Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes

doi:10.1073/pnas.0812798106

Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes

^aState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
^bArizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721;
^cDepartment of Agronomy, Purdue University, West Lafayette, IN 47907;
^dShanghai Key Laboratory of Bio-energy Crop, School of Life Sciences, Shanghai University, Shanghai 200444, China; and
^eDepartment of Genetics, University of Georgia, Athens, GA 30602-7223

Contributed by Jeffrey L. Bennetzen, December 17, 2008
↵¹F.L., J.S.S.A., A.S., S.Z., and R.S. contributed equally to this work. (received for review November 11, 2008)

Abstract

Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In the genus Oryza, this comparative approach can be used to investigate gene function, genome evolution, domestication, polyploidy, and ecological adaptation. A large genomic region surrounding the MONOCULM1 (MOC1) locus was chosen for study in 14 Oryza species, including 10 diploids and 4 allotetraploids. Sequencing and annotation of 18 bacterial artificial chromosome clones for these species revealed highly conserved gene colinearity and structure in the MOC1 region. Since the Oryza radiation about 14 Mya, differences in transposon amplification appear to be responsible for the different current sizes of the Oryza genomes. In the MOC1 region, transposons were only conserved between genomes of the same type (e.g., AA or BB). In addition to the conserved gene content, several apparent genes have been generated de novo or uniquely retained in the AA lineage. Two different 3-gene segments have been inserted into the MOC1 region of O. coarctata (KK) or O. sativa by unknown mechanism(s). Large and apparently noncoding sequences flanking the MOC1 gene were observed to be under strong purifying selection. The allotetraploids Oryza alta and Oryza minuta were found to be products of recent polyploidization, less than 1.6 and 0.4 Mya, respectively. In allotetraploids, pseudogenization of duplicated genes was common, caused by large deletions, small frame-shifting insertions/deletions, or nonsense mutations.

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Footnotes

³To whom correspondence may be addressed. E-mail: maize{at}uga.edu, mschen{at}genetics.ac.cn, rwing{at}ag.arizona.edu, or sjackson{at}purdue.edu
Author contributions: F.L., S.A.J., R.A.W., and M.C. designed research; F.L., J.S.S.A., A.S., S.Z., R.S., J.C., G.L., Y.S., X.S., Z.C., A.C.d.O., and M.C. performed research; F.L., J.S.S.A., A.S., S.Z., R.S., J.C., G.L., X.S., A.C.d.O., J.L.B., S.A.J., R.A.W., and M.C. analyzed data; and F.L., J.L.B., and M.C. wrote the paper.
↵²Present address: Key Discipline Open Laboratory on Crop Molecular Breeding, Henan Institute of Higher Learning/Henan Institute of Science and Technology, Xinxiang 453003, China.
The authors declare no conflict of interest.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. FJ032625–FJ032640).
This article contains supporting information online at www.pnas.org/cgi/content/full/0812798106/DCSupplemental.
Freely available online through the PNAS open access option.