PMID- 12481045
OWN - NLM
STAT- MEDLINE
DCOM- 20030530
LR  - 20181113
IS  - 0032-0889 (Print)
IS  - 1532-2548 (Electronic)
IS  - 0032-0889 (Linking)
VI  - 130
IP  - 4
DP  - 2002 Dec
TI  - Targeted analysis of orthologous phytochrome A regions of the sorghum, maize, and 
      rice genomes using comparative gene-island sequencing.
PG  - 1614-25
AB  - 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.
FAU - Morishige, Daryl T
AU  - Morishige DT
AD  - Institute for Plant Genomics and Biotechnology and Department of Biochemistry and 
      Biophysics, Texas A&M University, College Station, Texas 77843, USA.
FAU - Childs, Kevin L
AU  - Childs KL
FAU - Moore, L David
AU  - Moore LD
FAU - Mullet, John E
AU  - Mullet JE
LA  - eng
SI  - GENBANK/AF369906
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PL  - United States
TA  - Plant Physiol
JT  - Plant physiology
JID - 0401224
RN  - 0 (DNA, Plant)
RN  - 0 (Phytochrome A)
RN  - 11121-56-5 (Phytochrome)
SB  - IM
MH  - Base Sequence
MH  - Chromosomes, Artificial, Bacterial/genetics
MH  - Conserved Sequence/genetics
MH  - DNA, Plant/chemistry/genetics
MH  - *Genome, Plant
MH  - Molecular Sequence Data
MH  - Oryza/genetics
MH  - Phytochrome/*genetics
MH  - Phytochrome A
MH  - Poaceae/*genetics
MH  - Promoter Regions, Genetic/genetics
MH  - Sequence Alignment
MH  - Sequence Analysis, DNA
MH  - Sequence Homology, Nucleic Acid
MH  - Species Specificity
MH  - Zea mays/genetics
PMC - PMC166677
EDAT- 2002/12/14 04:00
MHDA- 2003/05/31 05:00
PMCR- 2003/12/01
CRDT- 2002/12/14 04:00
PHST- 2002/12/14 04:00 [pubmed]
PHST- 2003/05/31 05:00 [medline]
PHST- 2002/12/14 04:00 [entrez]
PHST- 2003/12/01 00:00 [pmc-release]
AID - 7589 [pii]
AID - 10.1104/pp.012567 [doi]
PST - ppublish
SO  - Plant Physiol. 2002 Dec;130(4):1614-25. doi: 10.1104/pp.012567.