{"entity": "researcher", "timestamp": "2026-09-23T14:43:12.506Z", "family": "Palacios-Gimenez", "given": "Octavio Manuel", "initials": "OM", "orcid": "0000-0002-1472-9949", "affiliations": ["Department of Organismal Biology-Systematic Biology, Science for Life Laboratory, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden.", "Department of Population Ecology, Institute of Ecology and Evolution, Friedrich Schiller University Jena, 07743 Jena, Germany.", "German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4d3d53ea54b4ec293da675c9c63a0de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4d3d53ea54b4ec293da675c9c63a0de"}}, "publications": [{"entity": "publication", "iuid": "551f331be02b4528af123d1ed081c27a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/551f331be02b4528af123d1ed081c27a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/551f331be02b4528af123d1ed081c27a"}}, "title": "Chromosome-level assembly of the club-legged grasshopper (Gomphocerus sibiricus) genome.", "authors": [{"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4d3d53ea54b4ec293da675c9c63a0de.json"}}, {"family": "Varma", "given": "Mahendra", "initials": "M", "orcid": "0000-0003-0271-4958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f043b78c7be4485c88e51781c06580fc.json"}}, {"family": "Cheng", "given": "Xinyi", "initials": "X"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "MB", "orcid": "0000-0002-6068-0971", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/174027286b1d4903a1a004c1c3bccdc6.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/185297e474cc4e09b1f2087fb7d902a1.json"}}], "type": "journal article", "published": "2025-12-10", "journal": {"title": "G3", "issn": "2160-1836", "volume": "15", "issue": "12", "issn-l": "2160-1836"}, "abstract": "Grasshoppers represent true outliers in genome sizes, both within insects and within animals in general. Their genomes are large and generally variable in sizes and feature a high abundance of repetitive DNA sequences. This has hampered the assembly of grasshopper genomes to the chromosome level. Here we present a chromosome-level reference genome for the club-legged grasshopper (Gomphocerus sibiricus, Acrididae: Gomphocerinae) using PacBio HiFi long-read and Hi-C sequencing technologies. In male haploid cells, the species has a chromosome set of n = 9 with an X0 sex-determination system, characterized by an absence of a Y chromosome. Our assembly spans 9.57 Gb in total, with 8.87 Gb organized into 9 chromosomes-8 autosomes and the X chromosome. The final assembly has a scaffold N50 value of 1.58 Gb, covers 96.7% single copy Insecta orthologs, and contains 42,665 predicted protein-coding genes and 43,385 mRNA transcripts. We compiled a curated, nonredundant, species-specific repeat library and used it to annotate repetitive DNA, covering 81.69% of the genome, mostly DNA transposons, long-interspersed nuclear element and long-terminal repeat retrotransposons. The genome of the club-legged grasshopper shows high degree of synteny with the locusts Schistocerca gregaria and Locusta migratoria, and the analysis strongly indicates 3 autosome-autosome centric fusions in Gomphocerinae. The genome offers a valuable resource for grasshopper genomics and for exploring the genetic basis of a transspecies color polymorphism.", "doi": "10.1093/g3journal/jkaf231", "pmid": "41029998", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12693501"}, {"db": "pii", "key": "8269502"}, {"db": "BioProject", "key": "PRJNA1250961"}, {"db": "GENBANK", "key": "JBPBLO000000000"}, {"db": "SRA", "key": "SRX29045381"}, {"db": "SRA", "key": "SRX29045382"}, {"db": "SRA", "key": "SRX29045386"}, {"db": "SRA", "key": "SRX29045393"}, {"db": "SRA", "key": "SRX29073929"}, {"db": "SRA", "key": "SRX29073928"}, {"db": "SRA", "key": "SRX29045383"}, {"db": "SRA", "key": "SRX29045385"}, {"db": "figshare", "key": "10.6084/m9.figshare.29476994"}, {"db": "figshare", "key": "10.6084/m9.figshare.29148779"}, {"db": "figshare", "key": "10.6084/m9.figshare.29148836"}, {"db": "figshare", "key": "10.6084/m9.figshare.29148746"}], "notes": [], "created": "2026-09-23T13:19:18.537Z", "modified": "2026-09-23T13:19:18.652Z"}, {"entity": "publication", "iuid": "ffae1e4181c347cb9177c68008efad8e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ffae1e4181c347cb9177c68008efad8e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ffae1e4181c347cb9177c68008efad8e"}}, "title": "Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.", "authors": [{"family": "Jayaprasad", "given": "Suvratha", "initials": "S"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12d645d316a64a54ad02fb915cf9b2d6.json"}}, {"family": "Ellerstrand", "given": "Simon J", "initials": "SJ", "orcid": "0000-0003-2674-6997", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e36f041d79c240d2aa669a1e24e168d7.json"}}, {"family": "Rossini", "given": "Roberto", "initials": "R"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Pettersson", "given": "Olga V", "initials": "OV", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f513ec3fb924415a9e579d1c829c7d2d.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2a00756397a4aa58f539513e5b8b37f.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc83e7c8e44145778f170d3ac49c52a6.json"}}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae255687b53f4926b4cb9ad06dcf6edc.json"}}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Bradford", "given": "Tessa M", "initials": "TM", "orcid": "0000-0003-0607-1398", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41bad8c13b55485c998822fa4c43d267.json"}}, {"family": "Cooper", "given": "Steven J B", "initials": "SJB", "orcid": "0000-0002-7843-8438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/771a0a9bd4174d10ab02a1f2a08da9fb.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0451b7e0a83450698af8d37c522279e.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Kawakami", "given": "Takeshi", "initials": "T", "orcid": "0000-0002-9204-6852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/843ff3f21fde4acdb15729e96cb0ae4c.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/185297e474cc4e09b1f2087fb7d902a1.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4d3d53ea54b4ec293da675c9c63a0de.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "33", "issue": "23", "pages": "e17567", "issn-l": "0962-1083"}, "abstract": "The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo-XY sex chromosomes have independently evolved multiple times by X-autosome fusions with different autosomes. Here, we generated new chromosome-level assemblies for two chromosomal races representing karyotypes with and without neo-sex chromosomes (P24XY and P24X0), and sequence data of a third chromosomal race with a different neo-XY chromosome system (P25XY). Interestingly, these two neo-XY chromosomal races are formed by different X-autosome fusions (involving chr1 and chrB, respectively), and we found that both neo-Y chromosomes have partly ceased to recombine with their neo-X counterpart. We show that the neo-XY chromosomes have diverged through accumulation of SNPs and structural mutations, and that many neo-Y-linked genes have degenerated since recombination ceased. However, the non-recombining regions of neo-Y chromosomes host non-degenerated genes crucial for sex determination, such as sex-lethal and transformer, alongside genes associated with spermatogenesis, fertility, and reproduction, illustrating their integrative role as a masculinizing supergene. Contrary to expectations, the neo-Y chromosomes showed (slightly) lower density of transposable elements (TEs) compared to other genomic regions. The study reveals the unique dynamics of young sex chromosomes, with evolution of recombination suppression and pronounced decay of (some) neo-sex chromosome genes, and provides a compelling case illustrating how chromosomal fusions and post-fusion mutational processes contribute to the evolution of supergenes.", "doi": "10.1111/mec.17567", "pmid": "39475093", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11589690"}], "notes": [], "created": "2026-09-23T11:34:42.294Z", "modified": "2026-09-23T11:34:42.591Z"}, {"entity": "publication", "iuid": "7a08a2edb60e44dc8dd34cc96cf412cd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a08a2edb60e44dc8dd34cc96cf412cd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a08a2edb60e44dc8dd34cc96cf412cd"}}, "title": "Chromosome-level genome assembly of the morabine grasshopper Vandiemenella viatica19.", "authors": [{"family": "Li", "given": "Xuan", "initials": "X", "orcid": "0000-0003-0066-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ce54ca4d2f64483b3f53700f53aed30.json"}}, {"family": "Jayaprasad", "given": "Suvratha", "initials": "S"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae255687b53f4926b4cb9ad06dcf6edc.json"}}, {"family": "Cooper", "given": "Steven J B", "initials": "SJB", "orcid": "0000-0002-7843-8438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/771a0a9bd4174d10ab02a1f2a08da9fb.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Palacios-Gimenez", "given": "Octavio Manuel", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4d3d53ea54b4ec293da675c9c63a0de.json"}}], "type": "journal article", "published": "2024-09-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "11", "issue": "1", "pages": "997", "issn-l": "2052-4463"}, "abstract": "Morabine grasshoppers in the Vandiemenella viatica species group, which show karyotype diversity, have been studied for their ecological distribution and speciation in relation to their genetic and chromosomal diversity. They are good models for studying sex chromosome evolution as \"old\" and newly emerged sex chromosomes co-exist within the group. Here we present a reference genome for the viatica19 chromosomal race, that possesses the ancestral karyotype within the group. Using PacBio HiFi and Hi-C sequencing, we generated a chromosome-level assembly of 4.09 Gb in span, scaffold N50 of 429 Mb, and complete BUSCO score of 98.1%, containing 10 pseudo-chromosomes. We provide Illumina datasets of males and females, used to identify the X chromosome. The assembly contains 19,034 predicted protein-coding genes, and a total of 75.21% of repetitive DNA sequences. By leveraging HiFi reads, we mapped the genome-wide distribution of methylated bases (5mC and 6 mA). This comprehensive assembly offers a robust reference for morabine grasshoppers and supports further research into speciation and sex chromosome diversification within the group and its related species.", "doi": "10.1038/s41597-024-03858-0", "pmid": "39266578", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11393057"}, {"db": "pii", "key": "10.1038/s41597-024-03858-0"}], "notes": [], "created": "2026-09-23T14:28:16.935Z", "modified": "2026-09-23T14:28:17.050Z"}, {"entity": "publication", "iuid": "49d66041d7f143fda8d8dbfa7dc1bbdd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/49d66041d7f143fda8d8dbfa7dc1bbdd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/49d66041d7f143fda8d8dbfa7dc1bbdd"}}, "title": "An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12d645d316a64a54ad02fb915cf9b2d6.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio Manuel", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4d3d53ea54b4ec293da675c9c63a0de.json"}}, {"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8fccaeeed5bd43e98eb49003c72f050b.json"}}, {"family": "Olsen", "given": "Remi Andr\u00e9", "initials": "RA"}, {"family": "Alaei Kakhki", "given": "Niloofar", "initials": "N"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8607ae348d9e43b18809e9c95c5fe8be.json"}}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4eaf573973047ecb18f4557675bf800.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/127271f95a954d1da12d2ae4d393d90f.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8b109ad7c724c3f9db1732c2f93b175.json"}}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "G3", "issn": "2160-1836", "volume": "13", "issue": "6", "issn-l": "2160-1836"}, "abstract": "Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern black-eared wheatear (Oenanthe melanoleuca). This species is part of the Oenanthe hispanica complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50, 12.6 Mb; scaffold N50, 70 Mb), with 96% of the genome assembled at the chromosome level and 95.5% benchmarking universal single-copy orthologs (BUSCO) completeness. The nuclear genome was annotated with 18,143 protein-coding genes and 31,333 mRNAs (annotation BUSCO completeness, 98.0%), and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern black-eared wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.", "doi": "10.1093/g3journal/jkad088", "pmid": "37097035", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10234393"}, {"db": "pii", "key": "7141353"}], "notes": [], "created": "2026-09-23T11:21:58.575Z", "modified": "2026-09-23T11:21:58.676Z"}, {"entity": "publication", "iuid": "e160c54974b54c0bab1945ded7b60333", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e160c54974b54c0bab1945ded7b60333.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e160c54974b54c0bab1945ded7b60333"}}, "title": "The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12d645d316a64a54ad02fb915cf9b2d6.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4d3d53ea54b4ec293da675c9c63a0de.json"}}, {"family": "Blommaert", "given": "Julie", "initials": "J", "orcid": "0000-0003-1411-2313", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a5bd00bde5f430c974744c740723b81.json"}}, {"family": "Liu", "given": "Jing", "initials": "J"}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e0d6a411e00490a8e8a612c34480c6a.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Zhou", "given": "Qi", "initials": "Q"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fbbdf5987064ce7954279ccbc3857fb.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}], "type": "posted-content", "published": "2020-07-31", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.07.31.230854", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T13:49:57.637Z", "modified": "2026-09-23T13:49:57.752Z"}]}