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A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis

The root systems of most plant species are aided by the soil-foraging capacities of symbiotic arbuscular mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM f...

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Autores principales: Manley, Bethan F, Lotharukpong, Jaruwatana S, Barrera-Redondo, Josué, Llewellyn, Theo, Yildirir, Gokalp, Sperschneider, Jana, Corradi, Nicolas, Paszkowski, Uta, Miska, Eric A, Dallaire, Alexandra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10234402/
https://www.ncbi.nlm.nih.gov/pubmed/36999556
http://dx.doi.org/10.1093/g3journal/jkad077
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author Manley, Bethan F
Lotharukpong, Jaruwatana S
Barrera-Redondo, Josué
Llewellyn, Theo
Yildirir, Gokalp
Sperschneider, Jana
Corradi, Nicolas
Paszkowski, Uta
Miska, Eric A
Dallaire, Alexandra
author_facet Manley, Bethan F
Lotharukpong, Jaruwatana S
Barrera-Redondo, Josué
Llewellyn, Theo
Yildirir, Gokalp
Sperschneider, Jana
Corradi, Nicolas
Paszkowski, Uta
Miska, Eric A
Dallaire, Alexandra
author_sort Manley, Bethan F
collection PubMed
description The root systems of most plant species are aided by the soil-foraging capacities of symbiotic arbuscular mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just emerging. Presented here is a close to T2T genome assembly of the model AM fungus Rhizophagus irregularis DAOM197198, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of R. irregularis, alongside short- and long-read RNA-Sequencing data, was used to produce a comprehensive annotation catalog of gene models, repetitive elements, small RNA loci, and DNA cytosine methylome. A phylostratigraphic gene age inference framework revealed that the birth of genes associated with nutrient transporter activity and transmembrane ion transport systems predates the emergence of Glomeromycotina. While nutrient cycling in AM fungi relies on genes that existed in ancestor lineages, a burst of Glomeromycotina-restricted genetic innovation is also detected. Analysis of the chromosomal distribution of genetic and epigenetic features highlights evolutionarily young genomic regions that produce abundant small RNAs, suggesting active RNA-based monitoring of genetic sequences surrounding recently evolved genes. This chromosome-scale view of the genome of an AM fungus genome reveals previously unexplored sources of genomic novelty in an organism evolving under an obligate symbiotic life cycle.
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spelling pubmed-102344022023-06-02 A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis Manley, Bethan F Lotharukpong, Jaruwatana S Barrera-Redondo, Josué Llewellyn, Theo Yildirir, Gokalp Sperschneider, Jana Corradi, Nicolas Paszkowski, Uta Miska, Eric A Dallaire, Alexandra G3 (Bethesda) Genome Report The root systems of most plant species are aided by the soil-foraging capacities of symbiotic arbuscular mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just emerging. Presented here is a close to T2T genome assembly of the model AM fungus Rhizophagus irregularis DAOM197198, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of R. irregularis, alongside short- and long-read RNA-Sequencing data, was used to produce a comprehensive annotation catalog of gene models, repetitive elements, small RNA loci, and DNA cytosine methylome. A phylostratigraphic gene age inference framework revealed that the birth of genes associated with nutrient transporter activity and transmembrane ion transport systems predates the emergence of Glomeromycotina. While nutrient cycling in AM fungi relies on genes that existed in ancestor lineages, a burst of Glomeromycotina-restricted genetic innovation is also detected. Analysis of the chromosomal distribution of genetic and epigenetic features highlights evolutionarily young genomic regions that produce abundant small RNAs, suggesting active RNA-based monitoring of genetic sequences surrounding recently evolved genes. This chromosome-scale view of the genome of an AM fungus genome reveals previously unexplored sources of genomic novelty in an organism evolving under an obligate symbiotic life cycle. Oxford University Press 2023-03-31 /pmc/articles/PMC10234402/ /pubmed/36999556 http://dx.doi.org/10.1093/g3journal/jkad077 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
Manley, Bethan F
Lotharukpong, Jaruwatana S
Barrera-Redondo, Josué
Llewellyn, Theo
Yildirir, Gokalp
Sperschneider, Jana
Corradi, Nicolas
Paszkowski, Uta
Miska, Eric A
Dallaire, Alexandra
A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis
title A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis
title_full A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis
title_fullStr A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis
title_full_unstemmed A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis
title_short A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis
title_sort highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus rhizophagus irregularis
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10234402/
https://www.ncbi.nlm.nih.gov/pubmed/36999556
http://dx.doi.org/10.1093/g3journal/jkad077
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