ArticlePlant physiology2002
Targeted analysis of orthologous phytochrome A regions of the sorghum, maize, and rice genomes using comparative gene-island sequencing.
Article in Plant physiology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea.Journal of biosciences · 2015Article
- Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.Journal of experimental botany · 2015Article
- A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling.PloS one · 2012Article
- Article
- Construction of a watermelon BAC library and identification of SSRs anchored to melon or Arabidopsis genomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2006Article
- Comparative structural and functional characterization of sorghum and maize duplications containing orthologous myb transcription regulators of 3-deoxyflavonoid biosynthesis.Plant molecular biology · 2006Article
- Article
- Article
- Molecular markers from the transcribed/expressed region of the genome in higher plants.Functional & integrative genomics · 2004Review
- Article
- Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution.The Plant cell · 2003Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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