We isolated one fungi from the soil, and from its morphology we concluded it must be a Cladosporium genera ( a filamentous fungi , a mold ). I've revised different methods, but I dont know what is the best one for our objectives, we only need to know what kind of Cladosporium it is. I revised for sequencing the ITS 1, ITS 2 and 5.8S of rRNA gene, or using specific gene sequences, like actin, calmodulin, translation elongation factor (1-α) and histone H3, but I dont know which one is better.
I think that would depend on how deep you want to go into the characterization of the species. As you can see in the link below, ITS1, ITS2 and 5.8S rDNA are enough to distinguish most of the species in the study. But for some closely-related species, such as C. psycrotolerans and C. langeronii, the use of the more variable sequences of tubulin or actin is necessary for identification.
So, depending on the species, you could go only with ITS sequences for identification (I guess that's all you need), or use other gene sequences if interested in distinguish without a doubt from other closely-related species.
http://www.cbs.knaw.nl/publications/1058/06%20Phylogeny%20and%20ecology%20of%20the%20ubiquitous%20saprobe%20Cladosporium%20sphaerospermum,with%20descriptions%20of%20seven%20new%20species%20from%20hypersaline%20environments.pdf
since you only need to know what cladosporum it is, i think sequencing the ITS regions should suffice for you
I have used ITS and beta-tubulin to identify some fungi. For me ITS was better than beta-tubulin, Just one of the fungi I could not identify using ITS. If you need protocols to ITS and beta-tubulin, I attached my paper for you. I hope it could be hopeful.
Fernanda
Dear, ITS 1, ITS 2 and 5.8S of rRNA are a good choice for species-level identification of fungi and many other species, and it is quite easy to do (most sequencer now can read the whole sequence, you just need 2 primers, Forward/Reverse).
However, if the comparison of your sequences with available sequences in NCBI does not give you a satisfactory identification of your fungi, you may consider other gene as well. As said Siddharth Anand, it may be enough for your objective.
IT'S is powerful for identification of several fungi.
However if you are considering Botryosphaeria species or forma specialis of Fusarium species, then IT'S is not enough. You need to go for the translation elongation factor gene.
All the best
Can we use the term molecular identification and molecular characterization interchangeably?
I, too, would start with the ITS region.
Some related reading:
https://www.researchgate.net/publication/235601668_Incorporating_molecular_data_in_fungal_systematics_a_guide_for_aspiringresearchers?ev=prf_pub
https://www.researchgate.net/publication/255483379_Towards_a_unified_paradigm_for_sequence-based_identification_of_Fungi?ev=prf_pub
Article Incorporating molecular data in fungal systematics: A guide ...
Article Towards a unified paradigm for sequence-based identification of Fungi
An ITS sequence is a good start.
https://www.researchgate.net/publication/235601668_Incorporating_molecular_data_in_fungal_systematics_a_guide_for_aspiringresearchers
Article Incorporating molecular data in fungal systematics: A guide ...
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