title: A gene expression atlas of the model legume Medicago truncatula.
abstract: Legumes played central roles in the development of agriculture and civilization, and today account for approximately one-third of the world's primary crop production. Unfortunately, most cultivated legumes are poor model systems for genomic research. Therefore, Medicago truncatula, which has a relatively small diploid genome, has been adopted as a model species for legume genomics. To enhance its value as a model, we have generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, with special emphasis on nodule and seed development. The atlas reveals massive differences in gene expression between organs that are accompanied by changes in the expression of key regulatory genes, such as transcription factor genes, which presumably orchestrate genetic reprogramming during development and differentiation. Interestingly, many legume-specific genes are preferentially expressed in nitrogen-fixing nodules, indicating that evolution endowed them with special roles in this unique and important organ. Comparative transcriptome analysis of Medicago versus Arabidopsis revealed significant divergence in developmental expression profiles of orthologous genes, which indicates that phylogenetic analysis alone is insufficient to predict the function of orthologs in different species. The data presented here represent an unparalleled resource for legume functional genomics, which will accelerate discoveries in legume biology.
authors.affiliation: Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
authors.forename: Vagner A
authors.initials: VA
authors.lastname: Benedito
authors.forename: Ivone
authors.initials: I
authors.lastname: Torres-Jerez
authors.forename: Jeremy D
authors.initials: JD
authors.lastname: Murray
authors.forename: Andry
authors.initials: A
authors.lastname: Andriankaja
authors.forename: Stacy
authors.initials: S
authors.lastname: Allen
authors.forename: Klementina
authors.initials: K
authors.lastname: Kakar
authors.forename: Maren
authors.initials: M
authors.lastname: Wandrey
authors.forename: Jérôme
authors.initials: J
authors.lastname: Verdier
authors.forename: Hélène
authors.initials: H
authors.lastname: Zuber
authors.forename: Thomas
authors.initials: T
authors.lastname: Ott
authors.forename: Sandra
authors.initials: S
authors.lastname: Moreau
authors.forename: Andreas
authors.initials: A
authors.lastname: Niebel
authors.forename: Tancred
authors.initials: T
authors.lastname: Frickey
authors.forename: Georg
authors.initials: G
authors.lastname: Weiller
authors.forename: Ji
authors.initials: J
authors.lastname: He
authors.forename: Xinbin
authors.initials: X
authors.lastname: Dai
authors.forename: Patrick X
authors.initials: PX
authors.lastname: Zhao
authors.forename: Yuhong
authors.initials: Y
authors.lastname: Tang
authors.forename: Michael K
authors.initials: MK
authors.lastname: Udvardi
mesh_terms: D016000:Cluster Analysis; D030541:Databases, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling; D023281:Genomics; D046913:Medicago truncatula / Q000235:genetics* / Q000378:metabolism / Q000382:microbiology; D009586:Nitrogen Fixation; D020411:Oligonucleotide Array Sequence Analysis; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D012333:RNA, Messenger / Q000378:metabolism; D053204:Root Nodules, Plant / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D016962:Sinorhizobium meliloti / Q000502:physiology; D013045:Species Specificity; D013559:Symbiosis
chemical_list: D012333:RNA, Messenger