Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass

BMC Evolutionary Biology

Research Article

Ross C Mann¹  Piyumi N Ekanayake²  Kathryn M Guthridge²  Timothy I Sawbridge²  Inoka K Hettiarachchige³  John W Forster⁴  German C Spangenberg⁴ 

[1] Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Melbourne, Victoria, Australia;Dairy Futures Cooperative Research Centre, 3083, Melbourne, Victoria, Australia;Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Melbourne, Victoria, Australia;Molecular Plant Breeding Cooperative Research Centre, 3083, Melbourne, Victoria, Australia;Dairy Futures Cooperative Research Centre, 3083, Melbourne, Victoria, Australia;Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Melbourne, Victoria, Australia;School of Applied Systems Biology, La Trobe University, Bundoora, 3086, Melbourne, Victoria, Australia;Dairy Futures Cooperative Research Centre, 3083, Melbourne, Victoria, Australia;Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Melbourne, Victoria, Australia;School of Applied Systems Biology, La Trobe University, Bundoora, 3086, Melbourne, Victoria, Australia;Molecular Plant Breeding Cooperative Research Centre, 3083, Melbourne, Victoria, Australia;Dairy Futures Cooperative Research Centre, 3083, Melbourne, Victoria, Australia;

关键词: Pasture grass;    Whole genome sequencing;    Taxonomy;    Nuclear gene;    Mating type;    Progenitor;   

DOI  :  10.1186/s12862-015-0349-6

 received in 2015-03-02, accepted in 2015-04-14,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundPerennial ryegrass (Lolium perenne L.) is one of the most important species for temperate pastoral agriculture, forming associations with genetically diverse groups of mutualistic fungal endophytes. However, only two taxonomic groups (E. festucae var. lolii and LpTG-2) have so far been described. In addition to these two well-characterised taxa, a third distinct group of previously unclassified perennial ryegrass-associated endophytes was identified as belonging to a putative novel taxon (or taxa) (PNT) in a previous analysis based on simple sequence repeat (SSR) marker diversity. As well as genotypic differences, distinctive alkaloid production profiles were observed for members of the PNT group.ResultsA detailed phylogenetic analysis of perennial ryegrass-associated endophytes using components of whole genome sequence data was performed using complete sequences of 7 nuclear protein-encoding genes. Three independently selected genes (encoding a DEAD/DEAH box helicase [Sbp4], a glycosyl hydrolase [family 92 protein] and a MEAB protein), none of which have been previously used for taxonomic studies of endophytes, were selected together with the frequently used ‘house-keeping’ genes tefA and tubB (encoding translation elongation factor 1-α and β-tubulin, respectively). In addition, an endophyte-specific gene (perA for peramine biosynthesis) and the fungal-specific MT genes for mating-type control were included. The results supported previous phylogenomic inferences for the known species, but revealed distinctive patterns of diversity for the previously unclassified endophyte strains, which were further proposed to belong to not one but two distinct novel taxa. Potential progenitor genomes for the asexual endophytes among contemporary teleomorphic (sexual Epichloë) species were also identified from the phylogenetic analysis.ConclusionsUnique taxonomic status for the PNT was confirmed through comparison of multiple nuclear gene sequences, and also supported by evidence from chemotypic diversity. Analysis of MT gene idiomorphs further supported a predicted independent origin of two distinct perennial ryegrass-associated novel taxa, designated LpTG-3 and LpTG-4, from different members of a similar founder population related to contemporary E. festucae. The analysis also provided higher resolution to the known progenitor contributions of previously characterised perennial ryegrass-associated endophyte taxa.

【 授权许可】

Unknown   
© Hettiarachchige et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.