{"entity": "researcher", "timestamp": "2026-07-14T04:31:20.461Z", "family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "affiliations": ["Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa"}}, "publications": [{"entity": "publication", "iuid": "c119e76b14514e52b934f2411b16aff8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c119e76b14514e52b934f2411b16aff8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c119e76b14514e52b934f2411b16aff8"}}, "title": "Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis.", "authors": [{"family": "Edelbroek", "given": "Bart", "initials": "B", "orcid": "0000-0002-5184-0873", "researcher": {"href": "https://publications.scilifelab.se/researcher/164d0bef1b3e48668e136dbe0d2e8736.json"}}, {"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Koskiniemi", "given": "Sanna", "initials": "S"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "dataset", "published": "2024-06-22", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "11", "issue": "1", "pages": "678", "issn-l": "2052-4463"}, "abstract": "Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni- to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.", "doi": "10.1038/s41597-024-03513-8", "pmid": "38909042", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11193728"}, {"db": "pii", "key": "10.1038/s41597-024-03513-8"}], "notes": [], "created": "2024-06-28T06:39:46.481Z", "modified": "2024-11-25T10:20:11.383Z"}, {"entity": "publication", "iuid": "7a0719a5a1cc4cef963a4832ec073fd7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a0719a5a1cc4cef963a4832ec073fd7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a0719a5a1cc4cef963a4832ec073fd7"}}, "title": "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.", "authors": [{"family": "Edelbroek", "given": "Bart", "initials": "B", "orcid": "0000-0002-5184-0873", "researcher": {"href": "https://publications.scilifelab.se/researcher/164d0bef1b3e48668e136dbe0d2e8736.json"}}, {"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Liao", "given": "Zhen", "initials": "Z"}, {"family": "Lundberg", "given": "Torgny", "initials": "T"}, {"family": "Noegel", "given": "Angelika A", "initials": "AA"}, {"family": "Eichinger", "given": "Ludwig", "initials": "L", "orcid": "0000-0003-1594-6117", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2b977ccf8604c2a9a048b21878fc828.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "journal article", "published": "2024-04-12", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "52", "issue": "6", "pages": "3121-3136", "issn-l": "0305-1048"}, "abstract": "MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.", "doi": "10.1093/nar/gkae109", "pmid": "38375870", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11014262"}, {"db": "pii", "key": "7611030"}], "notes": [], "created": "2024-10-22T07:38:55.161Z", "modified": "2024-11-25T10:25:30.684Z"}, {"entity": "publication", "iuid": "6c457acdccf942f7ad5f2a040919b53a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c457acdccf942f7ad5f2a040919b53a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c457acdccf942f7ad5f2a040919b53a"}}, "title": "Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas.", "authors": [{"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Avesson", "given": "Lotta", "initials": "L"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Liao", "given": "Zhen", "initials": "Z"}, {"family": "Eichinger", "given": "Ludwig", "initials": "L"}, {"family": "Noegel", "given": "Angelika", "initials": "A"}, {"family": "Gl\u00f6ckner", "given": "Gernot", "initials": "G"}, {"family": "Schaap", "given": "Pauline", "initials": "P"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "31", "issue": "3", "pages": "436-447", "issn-l": "1088-9051"}, "abstract": "Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, Dictyostelium discoideum However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal multicellular development. Here, we investigated Class I RNA evolution and its connection to multicellular development. We identified a large number of new Class I RNA genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis confirmed that our search approach identifies expressed Class I RNA genes with high accuracy and sensitivity and that the RNAs are developmentally regulated. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share highly conserved structure and sequence motifs. In addition, Class I RNA genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. Our results show that Class I RNA is an ancient class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Based on previous functional analyses and the presented evolutionary investigation, we hypothesize that Class I RNAs were involved in evolution of multicellularity in Dictyostelia.", "doi": "10.1101/gr.272856.120", "pmid": "33479022", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "gr.272856.120"}, {"db": "pmc", "key": "PMC7919456"}], "notes": [], "created": "2021-12-10T10:43:43.443Z", "modified": "2021-12-10T10:43:43.527Z"}]}