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PMID: 12368247 Published · ppublish English Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Mosaic organization of orthologous sequences in grass genomes.

Genome research ·Vol. 12 ·No. 10 ·2002-10-00 ·Pages 1549-55

Song R, Llaca V, Messing J

Abstract

Although comparative genetic mapping studies show extensive genome conservation among grasses, recent data provide many exceptions to gene collinearity at the DNA sequence level. Rice, sorghum, and maize are closely related grass species, once sharing a common ancestor. Because they diverged at different times during evolution, they provide an excellent model to investigate sequence divergence. We isolated, sequenced, and compared orthologous regions from two rice subspecies, sorghum, and maize to investigate the nature of their sequence differences. This study represents the most extensive sequence comparison among grasses, including the largest contiguous genomic sequences from sorghum (425 kb) and maize (435 kb) to date. Our results reveal a mosaic organization of the orthologous regions, with conserved sequences interspersed with nonconserved sequences. Gene amplification, gene movement, and retrotransposition account for the majority of the nonconserved sequences. Our analysis also shows that gene amplification is frequently linked with gene movement. Analyzing an additional 2.9 Mb of genomic sequence from rice not only corroborates our observations, but also suggests that a significant portion of grass genomes may consist of paralogous sequences derived from gene amplification. We propose that sequence divergence started from hotspots along chromosomes and expanded by accumulating small-scale genomic changes during evolution.

MeSH Terms

Chromosomes, Plant/genetics Conserved Sequence/genetics DNA, Plant/genetics Evolution, Molecular Gene Amplification/genetics Genome, Plant Molecular Sequence Data Mosaicism/genetics Mutagenesis, Insertional/genetics Oryza/genetics Poaceae/genetics Recombination, Genetic/genetics Sequence Analysis, DNA/methods Sequence Homology, Nucleic Acid Zea mays/genetics

Chemicals

DNA, Plant

Authors & Affiliations

3 authors, click to expand affiliations / ORCID

Song Rentao

Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-8020, USA.

Llaca Victor

Messing Joachim

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Article Info

Journal

Genome research

Abbr.

Genome Res

ISSN

1088-9051

DOI

10.1101/gr.268302

Published

2002-10-00

Pages

1549-55

Language

English

Region

United States

NLM ID

9518021

PMCID

PMC187525

Subset

Databases

GENBANK

AC025905, AC025906, AC025907, AC027657, AC027658, AC027659, AC027660, AC027661, AC027662, AC073391, AC073392, AC073393, AC087542, AC087543, AC087544, AC087545, AC087546, AC087547, AC087549, AC087550, AF090447, AF114171, AF119222, AF128457, AF229187, AF527807, AF527808, AF527809, AF528565

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PubMed source DOI: 10.1101/gr.268302 PMC Full Text View journal details

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Mosaic organization of orthologous sequences in grass genomes.

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