Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat

BMC Genomics
Zhen-Yong ChenJi-Rui Wang

Abstract

Wheat (Triticum aestivum) is one of the most important cereal crops, providing food for humans and feed for other animals. However, its productivity is challenged by various biotic and abiotic stresses such as fungal diseases, insects, drought, salinity, and cold. Transcription factors (TFs) regulate gene expression in different tissues and at various developmental stages in plants and animals, and they can be identified and classified into families according to their structural and specialized DNA-binding domains (DBDs). Transcription factors are important regulatory components of the genome, and are the main targets for engineering stress tolerance. In total, 2407 putative TFs were identified from wheat expressed sequence tags, and then classified into 63 families by using Hmm searches against hidden Markov model (HMM) profiles. In this study, 2407 TFs represented approximately 2.22% of all genes in the wheat genome, a smaller proportion than those reported for other cereals in PlantTFDB V3.0 (3.33%-5.86%) and PlnTFDB (4.30%-6.46%). We assembled information from the various databases for individual TFs, including annotations and details of their developmental stage- and tissue-specific expression patterns. Based on this infor...Continue Reading

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Citations

Jul 4, 2019·Genome Génome / Conseil National De Recherches Canada·Dae Yeon KimYong Weon Seo
Jul 13, 2017·G3 : Genes - Genomes - Genetics·Philippa BorrillCristobal Uauy
Mar 28, 2018·International Journal of Genomics·Lingjie MaZhengqiang Ma
Nov 21, 2020·Plant Physiology and Biochemistry : PPB·Yucui HanLingjian Ma

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Methods Mentioned

BETA
transgenic

Software Mentioned

hmmbuild
HMMER
InterProScan
DNAMAN
est
intrerPro
BlastX
ESTate package Tag Analysis Tools
Hmm
BLAT

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