Genome-wide analysis and comparison of the DNA-binding one zinc finger gene family in diploid and tetraploid cotton (Gossypium).

Yuzhe Li,Mengjie Liu,Zhen Liu,Senyi Chen,Kaiyue Zhang,Qingde Zhang,Eric Jellen

doi:10.1371/journal.pone.0235317

Abstract

The Dof (DNA-binding one zinc finger) transcription factor family is a representative of plant-specific classes of transcription factors. In this study, we performed a genome-wide screening and characterization of the Dof gene family within two tetraploid species Gossypium barbadense, Gossypium hirsutum, and two diploid species Gossypium arboreum, Gossypium raimondii. 115, 116, 55 and 56 Dof genes were identified respectively and all of the genes contain a sequence encoding the Dof DNA-binding domain. Those genes were unevenly distributed across 13/26 chromosomes of the cotton. Genome comparison revealed that segmental duplication may have played crucial roles in the expansion of the cotton Dof gene family, and tandem duplication also played a minor role. Analysis of RNA-Seq data indicated that cotton Dof gene expression levels varied across different tissues and in response to different abiotic stress. Overall, our results could provide valuable information for better understanding the evolution of cotton Dof genes, and lays a foundation for future investigation in cotton.

Highlights

Transcription factors play a very vital role in gene regulation at transcriptional level
The G. hirsutum [23] and G. barbadense [23] genome sequences were downloaded from CottonGen, The genome sequences of G. arboretum [24] were downloaded from NCBI (BioProject ID: PRJNA382310), and the G. raimondii [25]genome sequence was download from https://cottonfgd.org/
Our results revealed that the number of exons varied from 1 to 4 in cotton Dof gene family

Summary

Introduction

Transcription factors play a very vital role in gene regulation at transcriptional level. The Dof (DNA-binding one zinc finger) is a plant-specific transcription factor having multiple roles such as carbon assimilation, light-mediated regulation, seed maturation and germination [1]. Dof bind AAAG sequences of plant gene promoters with the Dof DNA-binding domain [2,3,4]. In spite of high level homology in the Dof domain, the rest of the sequences are divergent, coinciding with their expected diverse functions [1, 3]. Cotton is an excellent model system for studying polyploidization and cell elongation [5,6,7,8]. Current understanding recognizes more than 50 species within the cotton genus, with both diploid and polyploid members.

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Results

Conclusion