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      • Record: found
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      The genome sequence of a solitary sea squirt, Ascidia mentula (Müller, 1776)

      data-paper
      Author(s): 1 , 1 , Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective, Darwin Tree of Life Consortium a ,
      Publication date (Electronic):
      Journal: Wellcome Open Research
      Publisher: F1000 Research Limited
      Keywords: Ascidia mentula, (a solitary sea squirt), genome sequence, chromosomal, Phlebobranchia

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          Abstract

          We present a genome assembly from an individual Ascidia mentula (the (a solitary sea squirt); Chordata; Ascidiacea; Phlebobranchia; Ascidiidae). The genome sequence is 197.0 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.46 kilobases in length.

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          Most cited references30

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          BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

          Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis … (2015)
          Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
          Article 0 comments Cited 4269 times – based on 0 reviews     Review now
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            A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

            Suhas S.P. Rao, Miriam H Huntley, Neva C Durand … (2014)
            We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs "facing" one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats. Copyright © 2014 Elsevier Inc. All rights reserved.
            Article 0 comments Cited 2745 times – based on 0 reviews     Review now
            Article has an altmetric score of 433
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              MITOS: improved de novo metazoan mitochondrial genome annotation.

              Matthias Bernt, Alexander Donath, Frank Jühling … (2013)
              About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.
              Article 0 comments Cited 2181 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                John Bishop: Role: InvestigationRole: ResourcesRole: Writing – Original Draft PreparationRole: Writing – Review & Editing
                Christine Wood: Role: InvestigationRole: Resources
                Journal
                Journal ID (nlm-ta): Wellcome Open Res
                Journal ID (iso-abbrev): Wellcome Open Res
                Title: Wellcome Open Research
                Publisher: F1000 Research Limited (London, UK )
                ISSN (Electronic): 2398-502X
                Publication date (Electronic): 29 December 2023
                Publication date Collection: 2023
                Volume: 8
                Electronic Location Identifier: 583
                Affiliations
                [1 ]The Marine Biological Association, Plymouth, England, UK
                [1 ]Universidade do Porto, Porto, Porto District, Portugal
                [1 ]UMR7144, Sorbonne Universite, Roscoff, Bretagne, France
                [2 ]Department of Marine Sciences, Tjärnö Marine Laboratory, Gothenburg University, 452 96 Strömstad, Strömstad,, Sweden
                Author notes

                No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Article
                DOI: 10.12688/wellcomeopenres.20415.1
                PMC ID: 11109543
                PubMed ID: 38779044
                SO-VID: a6836a27-5bdb-489e-a800-ef84b8d65390
                Copyright © Copyright: © 2023 Bishop J et al.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 16 November 2023
                Funding
                Funded by: Wellcome Trust
                Award ID: 218328
                Funded by: Wellcome Trust
                Award ID: 206194
                This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194) and the Darwin Tree of Life Discretionary Award (218328).
                The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Data Note
                Subject: Articles

                Keywords: ascidia mentula,(a solitary sea squirt),genome sequence,chromosomal,phlebobranchia
                Data availability:
                Keywords: ascidia mentula, (a solitary sea squirt), genome sequence, chromosomal, phlebobranchia

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