Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton

Caiping Cai,Baohong Zhang,Wangzhen Guo

doi:10.1038/s41598-017-18673-4

Abstract

Plant specific transcription factors, SQUAMOSA promoter-binding protein-like (SPL), are involved in many biological processes. However, no systematical study has been reported in cotton. In this study, a total of 177 SPL genes were identified, including 29, 30, 59 and 59 SPLs in Gossypium arboreum, G. raimondii, G. barbadense, and G. hirsutum, respectively. These SPL genes were classified into eight phylogenetical groups. The gene structure, conserved motif, and clustering were highly conserved within each orthologs. Two zinc finger-like structures (Cys3His and Cys2HisCys) and NLS segments were existed in all GrSPLs. Segmental duplications play important roles in SPL family expansion, with 20 genes involved in segmental duplications and 2 in tandem duplications, and ten ortholog pairs in syntenic regions between G. raimondii and A. thaliana. Several putative cis-elements, involved in light, stresses and phytohormones response, were found in the promoter regions of GhSPLs, suggesting that plant responses to those environmental changes may be induced through targeting SPL transcription factors. RNA-seq analysis shows that SPL genes were differentially expressed in cotton; some were highly expressed during fiber initiation and early development. Comparing with other plants, SPL genes show subfunctionalization, lost and/or gain functions in cotton during long-term domestication and evolution.

Highlights

SQUAMOSA promoter-binding protein-like (SPL), one class of plant-specific transcription factors, have a highly conserved SBP domains with approximately 78 amino acids in length, and containing an eight Cys or His sequence motif and contained a nuclear localization signal (NLS) motif
Genome-wide identification of SPL gene family has been reported in several plant species
No genome-wide identification of SPL gene family has been reported in cotton there are four cotton species sequenced

Summary

Introduction

SQUAMOSA promoter-binding protein-like (SPL), one class of plant-specific transcription factors, have a highly conserved SBP domains (for SQUAMOSA-PROMOTER BINDING PROTEIN) with approximately 78 amino acids in length, and containing an eight Cys or His sequence motif (two Zn-finger like structure) and contained a nuclear localization signal (NLS) motif. Various functions of SPL genes were reported in other plant species, including governing yield-related traits in hexaploid wheat[6], redundantly initiating side tillers and affecting biomass yield of energy crop in switchgrass[7], regulating floral organ size and ovule production in cotton[8], and regulating ovary and fruit development in tomato[9]. The identification and functional analysis of SPL gene family is much beyond in cotton than that in other plant species. 3–7930,31 and their two diploid progenitors G. arboreum[32] and G. raimondii[33,34] Those genome sequences provide a possible to identify SPL genes at a genome-wide level in cotton. We built a phylogenetic tree of the SPL gene family in Gossypium, A. thaliana, O. sativa and P. trichocarpa, and carried out a genome-wide intra- and inter-genomic duplication analysis of G. raimondii and other three plant species. The results will provide a solid foundation to understand the distribution, structure and evolution of the SPL gene family in cotton, and will contribute to investigate of the detailed functional differentiation and application of these genes in the future

Methods

Results

Conclusion