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In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies

Montoliu-Nerin, Merce and Sanchez-Garcia, Marisol and Bergin, Claudia and Kutschera, Verena Esther and Johannesson, Hanna and Bever, James D. and Rosling, Anna (2021). In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies. Frontiers in fungal biology. 2 , 716385
[Research article]

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Abstract

Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.

Authors/Creators:Montoliu-Nerin, Merce and Sanchez-Garcia, Marisol and Bergin, Claudia and Kutschera, Verena Esther and Johannesson, Hanna and Bever, James D. and Rosling, Anna
Title:In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
Series Name/Journal:Frontiers in fungal biology
Year of publishing :2021
Volume:2
Article number:716385
Number of Pages:13
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Evolutionary Biology
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biological Systematics
Keywords:genomics, phylogenetic, single nuclei sequencing, topology, Glomeromycota
URN:NBN:urn:nbn:se:slu:epsilon-p-115524
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-115524
Additional ID:
Type of IDID
DOI10.3389/ffunb.2021.716385
ID Code:26757
Faculty:S - Faculty of Forest Sciences
Department:(NL, NJ) > Dept. of Forest Mycology and Plant Pathology
(S) > Dept. of Forest Mycology and Plant Pathology
Deposited By: SLUpub Connector
Deposited On:20 Jan 2022 08:25
Metadata Last Modified:20 Jan 2022 08:31

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