A classification of basic helix-loop-helix transcription factors of soybean

International Journal of Genomics
Karen A Hudson, Matthew E Hudson

Abstract

The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH) family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281) of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic sel...Continue Reading

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Citations

Mar 15, 2016·Frontiers in Plant Science·Cui-Lan MaLi-Song Chen
Jun 5, 2016·Journal of Experimental Botany·Indrajit KumarMatthew E Hudson
Mar 27, 2018·Journal of Integrative Plant Biology·Lin LiHuixia Shou
Mar 17, 2018·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·Fırat Kurt, Ertugrul Filiz
Feb 6, 2020·Frontiers in Plant Science·Juan Pariasca-TanakaMatthias Wissuwa
Aug 31, 2018·Cell Death & Disease·Cristina GalloAlessia Ciarrocchi
Feb 25, 2021·BMC Plant Biology·Hayato SuzukiToshiya Muranaka
May 16, 2021·Journal of Experimental & Clinical Cancer Research : CR·Xiao YangYa-Ling Tang

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Software Mentioned

HMMER
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hmmbuild
PHYLIP
Geneious Pro
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