Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana

Huihuang D Yan, J. Mudge, D. J. Kim, D. Larsen, R. C. Shoemaker, D. R. Cook, N. D. Young

Research output: Contribution to journalArticle

55 Citations (Scopus)

Abstract

A growing body of research indicates that microsynteny is common among dicot genomes. However, most studies focus on just one or a few genomic regions, so the extent of microsynteny across entire genomes remains poorly characterized. To estimate the level of microsynteny between Medicago truncatula (Mt) and Glycine max (soybean), and also among homoeologous segments of soybean, we used a hybridization strategy involving bacterial artificial chromosome (BAC) contigs. A Mt BAC library consisting of 30,720 clones was screened with a total of 187 soybean BAC subclones and restriction fragment length polymorphism (RFLP) probes. These probes came from 50 soybean contig groups, defined as one or more related BAC contigs anchored by the same low-copy probe. In addition, 92 whole soybean BAC clones were hybridized to filters of HindIII-digested Mt BAC DNA to identify additional cases of cross-hybridization after removal of those soybean BACs found to be repetitive in Mt. Microsynteny was inferred when at least two low-copy probes from a single soybean contig hybridized to the same Mt BAC or when a soybean BAC clone hybridized to three or more low-copy fragments from a single Mt BAC. Of the 50 soybean contig groups examined, 54% showed microsynteny to Mt. The degree of conservation among 37 groups of soybean contigs was also investigated. The results indicated substantial conservation among soybean contigs in the same group, with 86.5% of the groups showing at least some level of microsynteny. One contig group was examined in detail by a combination of physical mapping and comparative sequencing of homoeologous segments. A TBLASTX similarity search was performed between 1,085 soybean sequences on the 50 BAC contig groups and the entire Arabidopsis genome. Based on a criterion of sequence homologues <100 kb apart, each with an expected value of ≤1e-07, seven of the 50 soybean contig groups (14%) exhibited microsynteny with Arabidopsis.

Original languageEnglish (US)
Pages (from-to)1256-1265
Number of pages10
JournalTheoretical And Applied Genetics
Volume106
Issue number7
StatePublished - May 1 2003
Externally publishedYes

Fingerprint

Medicago truncatula
Soybeans
Arabidopsis
Bacterial Artificial Chromosomes
bacterial artificial chromosomes
Glycine max
Arabidopsis thaliana
Genome
soybeans
genome
Clone Cells
clones
hybridization
physical chromosome mapping
Magnoliopsida
Sequence Homology

Keywords

  • Evolution
  • Genome duplication
  • Glycine max
  • Medicago truncatula
  • Microsynteny

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Horticulture
  • Plant Science
  • Genetics
  • Genetics(clinical)

Cite this

Yan, H. D., Mudge, J., Kim, D. J., Larsen, D., Shoemaker, R. C., Cook, D. R., & Young, N. D. (2003). Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana. Theoretical And Applied Genetics, 106(7), 1256-1265.

Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana. / Yan, Huihuang D; Mudge, J.; Kim, D. J.; Larsen, D.; Shoemaker, R. C.; Cook, D. R.; Young, N. D.

In: Theoretical And Applied Genetics, Vol. 106, No. 7, 01.05.2003, p. 1256-1265.

Research output: Contribution to journalArticle

Yan, HD, Mudge, J, Kim, DJ, Larsen, D, Shoemaker, RC, Cook, DR & Young, ND 2003, 'Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana', Theoretical And Applied Genetics, vol. 106, no. 7, pp. 1256-1265.
Yan, Huihuang D ; Mudge, J. ; Kim, D. J. ; Larsen, D. ; Shoemaker, R. C. ; Cook, D. R. ; Young, N. D. / Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana. In: Theoretical And Applied Genetics. 2003 ; Vol. 106, No. 7. pp. 1256-1265.
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