title: Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula.
abstract: 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.
authors.affiliation: Department of Computer Science, Dong-A University, Busan, Republic of Korea.
authors.forename: Daejin
authors.initials: D
authors.lastname: Hyung
authors.affiliation: Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea.
authors.forename: Chaeyoung
authors.initials: C
authors.lastname: Lee
authors.affiliation: Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea.
authors.forename: Jin-Hyun
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Genetic Engineering, Dong-A University, Busan, Republic of Korea.
authors.forename: Dongwoon
authors.initials: D
authors.lastname: Yoo
authors.affiliation: Department of Microbiology, Busan National University, Busan, Republic of Korea.
authors.forename: Young-Su
authors.initials: YS
authors.lastname: Seo
authors.affiliation: Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Republic of Korea.
authors.forename: Soon-Chun
authors.initials: SC
authors.lastname: Jeong
authors.affiliation: Department of Genetic Engineering, Dong-A University, Busan, Republic of Korea.
authors.forename: Jai-Heon
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Department of Genetic Engineering, Dong-A University, Busan, Republic of Korea.
authors.forename: Youngsoo
authors.initials: Y
authors.lastname: Chung
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Graduate School of Biotechnology, Kyunghee University, Yongin, Republic of Korea.
authors.forename: Ki-Hong
authors.initials: KH
authors.lastname: Jung
authors.affiliation: Department of Plant Pathology, University of California Davis, Davis, California, United States of America.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Cook
authors.affiliation: Department of Genetic Engineering, Dong-A University, Busan, Republic of Korea.
authors.forename: Hong-Kyu
authors.initials: HK
authors.lastname: Choi
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D056426:Genetic Loci; D055106:Genome-Wide Association Study; D023281:Genomics; D046913:Medicago truncatula / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D060066:Protein Interaction Maps; D013312:Stress, Physiological / Q000235:genetics*
chemical_list: D010940:Plant Proteins