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- Title
Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization.
- Authors
Gimmler, Anna; Stoeck, Thorsten
- Abstract
Environmental high-throughput sequencing (env HTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4- SSU r DNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization ( FISH). This powerful strategy allows to benefit from env HTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms.
- Subjects
PROTISTA; PHYLOGENY; MINES &; mineral resources; MICROBIAL ecology; NUCLEOTIDE sequencing; FLUORESCENCE in situ hybridization
- Publication
Environmental Microbiology Reports, 2015, Vol 7, Issue 4, p679
- ISSN
1758-2229
- Publication type
Article
- DOI
10.1111/1758-2229.12307