title: Functional and structural divergence of an unusual LTR retrotransposon family in plants.
abstract: Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and in silico approaches were used to determine the origin of Retrosat2 and putative function of ORF0. Our data show that not only is Retrosat2 highly abundant in the Oryza genus, it may yet be active in rice. Homologs of Retrosat2 were identified in maize, sorghum, Arabidopsis and other plant genomes suggesting that the Retrosat2 family is of ancient origin. Several putatively cis-acting elements, some multicopy, that regulate retrotransposon replication or responsiveness to environmental factors were found in the LTRs of Retrosat2. Unlike the ORF1, the ORF0 sequences from Retrosat2 and homologs are divergent at the sequence level, 3D-structures and predicted biological functions. In contrast to other retrotransposon families, Retrosat2 and its homologs are dispersed throughout genomes and not concentrated in the specific chromosomal regions, such as centromeres. The genomic distribution of Retrosat2 homologs varies across species which likely reflects the differing evolutionary trajectories of this retrotransposon family across diverse species.
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America. dgao@uga.edu
authors.forename: Dongying
authors.initials: D
authors.lastname: Gao
authors.forename: Jose C
authors.initials: JC
authors.lastname: Jimenez-Lopez
authors.forename: Aiko
authors.initials: A
authors.lastname: Iwata
authors.forename: Navdeep
authors.initials: N
authors.lastname: Gill
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics; D017404:In Situ Hybridization, Fluorescence; D008958:Models, Molecular; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D010944:Plants / Q000145:classification / Q000235:genetics*; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D018626:Retroelements / Q000235:genetics*; D013045:Species Specificity; D020079:Terminal Repeat Sequences / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D018626:Retroelements