Genome-wide identification and characterization, phylogenetic comparison and expression profiles of SPL transcription factor family in B. juncea (Cruciferae).

Jian Gao,Baowei Chen,Fabo Chen,Wenbo Li,Yi Liu,Hua Peng,Maoteng Li

doi:10.1371/journal.pone.0224704

Abstract

SQUAMOSA promoter-binding protein-like (SPL), as plant specific transcription factors, is involved in many plant growth and development processes. However, there is less systematical study for SPL transcription factor in B. juncea (Cruciferae). Here, a total of 59 SPL genes classified into eight phylogenetic groups were identified in B. juncea, highly conserved within each ortholog were also found based on gene structure, conserved motif, as well as clustering level. In addition, clustering of SPL domain showed that two zinc finger-like structures and NLS segments were identified in almost of BjuSPLs. Analyzed of putative cis-elements for BjuSPLs demonstrated that SPL transcription factors were involved in adverse environmental changes, such as light, plant stresses and phytohormones response. Expression analysis showed that differentially expressed SPL genes were identified in flower and stem development of Cruciferae; such as BjuSPL3a-B, BjuSPL2b_B and BjuSPL2c_A were significantly expressed in flower; BjuSPL 3b_B and BjuSPL10a_A were significantly expressed in stem node (VP: vegetative period). Moreover, 28 of the 59 BjuSPLs were found involved in their posttranscriptional regulation targeted by miR156. We demonstrated that miR156 negatively regulated BjuSPL10a_A and BjuSPL3b_B to act for stem development in B. juncea.

Highlights

Plant SQUAMOSA promoter-binding protein-like (SPL), acts as fundamental roles in plant growth and development, and are defined by the SBP domains that have a highly conserved regions of 76 amino acids in length
We accurately named BjuSPL genes following their closest orthologs in A. thaliana and we coded their different paralogs as a, b, c, and so on, together with their order of the homologous chromosomes
The results showed that lengths and predicted molecular weight (Mw) of 59 SPL genes encoding protein ranged from 106 to 1,038 amino acids, as well as 12.161 to 114.796 kDa in B. juncea respectively (S4 Table)

Summary

Introduction

Plant SQUAMOSA promoter-binding protein-like (SPL), acts as fundamental roles in plant growth and development, and are defined by the SBP domains (for SQUAMOSA-PROMOTER BINDING PROTEIN) that have a highly conserved regions of 76 amino acids in length. We constructed phylogenetic tree for SPL gene family collected from A. thaliana, B. juncea and B. napa. Cis-acting elements, conserved motif, gene structure and expression pattern of all identified BjuSPL genes in B. juncea were systematically analyzed.

Results

Conclusion