title: Characterization of AFLAV, a Tf1/Sushi retrotransposon from Aspergillus flavus.
abstract: The plasmid, pAF28, a genomic clone from Aspergillus flavus NRRL 6541, has been used as a hybridization probe to fingerprint A. flavus strains isolated in corn and peanut fields. The insert of pAF28 contains a 4.5 kb region which encodes a truncated retrotransposon (AfRTL-1). In search for a full-length and intact copy of retrotransposon, we exploited a novel PCR cloning strategy by amplifying a 3.4 kb region from the genomic DNA of A. flavus NRRL 6541. The fragment was cloned into pCR 4-TOPO. Sequence analysis confirmed that this region encoded putative domains of partial reverse transcriptase, RNase H, and integrase of the predicted retrotransposon. The two flanking long terminal repeats (LTRs) and the sequence between them comprise a putative full-length LTR retrotransposon of 7799 bp in length. This intact retrotransposon sequence is named AFLAV (A. flavus Retrotransposon). The order of the predicted catalytic domains in the polyprotein (Pol) placed AFLAV in the Tf1/sushi subgroup of the Ty3/gypsy retrotransposon family. Primers derived from AFLAV sequence were used to screen this retrotransposon in other strains of A. flavus. More than fifty strains of A. flavus isolated from different geological origins were surveyed and the results show that many strains have extensive deletions in the regions encoding the capsid (Gag) and Pol.
authors.affiliation: U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA. ssth@pw.usda.gov
authors.forename: Sui-Sheng T
authors.initials: SS
authors.lastname: Hua
authors.forename: Alice S
authors.initials: AS
authors.lastname: Tarun
authors.forename: Sonal N
authors.initials: SN
authors.lastname: Pandey
authors.forename: Leo
authors.initials: L
authors.lastname: Chang
authors.forename: Perng-Kuang
authors.initials: PK
authors.lastname: Chang
mesh_terms: D010367:Arachis / Q000382:microbiology; D001231:Aspergillus flavus / Q000235:genetics*; D001483:Base Sequence; D015139:Blotting, Southern; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D010957:Plasmids / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000382:microbiology
chemical_list: D004271:DNA, Fungal; D018626:Retroelements