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PMID: 12481045 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Targeted analysis of orthologous phytochrome A regions of the sorghum, maize, and rice genomes using comparative gene-island sequencing.

Plant physiology ·Vol. 130 ·No. 4 ·2002-12-00 ·Pages 1614-25

Morishige DT, Childs KL, Moore LD, Mullet JE

Abstract

A "gene-island" sequencing strategy has been developed that expedites the targeted acquisition of orthologous gene sequences from related species for comparative genome analysis. A 152-kb bacterial artificial chromosome (BAC) clone from sorghum (Sorghum bicolor) encoding phytochrome A (PHYA) was fully sequenced, revealing 16 open reading frames with a gene density similar to many regions of the rice (Oryza sativa) genome. The sequences of genes in the orthologous region of the maize (Zea mays) and rice genomes were obtained using the gene-island sequencing method. BAC clones containing the orthologous maize and rice PHYA genes were identified, sheared, subcloned, and probed with the sorghum PHYA-containing BAC DNA. Sequence analysis revealed that approximately 75% of the cross-hybridizing subclones contained sequences orthologous to those within the sorghum PHYA BAC and less than 25% contained repetitive and/or BAC vector DNA sequences. The complete sequence of four genes, including up to 1 kb of their promoter regions, was identified in the maize PHYA BAC. Nine orthologous gene sequences were identified in the rice PHYA BAC. Sequence comparison of the orthologous sorghum and maize genes aided in the identification of exons and conserved regulatory sequences flanking each open reading frame. Within genomic regions where micro-colinearity of genes is absolutely conserved, gene-island sequencing is a particularly useful tool for comparative analysis of genomes between related species.

MeSH Terms
Base Sequence Chromosomes, Artificial, Bacterial/genetics Conserved Sequence/genetics DNA, Plant/chemistry,genetics Genome, Plant Molecular Sequence Data Oryza/genetics Phytochrome/genetics Phytochrome A Poaceae/genetics Promoter Regions, Genetic/genetics Sequence Alignment Sequence Analysis, DNA Sequence Homology, Nucleic Acid Species Specificity Zea mays/genetics
Chemicals
DNA, Plant Phytochrome A Phytochrome
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Morishige Daryl T
Institute for Plant Genomics and Biotechnology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA.
Childs Kevin L
Moore L David
Mullet John E
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Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.012567
Published
2002-12-00
Pages
1614-25
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC166677
Subset
IM
Databases
GENBANK
AF369906
External Links
PubMed source DOI: 10.1104/pp.012567 PMC Full Text View journal details
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