Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis.

Yanshu Qu,Changwei Bi,Tongming Yin,Li-An Xu,Bing He,Ning Ye

doi:10.7717/peerj.8019

Abstract

MADS-box genes encode transcription factors that participate in various plant growth and development processes, particularly floral organogenesis. To date, MADS-box genes have been reported in many species, the completion of the sequence of the willow genome provides us with the opportunity to conduct a comprehensive analysis of the willow MADS-box gene family. Here, we identified 60 willow MADS-box genes using bioinformatics-based methods and classified them into 22 M-type (11 Mα, seven Mβ and four Mγ) and 38 MIKC-type (32 MIKCc and six MIKC*) genes based on a phylogenetic analysis. Fifty-six of the 60 SsMADS genes were randomly distributed on 19 putative willow chromosomes. By combining gene structure analysis with evolutionary analysis, we found that the MIKC-type genes were more conserved and played a more important role in willow growth. Further study showed that the MIKC* type was a transition between the M-type and MIKC-type. Additionally, the number of MADS-box genes in gymnosperms was notably lower than that in angiosperms. Finally, the expression profiles of these willow MADS-box genes were analysed in five different tissues (root, stem, leave, bud and bark) and validated by RT-qPCR experiments. This study is the first genome-wide analysis of the willow MADS-box gene family, and the results establish a basis for further functional studies of willow MADS-box genes and serve as a reference for related studies of other woody plants.

Highlights

MADS-box genes, which are an important class of transcription factors in eukaryotes, are ubiquitous in animals, plants and yeast and play significant roles in the growth and development of these organisms (Alvarez-Buylla et al, 2000; Becker & Theissen, 2003)
Based on the latest S. suchowensis genome sequence and RNA-Seq data, we identified 60 SsMADS genes using bioinformatics methods and classified them as members were classified as type I (M-type) (Mα, Mβ, and Mγ) and MIKC-type (MIKC*(Mδ) and MIKCc) according to their evolutionary relationships and protein structure characteristics
Further bioinformatics analyses performed for the obtained gene family members showed that the MIKC* (Mδ) subclass was a transitional class between the M and MIKC types

Summary

Introduction

MADS-box genes, which are an important class of transcription factors in eukaryotes, are ubiquitous in animals, plants and yeast and play significant roles in the growth and development of these organisms (Alvarez-Buylla et al, 2000; Becker & Theissen, 2003). Almost all of these genes participate in all stages of growth and development in plants, the development of floral organs (Zhang et al, 2017). The name MADS-box is derived from the four first letters of MCM1 from Saccharomyces cerevisiae, AGAMOUS from Arabidopsis, DEFICIENS from snapdragon and SRF4 from humans, and the proteins encoded by these genes contain a highly conserved region called the. Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis. MADS-box that is approximately 60 amino acid residues in length (Messenguy & Dubois, 2003)

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Discussion

Conclusion