Telomere-targeted retrotransposons in the rice blast fungus Magnaporthe oryzae: agents of telomere instability.

The fungus Magnaporthe oryzae is a serious pathogen of rice and other grasses. Telomeric restriction fragments in Magnaporthe isolates that infect perennial ryegrass (prg) are hotspots for genomic rearrangement and undergo frequent, spontaneous alterations during fungal culture. The telomeres of rice-infecting isolates are very stable by comparison. Sequencing of chromosome ends from a number of prg-infecting isolates revealed two related non-LTR retrotransposons (M. oryzae Telomeric Retrotransposons or MoTeRs) inserted in the telomere repeats. This contrasts with rice pathogen telomeres that are uninterrupted by other sequences. Genetic evidence indicates that the MoTeR elements are responsible for the observed instability. MoTeRs represent a new family of telomere-targeted transposons whose members are found exclusively in fungi.

Male circumcision and human papillomavirus studies reviewed by infection stage and virus type.

The unkeratinized epithelium of the inner human foreskin is thought to be more susceptible to human papillomavirus (HPV) entry than the rest of the penis. However, studies exploring a potential association between male circumcision and HPV infection have produced conflicting results. The present review stratifies the evidence based on methods of sampling and detection of HPV infection, HPV type, and the stage of infection. This approach reveals that circumcision reduces the risk of HPV infection in a stage- and type-specific manner. There is no consistent association of HPV acquisition with circumcision status, indicating that circumcised men may be no more protected from initial HPV infection than their uncircumcised peers. Circumcision is not protective against nononcogenic types of HPV, but is associated with a reduced prevalence and persistence of oncogenic HPV infections. Circumcised men are also less susceptible to multiple infections. These findings indicate that circumcision modulates HPV persistence rather than acquisition. Through promoting HPV infection clearance, male circumcision could be an important adjunct to education, condom use, and vaccination in reducing the global burden of HPV morbidity and mortality.

The telomere-linked helicase (TLH) gene family in Magnaporthe oryzae: revised gene structure reveals a novel TLH-specific protein motif.

Telomere-linked RecQ helicase (TLH) genes have been identified in several fungi, where they occur as small gene families with each member copy residing within ~10 kb of a telomere. Here we describe the characterization of all 11 TLH gene copies in the reference strain of the fungus Magnaporthe oryzae. A consensus gene prediction revealed that the previously reported TLH1 gene is actually a mutated copy, and the full-length gene is almost two times longer. Only four full-length TLH genes were present in the strain that was analyzed, with the remaining copies containing premature stops caused by point mutations, indels, transposon insertions, and a telomere truncation. Interestingly, all of the TLH gene copies possessed numerous mutations indicative of the action of the repeat-induced point mutation process. However, there was evidence of purifying selection indicating maintenance of gene function. Alignment of full-length proteins from M. oryzae, Schizosaccharomyces pombe and M. anisopliae revealed the presence of a novel, highly conserved protein motif which suggests that the telomere-linked helicases have different functions and/or substrates to the RecQ helicases encoded by "internal" genes.

TruMatch--a BLAST post-processor that identifies bona fide sequence matches to genome assemblies.

SUMMARY: BLAST is a widely used alignment tool for detecting matches between a query sequence and entries in nucleotide sequence databases. Matches (high-scoring pairs, HSPs) are assigned a score based on alignment length and quality and, by default, are reported with the top-scoring matches listed first. For certain types of searches, however, this method of reporting is not optimal. This is particularly true when searching a genome sequence with a query that was derived from the same genome, or a closely related one. If the genome is complex and the assembly is far from complete, correct matches are often relegated to low positions in the results, where they may be easily overlooked. To rectify this problem, we developed TruMatch--a program that parses standard BLAST outputs and identifies HSPs that involve query segments with unique matches to the assembly. Candidates for bona fide matches between a query sequence and a genome assembly are listed at the top of the TruMatch output. AVAILABILITY: TruMatch is written in Perl and is freely available to non-commercial users via web download at the URL: http://genome.kbrin.uky.edu/fungi_tel/TruMatch/

TERMINUS--Telomeric End-Read Mining IN Unassembled Sequences.

UNLABELLED: TERMINUS is a set of tools to map telomeres on draft sequences of whole genome shotgun sequencing projects. It mines raw sequence reads (from a trace archive) for telomeric reads, assembles them into contigs representing individual chromosome ends and BLASTs the resulting consensus sequences against the genome assembly to identify telomere-proximal genomic contigs. Finally, it estimates the sizes of telomeric gaps and identifies clones for gap closure. TERMINUS is implemented as a set of Perl scripts that requires two sets of inputs: the NCBI Trace Archive files for a given genome project; and ancillary genome assembly information. Results are output in spreadsheets containing information that facilitates manual validation. AVAILABILITY: The TERMINUS package and supplementary information can be downloaded from http://www.genome.kbrin.uky.edu/fungi_tel/terminus/ CONTACT: farman@uky.edu.