180V Poster Online - Virtual Posters
Tuesday June 07, 11:00 AM - 3:00 PM

Authors:
Sruthi Srinivasan ¹; Eliana Herman ¹; Fay-Wei Li ²; Nasim Rahmatpour ²; Steve Mount ¹

Affiliations:
1) Department of Cell Biology and Molecular Genetics, University of Maryland, College Park; 2) Boyce Thompson Institute and Cornell University, Ithaca, New York

Keywords:
Comparative genomics & genome evolution

We have recently determined the genome sequence of the semi-aquatic, heterosporous fern Marsilea vestista. The estimated genome size is 1.27 Gb. and the assembly of 1.03 Gb. has an N50 of 2.97 Mb. Repeatmasker identifies 422 Mb. (41%) of the sequence as repetitive. Because the genomes of ferns have not been extensively analyzed, we have begun an analysis of the structural diversity of repetitive elements that characterize this genome.

The extremely abundant, and apparently active, retroelement TMv01 was selected for detailed analysis. TMv01 is a member of the gypsy LTR superfamily. There are over 2,000 copies of TMv01 in the genome, including 106 copies with identical LTRs (indicating recent transposition). The complete element has a length of 7,500-8,100 base pairs and an open reading frame of 1,485 amino acids with the expected gag, protease, reverse transcriptase, RNaseH, and integrase domains. An additional chromo domain at the C-terminus, although unusual, has been seen in angiosperm elements of the gypsy subfamily. LTRs are 455-458 nucleotides in length. Insertion generates 5 base pair target site duplications. An unusual feature of this element is the presence of a long noncoding region of over 2,900 nucleotides between the 5' LTR and the open reading frame.