Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Angst, Pascal, Pombert, Jean-François, Ebert, Dieter, Fields, Peter D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
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
_version_ 1785114059212849152
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
work_keys_str_mv AT angstpascal nearchromosomelevelgenomeassemblyofthemicrosporidiumhamiltosporidiumtvaerminnensis
AT pombertjeanfrancois nearchromosomelevelgenomeassemblyofthemicrosporidiumhamiltosporidiumtvaerminnensis
AT ebertdieter nearchromosomelevelgenomeassemblyofthemicrosporidiumhamiltosporidiumtvaerminnensis
AT fieldspeterd nearchromosomelevelgenomeassemblyofthemicrosporidiumhamiltosporidiumtvaerminnensis