Genome-Wide Identification and Analysis of Class III Peroxidases in Allotetraploid Cotton (Gossypium hirsutum L.) and their Responses to PK Deficiency.

Duan Duan,Wang Wang,Chao Chao,Zhang Zhang

doi:10.3390/genes10060473

Duan Duan, Wang Wang + Show 2 more

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https://doi.org/10.3390/genes10060473

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Abstract

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.

Highlights

Peroxidases (EC 1.11.1.x) are encoded by multigenic families and are involved in several important physiological and developmental processes
PODs are involved in a broad range of physiological processes such as auxin metabolism, lignin and suberin formation, cross-linking of cell wall components, phytoalexin synthesis, defense against biotic or abiotic stress, cell elongation, and the metabolism of reactive nitrogen species and reactive oxygen species (ROS), throughout the plant life cycle from the early stage of germination to the final step of senescence [11,12,13]
The local BLAST database was established with protein sequences of upland cotton

Summary

Introduction

Peroxidases (EC 1.11.1.x) are encoded by multigenic families and are involved in several important physiological and developmental processes. Class III peroxidases (EC 1.11.1.7), belonging to the haem peroxidase subfamily, exist only in plants and have an extremely widespread presence in the plant kingdom [1]. They are members of a large multigenic family with more than 200 members in. Class III peroxidases were abbreviated as PODs. PODs are involved in a broad range of physiological processes such as auxin metabolism, lignin and suberin formation, cross-linking of cell wall components, phytoalexin synthesis, defense against biotic or abiotic stress, cell elongation, and the metabolism of reactive nitrogen species and reactive oxygen species (ROS), throughout the plant life cycle from the early stage of germination to the final step of senescence [11,12,13]. It is probably due to their high number of enzymatic isoforms and to the versatility of their enzyme-catalyzed reactions

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