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

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

doi:10.7717/peerj.8019

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

PeerJ. 2019 Nov 7:7:e8019. doi: 10.7717/peerj.8019. eCollection 2019.

Authors

Yanshu Qu¹, Changwei Bi², Bing He¹, Ning Ye³, Tongming Yin¹, Li-An Xu¹

Affiliations

¹ Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
² School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
³ College of Information Science and Technology, Nanjing Forestry University, Nanjing, China.

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.

Keywords: Expression; Gene family; Genome-wide characterization; MADS-box; Phylogenetic analysis; Willow.

Associated data

figshare/10.6084/m9.figshare.9878582.v1

Grants and funding

This work was supported by the National Key Research and Development Plan of China (2016YFD0600101) and the Program Development of Jiangsu Higher Education Institutions (PAPD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.