Genome-wide identification and characterization of WRKY gene family in Salix suchowensis

Bi, Changwei; Xu, Yiqing; Ye, Qiaolin; Yin, Tongming; Ye, Ning

doi:10.7287/peerj.preprints.2167

Cited by 1 publication

(5 citation statements)

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“…Multi-sequence and Blastp alignments (E-value = 1e-20) were performed to obtain the similarities between these SsMADS genes. To estimate gene duplication events in the SsMADS genes, the following metrics were set: (1) the proportion of regions used for alignment of the longer gene should exceed 65% and (2) the similarity of the aligned regions should exceed 65% (Bi et al 2016).…”

Section: Gene Structure Analysis Of the Willow Mads-box Genesmentioning

confidence: 99%

“…Gene duplication events have always been considered vital sources of biological evolution (Chothia et al 2003). Two or more adjacent homologous genes located on a single chromosome are considered tandem duplication events (TDs), whereas homologous gene pairs between different chromosomes are defined as segmental duplication events (SDs) (Bi et al 2016;Liu & Ekramoddoullah 2009). In this study, we identified a total of 12 homologous gene pair (including 24 SsMADS genes) duplication events.…”

Section: Gene Duplication Events and Conserved Motifs In Willowsmentioning

confidence: 99%

“…In view of the important role of the MADS-box gene family in the plant lifecycle, researchers have identified this gene family in a variety of plants, including Arabidopsis thaliana, Oryza sativa, Brachypodium distachyon, Malus domestica, Ziziphus jujube, and Populus trichocarpa (Arora et al 2007;Bi et al 2016;Kaufmann et al 2005;Leseberg et al 2006;Ng & Yanofsky 2001;Parenicova et al 2003;Tian et al 2015;Wei et al 2014;Zhang et al 2017). Willow is a general term for the type of woody plants belonging to the genus Salix, which include deciduous shrubs and arbors with a long cultivation history in China.…”

Section: Introductionmentioning

confidence: 99%

“…Because of their strong adaptability to the environment and short generation period, willows have been widely recognized as an important renewable source of bioenergy that can be used in cogeneration to meet today's rapidly increasing demand for renewable resources. In addition, willows have good economic value; for example, they can be used to make boxes and process antirheumatic Chinese medicinal herbs and are cultivated as ornamental trees (Bi et al 2016;Kuzovkina & Quigley 2005). However, the MADS-box gene family in willows has not been identified.…”

Section: Introductionmentioning

confidence: 99%

“…The exon-intron structures of multiple gene families play crucial roles during plant evolution (Bi et al 2016). To gain insights into the structural diversity of willow MADS-box genes, we analysed the exon-intron organization of the coding sequences of each willow MADS-box gene.…”

Section: Exon-intron Structures Of the Ssmads Genesmentioning

confidence: 99%

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Supplemental Information 3: The Details of Total Transcript Abundance of SsMADS Genes by RPKM Annotation

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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 MADSbox 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 ( 32MIKCc 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.

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Section: Gene Structure Analysis Of the Willow Mads-box Genesmentioning

confidence: 99%