Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives.
We have newly identified five Terminal-repeat retrotransposon in miniature (TRIM) families, four from Brassica and one from Arabidopsis. A total of 146 elements, including three Arabidopsis families reported before, are extracted from genomics data of Brassica and Arabidopsis, and these are grouped into eight distinct lineages, Br1 to Br4 derived from Brassica and At1 to At4 derived from Arabidopsis. Based on the occurrence of TRIM elements in 434 Mb of B. oleracea shotgun sequences and 96 Mb of B. rapa BAC end sequences, total number of TRIM members of Br1, Br2, Br3, and Br4 families are roughly estimated to be present in 660 and 530 copies in B. oleracea and B. rapa genomes, respectively. Studies on insertion site polymorphisms of four elements across taxa in the tribe Brassiceae infer the taxonomic lineage and dating of the insertion time. Active roles of the TRIM elements for evolution of the duplicated genes are inferred in the highly replicated Brassica genome.
Yang
Tae-Jin
TJ
Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea.
Kwon
Soo-Jin
SJ
Choi
Beom-Soon
BS
Kim
Jung Sun
JS
Jin
Mina
M
Lim
Ki-Byung
KB
Park
Jee Young
JY
Kim
Jin-A
JA
Lim
Myung-Ho
MH
Kim
Ho-Il
HI
Lee
Hyo-Jin
HJ
Lim
Yong Pyo
YP
Paterson
Andrew H
AH
Park
Beom-Seok
BS
D001483:Base Sequence; D001937:Brassica / Q000235:genetics*; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology; D017931:DNA Primers; D019143:Evolution, Molecular; D018628:Gene Dosage / Q000235:genetics; D023281:Genomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D020079:Terminal Repeat Sequences / Q000235:genetics
D017931:DNA Primers; D018626:Retroelements