How to recover a 16S rRNA gene from genome reads?

Question

[fhsantanna]

I have sequenced a bacterial genome with Illumina 2x300 pb kit and after that I have assembled the genome using SPADES (and also A5 pipeline).

The problem is that the draft genome does not present a full 1500 pb rRNA 16S gene. It is expected, since assemblers do not do a great deal with repetitive regions.

However, I need the full-length 16S rRNA gene for my research purposes (taxonomy). Is that a way to recover it from the genome reads (>30 x coverage)?

PS: I have found a promising program named Reago, but it did not worked for me. It seems it does not deal with reads over 101 bp.

Answer 1

[Chris Fields]

I have used SortMeRNA in the past to filter rRNA, and it has been used for the flip purpose (e.g. retaining only rRNA reads for taxonomic analysis). You could try this in combination with assembly to see if you can get a more-resolved 16s region.

[Chris Fields]

I should add, I've also started looking into phyloFlash for this, which can use SortMeRNA 'under the hood'. Seems very nice.

Answer 2

[jeremieaauger]

I think that you should to use MetaPhlAn!

"MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data."

You are wasting sequencing information by concentrating on 16S only. The software uses all the marker genes available in your data. This software comes from the reputable microbiome software suite "Biobakery".

Check it out! http://huttenhower.sph.harvard.edu/metaphlan

Cheers, Jérémie

Answer 3

[cschu181]

I second the SortMeRNA approach from Chris Fields. Alternatively, you could align your reads against an as closely as possible related 16S rRNA sequence and then do guided assembly (StringTie?) or deNovo (using only the aligning reads) from there.

[fhsantanna]

Nice suggestions. I'll give a try. Soon I post a feedback.

Answer 4

[felipe.zoujiro]

Hi, you can/could use Metaxa2 (http://microbiology.se/software/metaxa2/). It is a software for extracting 16S rDNA reads from metagenomic/genomic reads. I have used it and worked pretty good.