First published online November 7, 2002; 10.1104/pp.012567
Plant Physiol, December 2002, Vol. 130, pp. 1614-1625
Targeted Analysis of Orthologous Phytochrome A
Regions of the Sorghum, Maize, and Rice Genomes using Comparative
Gene-Island Sequencing1
Daryl T.
Morishige,
Kevin L.
Childs,
L. David
Moore, and
John E.
Mullet*
Institute for Plant Genomics and Biotechnology and Department of
Biochemistry and Biophysics, Texas A&M University, College Station,
Texas 77843
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.
1
This material is based on work supported by the
National Science Foundation (grant no. 0077713), by the Texas
Agricultural Experiment Station, and by the Perry Adkisson Chair in
Agricultural Biology.
*
Corresponding author; e-mail jmullet{at}tamu.edu; fax
979-862-4718.
© 2002 American Society of Plant Biologists
This article has been cited by other articles:
|
|
|
|
 
J.-S. Kim, M. N. Islam-Faridi, P. E. Klein, D. M. Stelly, H. J. Price, R. R. Klein, and J. E. Mullet
Comprehensive Molecular Cytogenetic Analysis of Sorghum Genome Architecture: Distribution of Euchromatin, Heterochromatin, Genes and Recombination in Comparison to Rice
Genetics,
December 1, 2005;
171(4):
1963 - 1976.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C. D. Buchanan, P. E. Klein, and J. E. Mullet
Phylogenetic Analysis of 5'-Noncoding Regions From the ABA-Responsive rab16/17 Gene Family of Sorghum, Maize and Rice Provides Insight Into the Composition, Organization and Function of cis-Regulatory Modules
Genetics,
November 1, 2004;
168(3):
1639 - 1654.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. J. Sheehan, P. R. Farmer, and T. P. Brutnell
Structure and Expression of Maize Phytochrome Family Homeologs
Genetics,
July 1, 2004;
167(3):
1395 - 1405.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
L. E. Palmer, P. D. Rabinowicz, A. L. O'Shaughnessy, V. S. Balija, L. U. Nascimento, S. Dike, M. de la Bastide, R. A. Martienssen, and W. R. McCombie
Maize Genome Sequencing by Methylation Filtration
Science,
December 19, 2003;
302(5653):
2115 - 2117.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Guo and S. P. Moose
Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and Patterns of Promoter Evolution
PLANT CELL,
May 1, 2003;
15(5):
1143 - 1158.
[Abstract]
[Full Text]
|
|
|
|
|
