The fungal ITS region varies roughly, with some exceptions, between approximately 450 and 750 base pairs (bp) in length. This feature makes it hard to compute the phylogenetic diversity. I used the tranditional method to align sequences and builded phylogenetic tree, but the bootstrap value was very low (most branches < 50%). So I suspect the tree is not robust to evaluate the fungal phylogenetic diversity. I wonder are there any feasible method to evaluate the fungal phylogenetic diveristy by ITS2 sequencing?Thank you for your kind reply.
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Hi Zhang
Tou can read this reference1
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4110421/
2
https://www.mycobiology.or.kr/Synapse/Data/PDFData/0184MB/mb-29-121.pdf
3
https://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.2012.01473.x/full
4
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159043
5
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131069
6
https://dash.harvard.edu/bitstream/handle/1/3153301/Pfister_PhylogeneticDiversityCore.pdf?sequence=1
8
https://miuse.mie-u.ac.jp/bitstream/10076/2607/1/AA110034360370301.pdf
Hi Laith,
Thank you for your help. I will read the materials you suggested. Thank you！
Hi Laith,
Thanks for your suggestion, I know how to construct ITS2 phylogenetic tree, but I don't know how to find the secondary structures by MFOLD and generate consensus structure by 4SALE. Could you give me an example if you know how to do? Thank you!
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