101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens

Haridas, Sajeet; Castanera Andrés, Raúl; Culley, D. E.; Daum, C.; Ramírez Nasto, Lucía; Alfaro Sánchez, Manuel

101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens

dc.contributor.author	Haridas, Sajeet
dc.contributor.author	Castanera Andrés, Raúl
dc.contributor.author	Culley, D. E.
dc.contributor.author	Daum, C.
dc.contributor.author	Ramírez Nasto, Lucía
dc.contributor.author	Alfaro Sánchez, Manuel
dc.contributor.department	Institute for Multidisciplinary Research in Applied Biology - IMAB	en
dc.date.accessioned	2020-08-05T06:00:24Z
dc.date.available	2020-08-05T06:00:24Z
dc.date.issued	2020
dc.description.abstract	Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.	en
dc.description.sponsorship	This manuscript has been authored by an author at Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231 with the U.S. Department of Energy. R. A. and I. V. G. were supported by the NSF grants DEB-1354625 and IOS-1456958. Sequencing of Dothideomycetes genomes were conducted as part of the 1000 Fungal Genomes Project supported by the JGI Community Sequencing Project #662.	en
dc.format.extent	13 p.
dc.format.mimetype	application/pdf	en
dc.identifier.doi	10.1016/j.simyco.2020.01.003
dc.identifier.issn	0166-0616
dc.identifier.uri	https://academica-e.unavarra.es/handle/2454/37656
dc.language.iso	eng	en
dc.publisher	Westerdijk Fungal Biodiversity Institute	en
dc.relation.ispartof	Studies in Mycology, 2020, 96, 141-153	en
dc.relation.publisherversion	https://doi.org/10.1016/j.simyco.2020.01.003
dc.rights	© 2020 Westerdijk Fungal Biodiversity Institute. Production and hosting by ELSEVIER B.V. This is an open access article under the CC BY-NC-ND license.	en
dc.rights.accessRights	info:eu-repo/semantics/openAccess
dc.rights.uri	https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject	Fungal evolution	en
dc.subject	Genome-based prediction	en
dc.subject	Machine-learning	en
dc.subject	New taxa	en
dc.title	101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens	en
dc.type	info:eu-repo/semantics/article
dc.type.version	info:eu-repo/semantics/publishedVersion
dspace.entity.type	Publication
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