Affiliations: Department of Biology, Loyola University Chicago,
Chicago, IL, USA | Program in Bioinformatics, Loyola University Chicago,
Chicago, IL, USA | Department of Biology, Oberlin College, Oberlin, OH,
USA
Note: [] Corresponding author. Department of Biology, Loyola University
Chicago, 6525 N. Sheridan Rd., Chicago, IL 60626, USA. Tel.: +1 773 508 3640;
E-mail: [email protected]
Abstract: SIRE1 is a 2,000-copy member of the Ty1/copia retroelement
family found in the soybean genome and is closely related to sireviruses found
in the genomes of other legumes. Although these elements closely resemble
typical plant members of the Ty1/copia family, they are unusual in that they
possess an envelope-like coding region immediately downstream of the reverse
transcriptase gene. Despite its copy number, very few members of the
SIRE1 family are currently present in publicly available genomic assemblies or
draft contigs. However, fragments of family members are well-represented as
BAC-ends in the GenBank Genome Survey Sequence database. This database was
queried using the 5' and 3' ends of SIRE1 in order to catalog
sequences into which SIRE1 members have integrated. Seven hundred and
eighty-one unique SIRE1 insertions were identified and the majority of
insertion sites constituted other repetitive elements, including Class I and
Class II transposable elements and satellite DNAs. Ninety-four insertions were
in single- or low-copy number sequences and three of these were homologous to
characterized protein-coding genes. Examination of the ten bases flanking
either side of SIRE1 revealed no clear consensus sequence, but the the
distributions of A, C, G, and T at most of the positions were biased with
strong statistical significance.
