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Old 07-04-2012, 01:29 PM   #1
Chuckytah
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Location: Barcelos, Braga, Portugal

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Question Water stress and Mycorrhization - Alpha diversity conclusions??

Hello all,

first of all I will made a brief resume about my thesis:
I had 2 sub-projects, project A - abiotic stress (water stress) and project M - biotic stress (mycorrhization). I need to find the genes involved in this stresses but my question now will be about alpha diversity.

Project A - water stress - I had 3 plants growing in 1 - less water, 2- medium water and 3- full water. And then the mRNA was extracted and send to pyrosequencing.
PROBLEM: Considering the alpha diversity, it has been calculated by MG-RAST and the number that in case 1, with less water, has been found about 40.000 different species and in 3, full of water, only 22.000 species, in 2 was a middle number about 30.000 species. Why this is verified? In less water were found more species cause the organisms in sample (soil and plant with contaminants, eg, insects) prefer less water? I dunno what conclusion should I write about it... any suggestions of reading or articles about this theme?

Project M - 2 plants growing: 1 is control and other is mycorrhized.And then the mRNA was extracted and send to pyrosequencing.
PROBLEM: Considering the alpha diversity, it has been shown by number that in mycorrhized, were found about 65.000 different species and in control, only 44.0000 species. Why this is verified? It is normal that in mycorrhized has more species because of the fungi, right?

Thanks so much for the help.
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Old 07-04-2012, 02:41 PM   #2
ECO
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Cool biology.

Not being an expert (or even a novice) in that field (and not being completely clear where the mRNA came from, the plants only or plants +environment) I would say that a reasonable start is to investigate the functional classes of genes that are activating under stress. You'll have to do more reading on the actual process, but there is a start here:

http://seqanswers.com/wiki/How-to/RN...tology_testing

...and googling for "rna-seq gene ontology" found a ton of papers and tools.
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Old 07-04-2012, 03:16 PM   #3
Chuckytah
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Location: Barcelos, Braga, Portugal

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Quote:
Originally Posted by ECO View Post
Cool biology.

Not being an expert (or even a novice) in that field (and not being completely clear where the mRNA came from, the plants only or plants +environment) I would say that a reasonable start is to investigate the functional classes of genes that are activating under stress. You'll have to do more reading on the actual process, but there is a start here:

http://seqanswers.com/wiki/How-to/RN...tology_testing

...and googling for "rna-seq gene ontology" found a ton of papers and tools.
Thanks so much for the answer. The mRNA came only from root sample, but there were always contaminants. My concern now it's to discover why the variation in alpha diversity... not the genes but thanks anyway
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