Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

Abstract Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Hel...

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Autores principales:	Dániel G. Knapp, Julianna B. Németh, Kerrie Barry, Matthieu Hainaut, Bernard Henrissat, Jenifer Johnson, Alan Kuo, Joanne Hui Ping Lim, Anna Lipzen, Matt Nolan, Robin A. Ohm, László Tamás, Igor V. Grigoriev, Joseph W. Spatafora, László G. Nagy, Gábor M. Kovács
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e4ef080f84db41c5baa1fda4e96573be
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spelling	oai:doaj.org-article:e4ef080f84db41c5baa1fda4e96573be2021-12-02T15:07:57ZComparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi10.1038/s41598-018-24686-42045-2322https://doaj.org/article/e4ef080f84db41c5baa1fda4e96573be2018-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-24686-4https://doaj.org/toc/2045-2322Abstract Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.Dániel G. KnappJulianna B. NémethKerrie BarryMatthieu HainautBernard HenrissatJenifer JohnsonAlan KuoJoanne Hui Ping LimAnna LipzenMatt NolanRobin A. OhmLászló TamásIgor V. GrigorievJoseph W. SpataforaLászló G. NagyGábor M. KovácsNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-13 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dániel G. Knapp Julianna B. Németh Kerrie Barry Matthieu Hainaut Bernard Henrissat Jenifer Johnson Alan Kuo Joanne Hui Ping Lim Anna Lipzen Matt Nolan Robin A. Ohm László Tamás Igor V. Grigoriev Joseph W. Spatafora László G. Nagy Gábor M. Kovács Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi
description	Abstract Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.
format	article
author	Dániel G. Knapp Julianna B. Németh Kerrie Barry Matthieu Hainaut Bernard Henrissat Jenifer Johnson Alan Kuo Joanne Hui Ping Lim Anna Lipzen Matt Nolan Robin A. Ohm László Tamás Igor V. Grigoriev Joseph W. Spatafora László G. Nagy Gábor M. Kovács
author_facet	Dániel G. Knapp Julianna B. Németh Kerrie Barry Matthieu Hainaut Bernard Henrissat Jenifer Johnson Alan Kuo Joanne Hui Ping Lim Anna Lipzen Matt Nolan Robin A. Ohm László Tamás Igor V. Grigoriev Joseph W. Spatafora László G. Nagy Gábor M. Kovács
author_sort	Dániel G. Knapp
title	Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi
title_short	Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi
title_full	Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi
title_fullStr	Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi
title_full_unstemmed	Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi
title_sort	comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/e4ef080f84db41c5baa1fda4e96573be
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Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

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