Discrete lineages within Alternaria alternata species group: identification using new highly variable loci and support from morphological characters

5.00
Hdl Handle:
http://hdl.handle.net/10547/576985
Title:
Discrete lineages within Alternaria alternata species group: identification using new highly variable loci and support from morphological characters
Authors:
Armitage, A.D.; Barbara, D.J.; Harrison, R.J.; Lane, C.R.; Sreenivasaprasad, Surapareddy; Woodhall, J.W.; Clarkson, J.P.
Abstract:
The Alternaria alternata species group is ubiquitous in the environment acting as saprotrophs, human allergens, and plant pathogens. Many morphological species have been described within the group and it is unclear whether these represent re-descriptions of the same species or discrete evolutionary taxa. Evolutionary relationships within the A. alternata species group were established using a phylogenetic approach based on functional genes. Sequencing of five highly variable loci identified three major lineages within the A. alternata species group. These loci included two loci previously shown to be variable within the Alternaria genus (endo-PG, Alt a1) as well as three new phylogenetic loci (TMA22, PGS1, and REV3) identified as highly variable based on publically available genome sequence data for Dothideomycete species. Results indicated that the three lineages have recently diverged and as such were considered as subspecies within a single species A. alternata. Lineages were identified as A. alternata ssp. arborescens, A. alternata ssp. tenuissima, and A. alternata ssp. gaisen in accordance with the placement of reference isolates. The phylogenetic results were supported by morphological analysis, which differentiated strains in A. alternata ssp. arborescens and A. alternata ssp. tenuissima and also aligned with previous morphological species descriptions for A. arborescens and A. tenuissima. However, phylogenetic analysis placed the morphologically described species A. alternata and A. mali within the A. alternata ssp. tenuissima and did not support them as discrete taxa. As A. alternata are of phytosanitary importance, the molecular loci used in this study offer new opportunities for molecular identification of isolates by national plant protection organizations.
Citation:
Armitage, A., Barbara, D. J., Harrison, R. J., Lane, C. R., Sreenivasaprasad, S., Woodhall, J. W. and Clarkson, J.P. (2015) 'Discrete lineages within Alternaria alternata species group: Identification using new highly variable loci with support from morphological characters'. Fungal Biology doi:10.1016/j.funbio.2015.06.012
Publisher:
Elsevier
Journal:
Fungal Biology
Issue Date:
Jul-2015
URI:
http://hdl.handle.net/10547/576985
DOI:
doi:10.1016/j.funbio.2015.06.012
Additional Links:
http://www.sciencedirect.com/science/article/pii/S1878614615001117
Type:
Article
Language:
en
ISSN:
1878-6146
Sponsors:
A.D. Armitage acknowledges the support of a Defra Plant Health Taxonomic fellowship.
Appears in Collections:
Environmental Science

Full metadata record

DC FieldValue Language
dc.contributor.authorArmitage, A.D.en
dc.contributor.authorBarbara, D.J.en
dc.contributor.authorHarrison, R.J.en
dc.contributor.authorLane, C.R.en
dc.contributor.authorSreenivasaprasad, Surapareddyen
dc.contributor.authorWoodhall, J.W.en
dc.contributor.authorClarkson, J.P.en
dc.date.accessioned2015-09-09T09:08:08Zen
dc.date.available2015-09-09T09:08:08Zen
dc.date.issued2015-07en
dc.identifier.citationArmitage, A., Barbara, D. J., Harrison, R. J., Lane, C. R., Sreenivasaprasad, S., Woodhall, J. W. and Clarkson, J.P. (2015) 'Discrete lineages within Alternaria alternata species group: Identification using new highly variable loci with support from morphological characters'. Fungal Biology doi:10.1016/j.funbio.2015.06.012en
dc.identifier.issn1878-6146en
dc.identifier.doidoi:10.1016/j.funbio.2015.06.012en
dc.identifier.urihttp://hdl.handle.net/10547/576985en
dc.description.abstractThe Alternaria alternata species group is ubiquitous in the environment acting as saprotrophs, human allergens, and plant pathogens. Many morphological species have been described within the group and it is unclear whether these represent re-descriptions of the same species or discrete evolutionary taxa. Evolutionary relationships within the A. alternata species group were established using a phylogenetic approach based on functional genes. Sequencing of five highly variable loci identified three major lineages within the A. alternata species group. These loci included two loci previously shown to be variable within the Alternaria genus (endo-PG, Alt a1) as well as three new phylogenetic loci (TMA22, PGS1, and REV3) identified as highly variable based on publically available genome sequence data for Dothideomycete species. Results indicated that the three lineages have recently diverged and as such were considered as subspecies within a single species A. alternata. Lineages were identified as A. alternata ssp. arborescens, A. alternata ssp. tenuissima, and A. alternata ssp. gaisen in accordance with the placement of reference isolates. The phylogenetic results were supported by morphological analysis, which differentiated strains in A. alternata ssp. arborescens and A. alternata ssp. tenuissima and also aligned with previous morphological species descriptions for A. arborescens and A. tenuissima. However, phylogenetic analysis placed the morphologically described species A. alternata and A. mali within the A. alternata ssp. tenuissima and did not support them as discrete taxa. As A. alternata are of phytosanitary importance, the molecular loci used in this study offer new opportunities for molecular identification of isolates by national plant protection organizations.en
dc.description.sponsorshipA.D. Armitage acknowledges the support of a Defra Plant Health Taxonomic fellowship.en
dc.language.isoenen
dc.publisherElsevieren
dc.relation.urlhttp://www.sciencedirect.com/science/article/pii/S1878614615001117en
dc.subjectAlternaria malien
dc.subjectdothideomyceteen
dc.subjectfungal barcodingen
dc.subjectpathotypeen
dc.subjectsectionen
dc.subjectspecies complexen
dc.titleDiscrete lineages within Alternaria alternata species group: identification using new highly variable loci and support from morphological charactersen
dc.typeArticleen
dc.identifier.journalFungal Biologyen
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