Genome-Wide Identification and Analysis of Class III Peroxidases in Allotetraploid Cotton (Gossypium hirsutum L.) and their Responses to PK Deficiency
Genome-Wide Identification and Analysis of Class III Peroxidases in Allotetraploid Cotton (Gossypium hirsutum L.) and their Responses to PK Deficiency
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异源四倍体棉花 (Gossypium hirsutum L.) 中 III 类过氧化物酶的全基因组鉴定和分析及其对 PK 缺乏的反应
DOI：
10.3390/genes10060473
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发表时间：
2019-06-01
期刊：
影响因子：
3.5
通讯作者：
Zhang, Baohong
中科院分区：
文献类型：
--
作者：
Duan, Pengfei;Wang, Guo;Zhang, Baohong
III类过氧化物酶（Class III peroxidases, pod）通常被称为可分泌的III类植物过氧化物酶，是一种植物特异性酶，不仅在植物生长发育中起重要作用，而且在生物和非生物胁迫反应中起重要作用。在这项研究中，我们鉴定了198个非冗余POD基因，命名为ghpod，其中180个POD被预测分泌到外质体中。根据系统发育关系将这些POD基因划分为10个亚群。我们对POD基因进行了系统的生物信息学分析，包括基因结构、系统发育关系和基因表达谱分析。ghpod在陆地棉亚基因组A和D染色体上分布不均匀。此外，这些基因经历了15个片段重复和12个串联重复，表明片段重复和串联重复都对陆地棉POD基因家族的扩展做出了贡献。Ka/Ks分析表明，大多数重复的ghpod经历了负选择，在重复事件中功能分化有限。高通量RNA-seq数据表明，大多数高表达基因可能在根、茎、叶和纤维发育中发挥重要作用。缺钾缺磷条件下，pod在棉花根和叶片中表现出不同的表达模式。该研究为进一步分析陆地棉POD基因家族的功能提供了有益的信息。
Class III peroxidases (PODs), commonly known as secretable class III plant peroxidases, are plant-specific enzymes that play critical roles in not only plant growth and development but also the responses to biotic and abiotic stress. In this study, we identified 198 nonredundant POD genes, designated GhPODs, with 180 PODs being predicted to secrete into apoplast. These POD genes were divided into 10 sub-groups based on their phylogenetic relationships. We performed systematic bioinformatic analysis of the POD genes, including analysis of gene structures, phylogenetic relationships, and gene expression profiles. The GhPODs are unevenly distributed on both upland cotton sub-genome A and D chromosomes. Additionally, these genes have undergone 15 segmental and 12 tandem duplication events, indicating that both segmental and tandem duplication contributed to the expansion of the POD gene family in upland cotton. Ka/Ks analysis suggested that most duplicated GhPODs experienced negative selection, with limited functional divergence during the duplication events. High-throughput RNA-seq data indicated that most highly expressed genes might play significant roles in root, stem, leaf, and fiber development. Under K or P deficiency conditions, PODs showed different expression patterns in cotton root and leaf. This study provides useful information for further functional analysis of the POD gene family in upland cotton.