Transcription factors in alfalfa (Medicago sativa L.): genome-wide identification and a web resource center AlfalfaTFDB

Authors: Nemchinov, Lev; Shao, Jonathan; Grinstead, Sam; POSTNIKOVA, OLGA - National Institutes Of Health (NIH)

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 3/2/2021
Publication Date: 7/18/2021
Citation: Nemchinov L.G., Shao J., Grinstead S., Postnikova O.A. (2021) Transcription Factors in Alfalfa (Medicago sativa L.): Genome-Wide Identification and a Web Resource Center AlfalfaTFDB. In: Yu LX., Kole C. (eds) The Alfalfa Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-74466-3_7
DOI: https://doi.org/10.1007/978-3-030-74466-3_7

Interpretive Summary: Fundamental research is critical for improvement of alfalfa. Transcription factors (TFs), proteins that regulate gene expression, are at the center of the complex system controlling plant growth, development, and responses to the environment. Currently, information on TFs in alfalfa is limited to individual TF families. In this work, using genome-wide analysis, we computationally predicted alfalfa transcription factors based on the newly available genome of tetraploid alfalfa, classified them into families and combined all the data into database AlfalfaTFDB. We expect that this study will contribute toward understanding of the expression and regulation of genes associated with alfalfa development and stress tolerance and will be of interest to a wide range of researchers in academia and government organizations.

Technical Abstract: Research on the genomics of cultivated alfalfa (Medicago sativa L.), over many years hindered by the lack of the reference genome, has substantially progressed during the last decade. Cutting-edge high throughput sequencing technologies increased our understanding of transcriptomic processes in the plant in response to a variety of environmental factors, advanced whole genome sequencing and transformed plant genotyping and breeding strategies. This newly gained information presented unique opportunities for discovery of novel sequences, identification of genes, functional DNA elements and genetic markers. It also provided critical tools to decipher molecular mechanisms involved in the crop adaptation to the environment, evolution, plant productivity and biomass increase. This article pertains to transcription factors, the regulatory components of the alfalfa genome that coordinate gene expression and activity. In this research, taking advantage of the most recent developments in the field of alfalfa genomics, we have re-analyzed and significantly expanded repertoire of alfalfa transcription factors. We have also updated AlfalfaTFDB database to include new transcription factors identified since 2014. AlfalfaTFDB (http://plantpathology.ba.ars.usda.gov/alfalfatftb.html) is a comprehensive portal that includes classifications of TF families, their descriptions and coding sequences. In the absence of the broad and inclusive resource on M. sativa’s TFs, when only scattered knowledge on individual transcription factors is available through random published studies on individual alfalfa TF families, our data represent an essential information tool, addressing key proteins in the gene regulatory network of alfalfa, the word’s most important forage legume.