{"entity": "researcher", "timestamp": "2026-07-14T04:34:59.932Z", "family": "Powell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-6323-7791", "affiliations": ["Evolutionary Ecology, Biology Department Lund University Lund Sweden.", "Global Change Ecology, School of Science, Technology and Engineering University of the Sunshine Coast Sippy Downs QLD Australia."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/e8bd7fa790f9432d9d61cc1ab8d9b2d8.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/e8bd7fa790f9432d9d61cc1ab8d9b2d8"}}, "publications": [{"entity": "publication", "iuid": "960433d0e9d14c7baf59a3e9a519d1db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/960433d0e9d14c7baf59a3e9a519d1db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/960433d0e9d14c7baf59a3e9a519d1db"}}, "title": "A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest.", "authors": [{"family": "Powell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-6323-7791", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8bd7fa790f9432d9d61cc1ab8d9b2d8.json"}}, {"family": "Gro\u03b2e-Wilde", "given": "Ewald", "initials": "E"}, {"family": "Krokene", "given": "Paal", "initials": "P"}, {"family": "Roy", "given": "Amit", "initials": "A"}, {"family": "Chakraborty", "given": "Amrita", "initials": "A"}, {"family": "L\u00f6fstedt", "given": "Christer", "initials": "C", "orcid": "0000-0002-3116-6922", "researcher": {"href": "https://publications.scilifelab.se/researcher/68150ac5a3d44f26af3fa81a5209c535.json"}}, {"family": "Vogel", "given": "Heiko", "initials": "H"}, {"family": "Andersson", "given": "Martin N", "initials": "MN", "orcid": "0000-0001-9807-8524", "researcher": {"href": "https://publications.scilifelab.se/researcher/42bc7f90fad040c292fceed405df5ac3.json"}}, {"family": "Schlyter", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-1244-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/38df140cdd0e4a1693da808131833114.json"}}], "type": "journal article", "published": "2021-09-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "1059", "issn-l": "2399-3642"}, "abstract": "Conifer-feeding bark beetles are important herbivores and decomposers in forest ecosystems. These species complete their life cycle in nutritionally poor substrates and some can kill enormous numbers of trees during population outbreaks. The Eurasian spruce bark beetle (Ips typographus) can destroy >100 million m3 of spruce in a single year. We report a 236.8 Mb I. typographus genome assembly using PacBio long-read sequencing. The final phased assembly has a contig N50 of 6.65 Mb in 272 contigs and is predicted to contain 23,923 protein-coding genes. We reveal expanded gene families associated with plant cell wall degradation, including pectinases, aspartyl proteases, and glycosyl hydrolases. This genome sequence from the genus Ips provides timely resources to address questions about the evolutionary biology of the true weevils (Curculionidae), one of the most species-rich animal families. In forests of today, increasingly stressed by global warming, this draft genome may assist in developing pest control strategies to mitigate outbreaks.", "doi": "10.1038/s42003-021-02602-3", "pmid": "34504275", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02602-3"}, {"db": "pmc", "key": "PMC8429705"}, {"db": "figshare", "key": "10.6084/m9.figshare.14503065"}], "notes": [], "created": "2021-09-22T15:33:20.295Z", "modified": "2024-01-16T13:48:38.511Z"}, {"entity": "publication", "iuid": "f5bd5ff4af6e4311aaa2b84a04fff62b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5bd5ff4af6e4311aaa2b84a04fff62b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5bd5ff4af6e4311aaa2b84a04fff62b"}}, "title": "Urbanization is associated with modifications in DNA methylation in a small passerine bird.", "authors": [{"family": "Watson", "given": "Hannah", "initials": "H", "orcid": "0000-0003-4656-0647", "researcher": {"href": "https://publications.scilifelab.se/researcher/897ef477ef2e4fa290cb67b245bdf3f5.json"}}, {"family": "Powell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-6323-7791", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8bd7fa790f9432d9d61cc1ab8d9b2d8.json"}}, {"family": "Salm\u00f3n", "given": "Pablo", "initials": "P", "orcid": "0000-0001-9718-6611", "researcher": {"href": "https://publications.scilifelab.se/researcher/b60bfa8b60174680a1546f283c2ccbc1.json"}}, {"family": "Jacobs", "given": "Arne", "initials": "A", "orcid": "0000-0001-7635-5447", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c375694c76e48279bdc6e7dcc2808a6.json"}}, {"family": "Isaksson", "given": "Caroline", "initials": "C", "orcid": "0000-0002-6889-1386", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ddbca044f64cb1b1feef58baf539ba.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "14", "issue": "1", "pages": "85-98", "issn-l": "1752-4571"}, "abstract": "Urbanization represents a fierce driver of phenotypic change, yet the molecular mechanisms underlying observed phenotypic patterns are poorly understood. Epigenetic changes are expected to facilitate more rapid adaption to changing or novel environments, such as our towns and cities, compared with slow changes in gene sequence. A comparison of liver and blood tissue from great tits Parus major originating from an urban and a forest site demonstrated that urbanization is associated with variation in genome-wide patterns of DNA methylation. Combining reduced representation bisulphite sequencing with transcriptome data, we revealed habitat differences in DNA methylation patterns that suggest a regulated and coordinated response to the urban environment. In the liver, genomic sites that were differentially methylated between urban- and forest-dwelling birds were over-represented in regulatory regions of the genome and more likely to occur in expressed genes. DNA methylation levels were also inversely correlated with gene expression at transcription start sites. Furthermore, differentially methylated CpG sites, in liver, were over-represented in pathways involved in (i) steroid biosynthesis, (ii) superoxide metabolism, (iii) secondary alcohol metabolism, (iv) chylomicron remodelling, (v) cholesterol transport, (vi) reactive oxygen species (ROS) metabolic process and (vii) epithelial cell proliferation. This corresponds with earlier studies identifying diet and exposure to ROS as two of the main drivers of divergence between organisms in urban and nonurban environments. Conversely, in blood, sites that were differentially methylated between urban- and forest-dwelling birds were under-represented in regulatory regions, more likely to occur in nonexpressed genes and not over-represented in specific biological pathways. It remains to be determined whether diverging patterns of DNA methylation represent adaptive evolutionary responses and whether the conclusions can be more widely attributed to urbanization.", "doi": "10.1111/eva.13160", "pmid": "33519958", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EVA13160"}, {"db": "pmc", "key": "PMC7819559"}], "notes": [], "created": "2021-02-02T12:30:56.264Z", "modified": "2024-01-16T13:48:40.994Z"}]}