Marine Microorganisms Mining

Question

[August]

How did people get marine microorganisms' gene sequence? Is there a database that contains a lot of sequences? How do the experiments proceed?

[Joe]

Get water -> extract DNA -> sequence genomes.

You might want to look at initiatives like TARA:

http://ocean-microbiome.embl.de/companion.html

https://www.ebi.ac.uk/services/tara-oceans-data

Of course NCBI is full of marine microbial data, though it is not necessarily curated as such.

There are lots of resources out there for these types of data - this is by no means an exhaustive list, and TARA probably isn't even the de facto data source, though it is one of the biggest studies AFAIK. This is not really my area though.

[Dunois]

Marine prokaryotes or eukaryotes? Most prokaryotes are sequenced "directly" via metagenomics approaches. Eukaryotes (mostly) depending on their size can be isolated by hand, or under a microscope, and sacrificed thereafter to extract nucleic acids for sequencing. (I do believe "eukaryotic" metagenomics exists as well.)

Answer 1

[Fatima]

Marine Sediment Metagenome

You can use a gene predictor (e.g. FragGeneScan) to predict the genes ....