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Near chromosome–level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis
Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magni...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10542269/ https://www.ncbi.nlm.nih.gov/pubmed/37565496 http://dx.doi.org/10.1093/g3journal/jkad185 |
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author | Angst, Pascal Pombert, Jean-François Ebert, Dieter Fields, Peter D |
author_facet | Angst, Pascal Pombert, Jean-François Ebert, Dieter Fields, Peter D |
author_sort | Angst, Pascal |
collection | PubMed |
description | Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents the first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences (PacBio), and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56% interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism. |
format | Online Article Text |
id | pubmed-10542269 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-105422692023-10-03 Near chromosome–level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis Angst, Pascal Pombert, Jean-François Ebert, Dieter Fields, Peter D G3 (Bethesda) Genome Report Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents the first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences (PacBio), and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56% interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism. Oxford University Press 2023-08-11 /pmc/articles/PMC10542269/ /pubmed/37565496 http://dx.doi.org/10.1093/g3journal/jkad185 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/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. |
spellingShingle | Genome Report Angst, Pascal Pombert, Jean-François Ebert, Dieter Fields, Peter D Near chromosome–level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis |
title | Near chromosome–level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis |
title_full | Near chromosome–level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis |
title_fullStr | Near chromosome–level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis |
title_full_unstemmed | Near chromosome–level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis |
title_short | Near chromosome–level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis |
title_sort | near chromosome–level genome assembly of the microsporidium hamiltosporidium tvaerminnensis |
topic | Genome Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10542269/ https://www.ncbi.nlm.nih.gov/pubmed/37565496 http://dx.doi.org/10.1093/g3journal/jkad185 |
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