Hi everyone,
I'm firstly interested in identifying Alternaria cultures to species level. After this, I will have a look at a specific pathotype. In this regard, would it be sufficient to use the ITS region for the initial identification to species level? I'll be happy if it can just tell me if a specific culture is Alternaria alternate or not. I appreciate your time.
Thanks,
Pieter
ITS region along with Inter simple sequence repeat markers (ISSR) can be used to identify and differentiate between Alternaria sp. Just sequencing the ITS region and comparing from NCBI database (blast) can also be done for identification.
You can refer the following publications.
1. Molecular identification and genetic variation of Alternaria species isolated from tomatoes using ITS1 sequencing and inter simple sequence repeat methods (Mohammadi A and Seifollah B, 2019).
Morphological-based Identification and molecular confirmation is important.
In addition to ITS region other marker genes are used
please check the files below
Article Alternaria redefined
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4774270/
ITS region considered the universal barcode region to differentiate between fungal species (Schoch et al. 2012: https://www.pnas.org/content/109/16/6241/). The ITS region can efficiently discriminate between closely related species and has been used to differentiate between different species within the genus Altenaria. The link below provide detailed information on using ITS to differentiate between toxigenic Alternaria species and also provide different primer pairs and PCR conditions to amplify the ITS region. Sequencing the ITS region and BLAST search within NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) can accurately identify the Alternaria species.
Phologeny of Alternaria fungi known to produce host-specific toxins on the basis of variation in internal transcribed spacers of ribosomal DNA
https://link.springer.com/content/pdf/10.1007/BF00310821.pdf
All the best
Hello Johannes, ITS is a good starting locus for most Fungi, but most genera require additional markers to identify taxa to an accurately monophyletic species. The One Stop Shop and GOPHY series of articles provide good reviews of proven multilocus markers for many plant pathogenic genera, including Alternaria:
Article Genera of phytopathogenic fungi: GOPHY 3
https://onestopshopfungi.org/16097-2/
For most Pleosporalean fungi like Alternaria we use ITS, GPD, and TEF1a.
Good Luck!
ITS region +ISSR is a very good tool to differentiate among Alternaria species, in addition, you need also to go deeply to differentiate between races with biochemical tools
ITS and mt ssu rDNA can also used for identification of Alternaria spp.
Best Regard
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