TY - JOUR
T1 - Dynamic Oryza genomes
T2 - Repetitive DNA sequences as genome modeling agents
AU - Gill, Navdeep
AU - SanMiguel, Phillip
AU - Dhillon, Braham Deep Singh
AU - Abernathy, Brian
AU - Kim, Hye Ran
AU - Stein, Lincoln
AU - Ware, Doreen
AU - Wing, Rod
AU - Jackson, Scott A.
N1 - Funding Information:
Acknowledgments This work was funded by the NSF Plant Genome Award # DBI-0321678 to SAJ, RW, and LS. We thank Dr. Ning Jiang from the Michigan State University, USA and Dr. Tom Bureau from McGill University, Canada for generously sharing their TE databases. We also thank the AGI technical staff, especially members of the BAC/EST Resource, BAC Library Construction, Sequencing, Genome Finishing, and Annotation Centers for supporting this project.
PY - 2010/12
Y1 - 2010/12
N2 - Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome. In an attempt to address this question, we performed a comparative analysis of repetitive DNA sequences in the genus Oryza, representing ~15 million years of evolution. Both Class I and Class II transposable elements, through their expansion, loss and movement in the genome, were found to influence genome size variation in this genus. We identified 38 LTRretrotransposon families that are present in 1,500 or more copies throughout Oryza, and many are preferentially amplified in specific lineages. The data presented here, besides furthering our understanding of genome organization in the genus Oryza, will aid in the assembly, annotation and analysis of genomic data, as part of the future genome sequencing projects of O. sativa wild relatives.
AB - Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome. In an attempt to address this question, we performed a comparative analysis of repetitive DNA sequences in the genus Oryza, representing ~15 million years of evolution. Both Class I and Class II transposable elements, through their expansion, loss and movement in the genome, were found to influence genome size variation in this genus. We identified 38 LTRretrotransposon families that are present in 1,500 or more copies throughout Oryza, and many are preferentially amplified in specific lineages. The data presented here, besides furthering our understanding of genome organization in the genus Oryza, will aid in the assembly, annotation and analysis of genomic data, as part of the future genome sequencing projects of O. sativa wild relatives.
KW - Genome size variation
KW - LTR-retrotransposons
KW - Oryza
KW - Repetitive sequences
KW - Transposable elements
UR - http://www.scopus.com/inward/record.url?scp=84856615026&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84856615026&partnerID=8YFLogxK
U2 - 10.1007/s12284-010-9054-7
DO - 10.1007/s12284-010-9054-7
M3 - Article
AN - SCOPUS:84856615026
SN - 1939-8425
VL - 3
SP - 251
EP - 269
JO - Rice
JF - Rice
IS - 4
ER -