A de novo approach to disentangle partner identity and function in holobiont systems.

ABSTRACT:

Background

Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept.

Results

We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defin

SUBMITTER: Meng A 

PROVIDER: S-EPMC5994019 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature