Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization

Zhu, H., Kim, D. J., Baek, J. M., Choi, H. K., Ellis, L. C., Küester, H., McCombie, W. R., Peng, H. M., Cook, D. R. (2003) Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization. Plant Physiology, 131 (3). pp. 1018-1026. ISSN 00320889 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/12644654
DOI: 10.1104/pp.102.016436

Abstract

Arabidopsis and Medicago truncatula represent sister clades within the dicot subclass Rosidae. We used genetic map-based and bacterial artificial chromosome sequence-based approaches to estimate the level of synteny between the genomes of these model plant species. Mapping of 82 tentative orthologous gene pairs reveals a lack of extended macrosynteny between the two genomes, although marker collinearity is frequently observed over small genetic intervals. Divergence estimates based on non-synonymous nucleotide substitutions suggest that a majority of the genes under analysis have experienced duplication in Arabidopsis subsequent to divergence of the two genomes, potentially confounding synteny analysis. Moreover, in cases of localized synteny, genetically linked loci in M. truncatula often share multiple points of synteny with Arabidopsis; this latter observation is consistent with the large number of segmental duplications that compose the Arabidopsis genome. More detailed analysis, based on complete sequencing and annotation of three M. truncatula bacterial artificial chromosome contigs suggests that the two genomes are related by networks of microsynteny that are often highly degenerate. In some cases, the erosion of microsynteny could be ascribed to the selective gene loss from duplicated loci, whereas in other cases, it is due to the absence of close homologs of M. truncatula genes in Arabidopsis.

Item Type: Paper
Uncontrolled Keywords: Bacteria Biodiversity Genes Mapping Arabidopsis Plant cell culture Chromosome Mapping Chromosomes, Plant Cloning, Molecular Gene Duplication Gene Order Genome, Plant Linkage (Genetics) Medicago Molecular Sequence Data Phylogeny Species Specificity Synteny Variation (Genetics) Bacteria (microorganisms) Embryophyta Medicago truncatula Rosidae
Subjects: organism description > plant > Arabidopsis
bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > plant
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > synteny
CSHL Authors:
Communities: CSHL labs > McCombie lab
Depositing User: Matt Covey
Date Deposited: 23 Apr 2013 15:22
Last Modified: 23 Apr 2013 15:22
PMCID: PMC166867
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28247

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