Genetics and Genomic Sciences

Yeast glycoproteins are representative of low-complexity sequences, those sequences rich in a few types of amino acids. Low-complexity protein sequences comprise more than 10% of the proteome but are poorly aligned by existing methods. Under default conditions, BLAST and FASTA use the scoring matrix BLOSUM62, which is optimized for sequences with diverse amino acid compositions. Because low-complexity sequences are rich in a few amino acids, these tools tend to align the most common residues in nonhomologous positions, thereby generating anomalously high scores, deviations from the expected extreme value distribution, and small e values. This anomalous scoring prevents BLOSUM62-based BLAST and FASTA from identifying correct homologs for proteins with low-complexity sequences, including Saccharomyces cerevisiae wall proteins.

Motivation: Finding genomic distance based on gene order is a classic problem in genome rearrangements. Efficient exact algorithms for genomic distances based on inversions and/or translocations have been found but are complicated by special cases, rare in simulations and empirical data. We seek a universal operation underlying a more inclusive set of evolutionary operations and yielding a tractable genomic distance with simple mathematical form. Results: We study a universal double-cut-and-join operation that accounts for inversions, translocations, fissions and fusions, but also produces circular intermediates which can be reabsorbed. The genomic distance, computable in linear time, is given by the number of breakpoints minus the number of cycles (b − c) in the comparison graph of the two genomes; the number of hurdles does not enter into it. Without changing the formula, we can replace generation and re-absorption of a circular intermediate by a generalized transposition, equivalent to a block interchange, with weight two. Our simple algorithm converts one multi-linear chromosome genome to another in the minimum distance.

We determined 8-fold coverage draft sequences of B. burgdorferi JD1 and N40 genomes as described . Genome assembly of JD1 and N40 (in particular, the assembly of the highly paralogous cp32 plasmids) is not yet complete. Sequencing of selected genes (both strands) from additional clinical isolates was performed by the Stony Brook University Core DNA Sequencing Facility (see Supporting Materials and Methods, which is published as supporting information on the PNAS web site).

In a liver transplant recipient with vancomycin-resistant Enterococcus (VRE) surgical site and bloodstream infection, a combination of pulsed-field gel electrophoresis, multilocus sequence typing, and whole genome sequencing identified that donor and recipient VRE isolates were highly similar when compared to time-matched hospital isolates. Comparison of de novo assembled isolate genomes was highly suggestive of transplant transmission rather than hospital-acquired transmission and also identified subtle internal rearrangements between donor and recipient missed by other genomic approaches. Given the improved resolution, whole-genome assembly of pathogen genomes is likely to become an essential tool for investigation of potential organ transplant transmissions.

Clinical and tick isolates of Borrelia burgdorferi sensu stricto, the bacterial agent of Lyme disease, from the northeastern United States were sequenced at 12 loci located on the main chromosome and 7 plasmids (lp54, cp26, cp9, lp17, lp25, lp28-2, and lp38). The outer surface protein C gene (ospC) showed the highest number (12) of major alleles (defined as alleles differing by 5% or more in nucleotide sequence) while other ORFs had only two to four major alleles. A non-recombining chromosomal marker, the rrs-rrlA ribosomal RNA spacer, was used to infer the intraspecific phylogeny among these B. burgdorferi isolates. We were thus able to analyze the multilocus genotypes in the context of a B. burgdorferi intraspecific phylogeny. Except for ospC, sequence variations at plasmid-borne loci showed broad inconsistency with the intraspecific phylogeny, supporting DNA exchanges mediated by plasmid transfers. The multilocus linkage frequently observed in B. burgdorferi populations is due more likely to a ''founder effect'' than to a lack of recombination. The exceptional phylogenetic consistency of ospC, in conjunction with its selectively maintained high intraspecific diversity, suggested a dominant role ospC plays in the initiation and maintenance of adaptive differentiation in B. burgdorferi. #

Three-prime untranslated regions (3′UTRs) of metazoan mRNAs contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3′RACE, full-length cDNAs, and RNA-seq, we define ~26,000 distinct 3′UTRs in Caenorhabditis elegans for ~85% of the 18,328 experimentally supported protein coding genes and revise ~40% of gene models. Alternative 3′UTR isoforms are frequent, often differentially expressed during development. Average 3′UTR length decreases with animal age. Surprisingly, no polyadenylation signal (PAS) is detected for 13% of polyA sites, predominantly among shorter alternative isoforms. Trans-spliced (versus non-trans-spliced) mRNAs possess longer 3′UTRs and frequently contain no PAS or variant PAS. We identify conserved 3′UTR motifs, isoformspecific predicted microRNA target sites, and polyadenylation of most histone genes. Our data reveal a rich complexity of 3′UTRs genome-wide and throughout development.