Suggest Papers In Metagenomics

Question

[User 9158]

Can anyone suggest me a recent paper (say after 2009) which talks about application/effect of metagenomics in agriculture or plant genome analysis?

Answer 1

[Michael]

I have to disappoint you partially regarding plant genome analysis, because metagenomics involves communities of organisms, mainly microbial, (something that possibly also the paper mentioned by Khader will tell you). So, metagenomics does not apply if you have a single organism, like a plant. One application of metagenomics to agriculture, and that is possibly what you meant, is the study of bacterial communities in the soil, or specifically root associated bacteria, e.g. bacteria involved in nitrogen fixation.

Searched for 'soil metagenomics' in pubmed, here is one paper which seems to be an introduction: http://www.ncbi.nlm.nih.gov/pubmed/21076656

Or this one: about rhizobial communities: Effects of Medicago truncatula genetic diversity, rhizobial competition, and strain effectiveness on the diversity of a natural sinorhizobium species community. Rangin C, Brunel B, Cleyet-Marel JC, Perrineau MM, Béna G. Appl Environ Microbiol. 2008
http://www.ncbi.nlm.nih.gov/pubmed/18658290 This comes maybe closest to what you were asking as it investigates the interaction of the plant genetic variation and the rhizobial commity. (It is not a metagenomics approach in the strict sense, because they use few loci, instead of whole-metagenome sequencing)

Here is a recent article about metagenomics and biogas production, another different but agriculture-related topic: http://www.ncbi.nlm.nih.gov/pubmed/21297863

Answer 2

[Khader Shameer]

A primer on metagenomics Wooley JC, Godzik A, Friedberg I. PLoS Comput Biol. 2010 Feb 26;6(2):e1000667.

Answer 3

[Science_Robot]

Complete Genome Sequence of Citrus Huanglongbing Bacterium, Candidatus Liberibacter asiaticus Obtained Through Metagenomics

http://ddr.nal.usda.gov/bitstream/10113/33731/1/IND44241273.pdf

Answer 4

[Larry_Parnell]

Just out - taking a proteomics view:

Characterization of plant-bacterial interactions using proteomic approaches by Cheng, Z., Woody, O.Z., Glick, B.R., McConkey, B.J. in Current Proteomics, 7 ( 4 ) pp. 244 - 257.

Added 27 Apr 2011: Or you may want to look at the paper entitled Targeted metabolic reconstruction: A novel approach for the characterization of plant-pathogen interactions, by Pinzón, A., Rodriguez-R, L.M., González, A., Bernal, A., Restrepo, S. 2011 Briefings in Bioinformatics, 12, art. no. bbq009, pp. 151-162.

Added 6 May 2011: Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria by Rodrigo Mendes, Marco Kruijt, et al. at http://www.sciencemag.org/content/early/2011/05/04/science.1203980.full.pdf