Genome-wide identification and expression analysis along the leaf developmental gradient of the sigma factor gene family in foxtail millet (Setaria italica)

Hongyun Liu; Jinjin Cheng; Siyuan Cheng; Hui Fan; Bo Wen; Zheng Liu

doi:10.7324/JABB.2016.40402

Abstract

Sigma factors are necessary for the initiation of transcription by RNA polymerase in bacteria and plastids of plants. In plants, a small family of nuclear genes is responsible for encoding the sigma factor proteins. In this study, a genome-wide identification and expression analysis of leaf gradient in millet (Setaria italica) were performed to characterize sigma factor genes and their proteins. By applying several bioinformatics tools, we identified chromosome locations of seven sigma factor genes in millet and their protein 3D structures. All these proteins contained three conserved domains of σ-70 family. These sigma factor genes have a closer phylogenetic relationship with their orthologs in maize than that in rice. The digital gene expression (DGE) analysis along the millet leaf developmental gradient indicated that Sisig1, Sisig5, Sisig6 showed extremely high expression levels in leaf middle and tip regions. Combining the conservation analysis of residues of each sigma factor protein with the DGE profiles of these proteins, it reveals that Sisig5 plays the housekeeping role compared with other Sisig proteins. Our study will facilitate the future research on crop evolution and the functional studies of sigma factor genes in millet.

Keyword: Setaria italica sigma factors gene family phylogenetic tree protein domain digital gene expression.

Citation:

Hongyun Liu, Jinjin Cheng, Siyuan Cheng, Hui Fan, Bo Wen, Zheng Liu., Genome-wide identification and expression analysis along the leaf developmentalgradient of the sigma factor gene family in foxtail millet (Setaria italica). J App Biol Biotech. 2016; 4 (04): 011-030. DOI: 10.7324/JABB.2016.40102

Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

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