Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.

/pdf/comparative-genomics-reveals-mobile-pathogenicity-4un6wxzvar.pdf

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Advances in DNA sequencing technology have fueled a rapid increase in the number of sequenced vertebrate genomes, and we anticipate an explosion in the number of genomes sequenced in the near future. Detecting similarities between genomes is a valuable technique in discovering functional elements, and sequence alignment is the primary tool for discovering similarities. The quality of alignments is affected by several user-specified control parameters. The parameters are so little understood that most users simply use default settings. We seek to change that, to have the program automatically infer appropriate parameter choices from statistics derived automatically from the sequences. 
We introduce a program, INFERZ, which addresses part of the inference problem, inferring substitution and gap scores according to a mathematically sound model. Further, we explore the usefulness of iterating inferred scores to convergence. We test this process on both simulated and actual genomic data, and show that iteration will converge in general, but found that converged scores were not a consistent improvement. 
INFERZ has a synergistic relationship with LASTZ, our improved drop-in replacement for the widely used alignment program BLASTZ. INFERZ makes repeated calls to LASTZ to test score sets, and LASTZ provides the user an option to have INFERZ decide what scoring parameters to use. Compared to BLASTZ, LASTZ adds a richer set of seeding strategy choices, supports alignment to probabilistic sequences and reduces memory requirements. Additionally, disciplined software techniques make it a better platform for continued experimentation.

Improved pairwise alignment of genomic dna

The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp.

/pdf/shrimp-accurate-mapping-of-short-color-space-reads-4xqnzannoy.pdf

SHRiMP: Accurate Mapping of Short Color-space Reads

Background
The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome [1] would not have been possible without advanced assembly algorithms. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there is a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use.

/pdf/seqan-an-efficient-generic-c-library-for-sequence-analysis-17rjjoukn1.pdf

SeqAn An efficient, generic C++ library for sequence analysis

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

/pdf/analysis-of-the-genome-and-transcriptome-of-cryptococcus-2r327p0b04.pdf

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Extending the single optimized spaced seed of PatternHunter(20) to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search methodology research back to a full circle.

Patternhunter II: highly sensitive and fast homology search.

Extending the single optimized spaced seed of PatternHunter to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle.

PatternHunter II: highly sensitive and fast homology search.

Summary: New ideas, spaced seeds and gapped alignment before 6-frame translation are implemented for translated homology search in tPatternHunter. The new software compares favorably with tBLASTx.

Availability: The software is free to academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/

Contact: [email protected]

/pdf/tpatternhunter-gapped-fast-and-sensitive-translated-homology-59ypbdy1in.pdf

Derek Kisman

Papers

Patternhunter II: highly sensitive and fast homology search.

PatternHunter II: highly sensitive and fast homology search.

tPatternHunter: gapped, fast and sensitive translated homology search