Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis
- Published
- Accepted
- Subject Areas
- Bioinformatics, Genomics
- Keywords
- gene family, MADS-box, phylogenetic analysis, expression, genome-wide characterization, willow
- Copyright
- © 2018 Qu et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis. PeerJ Preprints 6:e27195v1 https://doi.org/10.7287/peerj.preprints.27195v1
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, 7 Mβ and 4 Mγ) and 38 MIKC-type (32 MIKCc and 6 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). 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.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Homologous genes in the willow MADS-box gene family
The details of fifteen conserved motif sequences identified in SsMADS genes
The details of total transcript abundance of SsMADS genes by RPKM annotation
Sequence logo of the 60 willow MADS-box domains
The logo was generated using the web-based application WebLogo3 ( http://weblogo.threeplusone.com ) with the default parameters. The heights of the symbols within each stack indicate the relative frequency of each amino acid at that position.
Phylogenetic tree of S. suchowensis and O. sativa MADS-box domains
A total of 60 MADS-box domains from S. suchowensis and 66 from O. sativa were used to construct a NJ tree using MEGA 7. Different shapes and colours represent different species and gene categories.
Phylogenetic tree of S. suchowensis and P. trichocarpa MADS-box domains
A total of 60 MADS-box domains from S. suchowensis and 103 from P. trichocarpa were used to construct a NJ tree using MEGA 7. Different shapes and colours represent different species and gene categories.
