Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula

• Published in: PloS one Vol. 9; no. 3; p. e91721
• Main Authors: Hyung, Daejin, Lee, Chaeyoung, Kim, Jin-Hyun, Yoo, Dongwoon, Seo, Young-Su, Jeong, Soon-Chun, Lee, Jai-Heon, Chung, Youngsoo, Jung, Ki-Hong, Cook, Douglas R, Choi, Hong-Kyu
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 27.03.2014; Public Library of Science (PLoS)
• Subjects: Abscisic acid; Alfalfa; Alignment; Anopheles; Arabidopsis; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis thaliana; Biology and Life Sciences; Biotechnology; Brassicaceae; Chromosome Mapping; Comparative analysis; Cues; Data analysis; Data processing; Drought; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Ontology; Gene Regulatory Networks; Genes; Genes, Plant; Genetic engineering; Genetic Loci; Genome-Wide Association Study; Genomes; Genomics; Glycine max; Hand tools; Information management; Inspection; Kinases; Legumes; Medicago truncatula; Medicago truncatula - genetics; Medicago truncatula - metabolism; Mutation; Oryza; Plant Proteins - genetics; Plant Proteins - metabolism; Protein Binding; Protein Interaction Maps; Proteins; Research and Analysis Methods; Salinity; Signal transduction; Stress; Stress, Physiological - genetics; Stresses; Synteny; Translation; Translation (Genetics); South Korea; California
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0091721

Cross-species translation of genomic information may play a pivotal role in applying biological knowledge gained from relatively simple model system to other less studied, but related, genomes. The information of abiotic stress (ABS)-responsive genes in Arabidopsis was identified and translated into the legume model system, Medicago truncatula. Various data resources, such as TAIR/AtGI DB, expression profiles and literatures, were used to build a genome-wide list of ABS genes. tBlastX/BlastP similarity search tools and manual inspection of alignments were used to identify orthologous genes between the two genomes. A total of 1,377 genes were finally collected and classified into 18 functional criteria of gene ontology (GO). The data analysis according to the expression cues showed that there was substantial level of interaction among three major types (i.e., drought, salinity and cold stress) of abiotic stresses. In an attempt to translate the ABS genes between these two species, genomic locations for each gene were mapped using an in-house-developed comparative analysis platform. The comparative analysis revealed that fragmental colinearity, represented by only 37 synteny blocks, existed between Arabidopsis and M. truncatula. Based on the combination of E-value and alignment remarks, estimated translation rate was 60.2% for this cross-family translation. As a prelude of the functional comparative genomic approaches, in-silico gene network/interactome analyses were conducted to predict key components in the ABS responses, and one of the sub-networks was integrated with corresponding comparative map. The results demonstrated that core members of the sub-network were well aligned with previously reported ABS regulatory networks. Taken together, the results indicate that network-based integrative approaches of comparative and functional genomics are important to interpret and translate genomic information for complex traits such as abiotic stresses.