@article{LahLoeberHsiangetal.2017,
  author    = {Lah, Ljerka and L{\"o}ber, Ulrike and Hsiang, Tom and Hartmann, Stefanie},
  title     = {A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles},
  series = {Fungal biology},
  volume    = {121},
  journal   = {Fungal biology},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {1878-6146},
  doi       = {10.1016/j.funbio.2016.12.002},
  pages     = {234 -- 252},
  year      = {2017},
  abstract  = {Ophiostomatoid fungi are vectored by their bark-beetle associates and colonize different host tree species. To survive and proliferate in the host, they have evolved mechanisms for detoxification and elimination of host defence compounds, efficient nutrient sequestration, and, in pathogenic species, virulence towards plants. Here, we assembled a draft genome of the spruce pathogen Ophiostoma bicolor. For our comparative and phylogenetic analyses, we mined the genomes of closely related species (Ophiostoma piceae, Ophiostoma ulmi, Ophiostoma novo-ulmi, and Grosmannia clavigera). Our aim was to acquire a genomic and evolutionary perspective of gene families important in host colonization. Genome comparisons showed that both the nuclear and mitochondrial genomes in our assembly were largely complete. Our O. bicolor 25.3 Mbp draft genome had 10 018 predicted genes, 6041 proteins with gene ontology (GO) annotation, 269 carbohydrate-active enzymes (CAZymes), 559 peptidases and inhibitors, and 1373 genes likely involved in pathogen-host interactions. Phylogenetic analyses of selected protein families revealed core sets of cytochrome P450 genes, ABC transporters and backbone genes involved in secondary metabolite (SM) biosynthesis (polyketide synthases (PKS) and non-ribosomal synthases), and species-specific gene losses and duplications. Phylogenetic analyses of protein families of interest provided insight into evolutionary adaptations to host biochemistry in ophiostomatoid fungi.},
  language  = {en}
}
@article{AutenriethHartmannLahetal.2018,
  author    = {Autenrieth, Marijke and Hartmann, Stefanie and Lah, Ljerka and Roos, Anna and Dennis, Alice B. and Tiedemann, Ralph},
  title     = {High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)},
  series = {Molecular ecology resources},
  volume    = {18},
  journal   = {Molecular ecology resources},
  number    = {6},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/1755-0998.12932},
  pages     = {1469 -- 1481},
  year      = {2018},
  abstract  = {The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50\% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.},
  language  = {en}
}