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      Genome assembly and annotation of the mermithid nematode Mermis nigrescens

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          Abstract

          Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. A lack of genomic resources has limited the expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long reads and 10X Chromium link reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 83.98%. mRNA-seq reads from different sized nematodes (≤2 cm, 3.5–7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host–parasite interactions of mermithid nematodes.

          Most cited references55

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

            Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
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              Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

              Massively-parallel cDNA sequencing has opened the way to deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here, we present the Trinity methodology for de novo full-length transcriptome reconstruction, and evaluate it on samples from fission yeast, mouse, and whitefly – an insect whose genome has not yet been sequenced. Trinity fully reconstructs a large fraction of the transcripts present in the data, also reporting alternative splice isoforms and transcripts from recently duplicated genes. In all cases, Trinity performs better than other available de novo transcriptome assembly programs, and its sensitivity is comparable to methods relying on genome alignments. Our approach provides a unified and general solution for transcriptome reconstruction in any sample, especially in the complete absence of a reference genome.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press (US )
                2160-1836
                April 2024
                01 February 2024
                01 February 2024
                : 14
                : 4
                : jkae023
                Affiliations
                Department of Anatomy, University of Otago , Dunedin 9016, New Zealand
                Department of Organismic & Evolutionary Biology, Harvard University , Cambridge, MA 02138, USA
                Department of Zoology, University of Otago , Dunedin 9016, New Zealand
                Department of Anatomy, University of Otago , Dunedin 9016, New Zealand
                Department of Anatomy, University of Otago , Dunedin 9016, New Zealand
                Author notes
                Corresponding author: Department of Anatomy, University of Otago, Dunedin 9016, New Zealand. Email: eddy.dowle@ 123456otago.ac.nz (E.D.)
                Corresponding author: Department of Anatomy, University of Otago, Dunedin 9016, New Zealand. Email: neil.gemmell@ 123456otago.ac.nz (N.J.G.)

                Conflicts of interest. The author(s) declare no conflicts of interest.

                Author information
                https://orcid.org/0000-0003-1512-7218
                https://orcid.org/0000-0003-1390-1206
                Article
                jkae023
                10.1093/g3journal/jkae023
                10989877
                38301266
                0ae4dbdb-206f-4f6f-ac40-2c2b0dfd36be
                © The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 29 December 2023
                : 22 January 2024
                : 05 March 2024
                Page count
                Pages: 7
                Funding
                Funded by: Royal Society Te Apārangi Marsden Fund;
                Award ID: 16-UOO-152
                Categories
                Genome Report
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140

                Genetics
                mermis nigrescens,nematode,hybrid genome assembly,repeatome,genome annotation
                Genetics
                mermis nigrescens, nematode, hybrid genome assembly, repeatome, genome annotation

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