I would like to the phylogenetic study on clinical isolate of Yeast.
I have some Yeast isolates most likely to be Saccharomyces sp, as tested by culture.
I found some genes were used for phylogenetic study on Yeast typing, including 18S rRNA, 26S RNA and Internal Transcribed Spacer Regions (ITS 1 and ITS 2).
Anyway, which one is the common one and any other suggestion.
Regards
One way to explore this, is to go to the NCBI/GenBank taxonomy browser and poke around there. Saccharomyces for example is here:
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4930
If you click the top link (Saccharomyces) it shows that there are over one million gene sequences from within this genus.
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4930&lvl=3&lin=f&keep=1&srchmode=1&unlock
Also in the table at the top right of that page are links to complete genome projects and "popsets".
"Popsets" are sets of sequences from population surveys, where the researchers have wanted to study the diversity of organisms in some type of population. An example from the Sacchaormyces taxonomy link that includes some Saccharomyces plus many other yeasts, is this one:
http://www.ncbi.nlm.nih.gov/popset/141603920
In this set, they used 26S rRNA sequences. 26S rRNA is very good for identifying which species a given isolate belongs to. It is helpful, if you have "unknown" organisms, to use a gene sequence such as 26S that has been sequenced in thousands of other isolates, so you can find out what others yours is closest to.
ITS (internal transcribed spacer) and other regions evolve more quickly than 26S rRNA and are more useful for studying strains or isolates within a single species.
For 26S rRNA the sequences from various Saccharomyces species are all more than 95% identical to each other. Saccharomyces vs Candida species are roughly 83% identical to each other.
Hi, those genes that you mentioned (18s, 26s and ITS) are the most commonly used. I would probably try 26s first, since it gives a nice resolution and has been historically used for species delimitation among yeasts, leading to the availability of a very large database of sequences. Best!
One way to explore this, is to go to the NCBI/GenBank taxonomy browser and poke around there. Saccharomyces for example is here:
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4930
If you click the top link (Saccharomyces) it shows that there are over one million gene sequences from within this genus.
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4930&lvl=3&lin=f&keep=1&srchmode=1&unlock
Also in the table at the top right of that page are links to complete genome projects and "popsets".
"Popsets" are sets of sequences from population surveys, where the researchers have wanted to study the diversity of organisms in some type of population. An example from the Sacchaormyces taxonomy link that includes some Saccharomyces plus many other yeasts, is this one:
http://www.ncbi.nlm.nih.gov/popset/141603920
In this set, they used 26S rRNA sequences. 26S rRNA is very good for identifying which species a given isolate belongs to. It is helpful, if you have "unknown" organisms, to use a gene sequence such as 26S that has been sequenced in thousands of other isolates, so you can find out what others yours is closest to.
ITS (internal transcribed spacer) and other regions evolve more quickly than 26S rRNA and are more useful for studying strains or isolates within a single species.
For 26S rRNA the sequences from various Saccharomyces species are all more than 95% identical to each other. Saccharomyces vs Candida species are roughly 83% identical to each other.
Dear all,
These are such very comprehensive answer. SIncerly thanks, Regards
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