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BMC Genomics. 2018 Sep 12;19(1):665. doi: 10.1186/s12864-018-5051-9.

Genomic, expressional, protein-protein interactional analysis of Trihelix transcription factor genes in Setaria italia and inference of their evolutionary trajectory.

Wang Z1,2, Zhao K3, Pan Y3,4, Wang J3,4, Song X3,4, Ge W3,4, Yuan M3,4, Lei T3,4, Wang L3,4, Zhang L3,4, Li Y3,4, Liu T4,5, Chen W4,5, Meng W3, Sun C3, Cui X3, Bai Y3, Wang X6,7.

Author information

1
College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. zhenyiwang0301@163.com.
2
Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. zhenyiwang0301@163.com.
3
College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.
4
Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.
5
College of Science, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.
6
College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. wangxiyin@vip.sina.com.
7
Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. wangxiyin@vip.sina.com.

Abstract

BACKGROUND:

Trihelix transcription factors (TTF) play important roles in plant growth and response to adversity stress. Until now, genome-wide identification and analysis of this gene family in foxtail millet has not been available. Here, we identified TTF genes in the foxtail millet and its grass relatives, and characterized their functional domains.

RESULTS:

As to sequence divergence, TTF genes were previously divided into five subfamilies, I-V. We found that Trihelix family members in foxtail millet and other grasses mostly preserved their ancestral chromosomal locations during millions of years' evolution. Six amino acid sites of the SIP1 subfamily possibly were likely subjected to significant positive selection. Highest expression level was observed in the spica, with the SIP1 subfamily having highest expression level. As to the origination and expansion of the gene family, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Overtime, starting from the subfamily O, certain genes evolved to form subfamilies III and I, and later from subfamily I to develop subfamilies II and V. The oldest gene, Si1g016284, has the most structural changes, and a high expression in different tissues. What's more interesting is that it may have bridge the interaction with different proteins.

CONCLUSIONS:

By performing phylogenetic analysis using non-plant species, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Starting from the subfamily O, certain genes evolved to form other subfamilies. Our work will contribute to understanding the structural and functional innovation of Trihelix transcription factor, and the evolutionary trajectory.

KEYWORDS:

Evolution; Foxtail millet; Grass; Selection; Transcription factor; Trihelix

PMID:
30208846
PMCID:
PMC6134603
DOI:
10.1186/s12864-018-5051-9
[Indexed for MEDLINE]
Free PMC Article

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