{"doi":"10.1371/journal.pone.0252213","title":"Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of LIM gene family in Medicago sativa L.","abstract":"<jats:p>The LIM (Lin-11, Isl-1 and Mec-3 domains) family is a key transcription factor widely distributed in animals and plants. The LIM proteins in plants are involved in the regulation of a variety of biological processes, including cytoskeletal organization, the development of secondary cell walls, and cell differentiation. It has been identified and analyzed in many species. However, the systematic identification and analysis of the LIM genes family have not yet been reported in alfalfa (<jats:italic>Medicago sativa</jats:italic>L.). Based on the genome-wide data of alfalfa, a total of 21 LIM genes were identified and named MsLIM01-MsLIM21. Comprehensive analysis of the chromosome location, physicochemical properties of the protein, evolutionary relationship, conserved motifs, and responses to abiotic stresses of the LIM gene family in alfalfa using bioinformatics methods. The results showed that these MsLIM genes were distributed unequally on 21 of the 32 chromosomes in alfalfa. Gene duplication analysis showed that segmental duplications were the major contributors to the expansion of the alfalfa LIM family. Based on phylogenetic analyses, the LIM gene family of alfalfa can be divided into four subfamilies: αLIM subfamily, βLIM subfamily, γLIM subfamily, and δLIM subfamily, and approximately all the LIM genes within the same subfamily shared similar gene structure. The 21 MsLIM genes of alfalfa contain 10 Motifs, of which Motif1 and Motif3 are the conserved motifs shared by these genes. Furthermore, the analysis of cis-regulatory elements indicated that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundant in the promoter sequence of MsLIM genes. Real-time quantitative PCR demonstrated that MsLIM gene expression is induced by low temperature and salt. The present study serves as a basic foundation for future functional studies on the alfalfa LIM family.</jats:p>","journal":"PLOS ONE","year":2021,"id":44093,"datarank":0.802820696764688,"base_score":2.70805020110221,"endowment":2.70805020110221,"self_citation_contribution":0.40620753016533157,"citation_network_contribution":0.3966131665993565,"self_endowment_contribution":0.40620753016533157,"citer_contribution":0.3966131665993565,"corpus_percentile":null,"corpus_rank":null,"citation_count":14,"citer_count":10,"citers_with_citation_signal":10,"citers_with_endowment":10,"datacite_reuse_total":16,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":208201,"name":"Xuelu 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Start-up Funds for Openly-Recruited Doctors of Gansu Agriculture University","grant_id":"2017RCZX-32","title":null},{"funder_name":"The Youth Science and Technology Fund of Gansu Province","grant_id":"20JR5RA014","title":null},{"funder_name":"Basic Scientific Research Funds of Guangxi Institute of Animal Sciences","grant_id":"2017-20, 2018-27","title":null}],"total_grants":4,"fwci":2.1983,"citation_percentile":0.88657668,"influential_citations":0,"citation_trend":[{"year":2021,"count":1},{"year":2022,"count":3},{"year":2023,"count":3},{"year":2024,"count":6},{"year":2025,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1371/journal.pone.0252213","host_type":"journal"},{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0252213&type=printable","host_type":"GOLD"},{"url":"https://doi.org/10.1371/journal.pone.0252213","host_type":"publisher"},{"url":"https://dx.plos.org/10.1371/journal.pone.0252213","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/34191816","host_type":"repository"},{"url":"https://doaj.org/article/01f42dcb90754cda9c9c9463050d83c0","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8244919","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC8244919","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC8244919?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Studies on Chitinases and Chitosanases","Galectins and Cancer Biology","14-3-3 protein interactions","Medicine","Biology","Environmental Science","Medicago sativa","Phylogeny","Gene Expression Regulation, Plant","Stress, Physiological","Plant Proteins","Multigene Family","Genome, Plant","Gene Duplication","Transcription Factors"],"mesh_terms":["Medicago sativa","Multigene Family","Phylogeny","Plant Proteins","Stress, Physiological","Transcription Factors","Genes, Plant","Gene Expression Regulation, Plant","Genome, Plant","Gene Duplication","Genomics","Medicago"],"keywords":["Subfamily","Biology","Gene family","Gene","Genetics","Gene duplication","Genome","Phylogenetic tree","Segmental duplication","Transcription factor","Conserved sequence","Peptide sequence"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[{"doi":"10.6084/m9.figshare.26757985.v1","title":"Additional file 8 of Global identification of LIM genes in response to different heat stress regimes in 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