@article{GrauHacklKoepflietal.2018,
  author    = {Grau, Jos{\´e} Horacio and Hackl, Thomas and Koepfli, Klaus-Peter and Hofreiter, Michael},
  title     = {Improving draft genome contiguity with reference-derived in silico mate-pair libraries},
  series = {GigaScience},
  volume    = {7},
  journal   = {GigaScience},
  number    = {5},
  publisher = {Oxford University Press},
  address   = {Oxford},
  issn      = {2047-217X},
  doi       = {10.1093/gigascience/giy029},
  pages     = {1 -- 6},
  year      = {2018},
  abstract  = {Background Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. Findings In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. Conclusions We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.},
  language  = {en}
}
@misc{GrauHacklKoepflietal.2018,
  author    = {Grau, Jos{\´e} Horacio and Hackl, Thomas and Koepfli, Klaus-Peter and Hofreiter, Michael},
  title     = {Improving draft genome contiguity with reference-derived in silico mate-pair libraries},
  series = {GigaScience},
  journal   = {GigaScience},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-419225},
  pages     = {6},
  year      = {2018},
  abstract  = {Background Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. Findings In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. Conclusions We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.},
  language  = {en}
}
@article{DerežaninBlažytėDobryninetal.2022,
  author    = {Derežanin, Lorena and Blažytė, Asta and Dobrynin, Pavel and Duch{\^e}ne, David A. and Grau, Jos{\´e} Horacio and Jeon, Sungwon and Kliver, Sergei and Koepfli, Klaus-Peter and Meneghini, Dorina and Preick, Michaela and Tomarovsky, Andrey and Totikov, Azamat and Fickel, J{\"o}rns and F{\"o}rster, Daniel W.},
  title     = {Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae},
  series = {Molecular ecology},
  volume    = {31},
  journal   = {Molecular ecology},
  number    = {10},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0962-1083},
  doi       = {10.1111/mec.16443},
  pages     = {2898 -- 2919},
  year      = {2022},
  abstract  = {Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.},
  language  = {en}
}