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Population genomics of domestic and wild yeasts
TLDR
Rather than one or two domestication events leading to the extant baker’s yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations. Expand
Population genomics of domestic and wild yeasts
TLDR
Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae shows a few well defined geographically isolated lineages and many different mosaics of these lineages, supporting the notion that human influence provided the opportunity for outbreeding and production of new combinations of pre-existing variation. Expand
The genomes of four tapeworm species reveal adaptations to parasitism
TLDR
An analysis of tapeworm genome sequences using the human-infective species Echinococcus multilocularis, E. granulosus, Taenia solium and the laboratory model Hymenolepis microstoma offers insights into the evolution of parasitism and identifies new potential drug targets. Expand
A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni
TLDR
The upgraded genome of Schistosoma mansoni will form a fundamental dataset to underpin further advances in schistosome research and is consolidated into a searchable format within the GeneDB and SchistoDB databases. Expand
Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle
TLDR
The utility of population genomic data in quantifying life cycles is illustrated with the life cycle of the wild yeast Saccharomyces paradoxus, which goes through a sexual cycle approximately once in every 1,000 asexual generations. Expand
Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus
TLDR
A high-quality draft genome sequence from an inbred line of B. xylophilus is presented, and the lack of proteins homologous to effectors from other plant parasitic nematodes confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage. Expand
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
TLDR
This work presents a practical approach that uses Illumina sequences to improve draft genome assemblies by aligning sequences against contig ends and performing local assemblies to produce gap-spanning contigs. Expand
The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode
TLDR
The complete genome sequence of G. pallida is presented, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Expand
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
TLDR
This protocol describes software (PAGIT) that is used to improve the quality of draft genomes and offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence and exploit reference genomes in order to improve scaffolding and generating annotations. Expand
The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery
TLDR
The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites and provide the most comprehensive understanding yet of the action of several important anthelmintics. Expand
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