular evolution, and expression divergence of the hexokinase gene family in apple[J]. Journal of Integrative Agriculture, 2021, 20(8): 2112-2125.

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Genome-wide identification, molecular evolution, and expression divergence of the hexokinase gene family in apple

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