{"entity": "researcher", "timestamp": "2026-09-26T15:10:11.994Z", "family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "affiliations": ["Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/d330af7e23ac4cc186393d46bd2892d1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/d330af7e23ac4cc186393d46bd2892d1"}}, "publications": [{"entity": "publication", "iuid": "1d986d1f918f4308b85334633a9d0ef9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1d986d1f918f4308b85334633a9d0ef9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1d986d1f918f4308b85334633a9d0ef9"}}, "title": "A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements.", "authors": [{"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d567e64775294426ba2297674b148121.json"}}, {"family": "Westerberg", "given": "Ivar", "initials": "I"}, {"family": "Galbraith", "given": "James", "initials": "J"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a2cc7a4bad04f5ab664027a374f5698.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d330af7e23ac4cc186393d46bd2892d1.json"}}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "Suh", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2024-02-07", "journal": {"title": "G3", "issn": "2160-1836", "volume": "14", "issue": "2", "issn-l": "2160-1836"}, "abstract": "Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.", "doi": "10.1093/g3journal/jkad266", "pmid": "38092066", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10849321"}, {"db": "pii", "key": "7471854"}], "notes": [], "created": "2026-09-23T11:22:32.664Z", "modified": "2026-09-23T11:22:32.716Z"}, {"entity": "publication", "iuid": "63ce6e9fb2014b008f9469c6ec18123d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/63ce6e9fb2014b008f9469c6ec18123d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/63ce6e9fb2014b008f9469c6ec18123d"}}, "title": "Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles.", "authors": [{"family": "Kaufmann", "given": "Philipp", "initials": "P", "orcid": "0000-0002-7164-6867", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e99dae220b24d2292f62f49f9c8680f.json"}}, {"family": "Wiberg", "given": "R Axel W", "initials": "RAW"}, {"family": "Papachristos", "given": "Konstantinos", "initials": "K"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d330af7e23ac4cc186393d46bd2892d1.json"}}], "type": "journal article", "published": "2023-08-03", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "40", "issue": "8", "issn-l": "0737-4038"}, "abstract": "The Y chromosome is theorized to facilitate evolution of sexual dimorphism by accumulating sexually antagonistic loci, but empirical support is scarce. Due to the lack of recombination, Y chromosomes are prone to degenerative processes, which poses a constraint on their adaptive potential. Yet, in the seed beetle, Callosobruchus maculatus segregating Y linked variation affects male body size and thereby sexual size dimorphism (SSD). Here, we assemble C. maculatus sex chromosome sequences and identify molecular differences associated with Y-linked SSD variation. The assembled Y chromosome is largely euchromatic and contains over 400 genes, many of which are ampliconic with a mixed autosomal and X chromosome ancestry. Functional annotation suggests that the Y chromosome plays important roles in males beyond primary reproductive functions. Crucially, we find that, besides an autosomal copy of the gene target of rapamycin (TOR), males carry an additional TOR copy on the Y chromosome. TOR is a conserved regulator of growth across taxa, and our results suggest that a Y-linked TOR provides a male specific opportunity to alter body size. A comparison of Y haplotypes associated with male size difference uncovers a copy number variation for TOR, where the haplotype associated with decreased male size, and thereby increased sexual dimorphism, has two additional TOR copies. This suggests that sexual conflict over growth has been mitigated by autosome to Y translocation of TOR followed by gene duplications. Our results reveal that despite of suppressed recombination, the Y chromosome can harbor adaptive potential as a male-limited supergene.", "doi": "10.1093/molbev/msad167", "pmid": "37479678", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10414808"}, {"db": "pii", "key": "7227908"}], "notes": [], "created": "2026-09-23T11:18:10.287Z", "modified": "2026-09-23T11:18:10.434Z"}, {"entity": "publication", "iuid": "4ed3c4f1b4fe4eac91dfc8f0f02cfcf2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4ed3c4f1b4fe4eac91dfc8f0f02cfcf2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4ed3c4f1b4fe4eac91dfc8f0f02cfcf2"}}, "title": "Y-linked copy number polymorphism of target of rapamycin (TOR) is associated with sexual size dimorphism in seed beetles", "authors": [{"family": "Kaufmann", "given": "Philipp", "initials": "P"}, {"family": "Wiberg", "given": "R Axel W", "initials": "RAW"}, {"family": "Papachristos", "given": "Konstantinos", "initials": "K"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d330af7e23ac4cc186393d46bd2892d1.json"}}], "type": "posted-content", "published": "2023-04-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.04.14.536871", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T14:48:31.574Z", "modified": "2026-09-23T14:48:31.636Z"}]}