PMID- 26061246
OWN - NLM
STAT- MEDLINE
DCOM- 20160414
LR  - 20150722
IS  - 1758-2229 (Electronic)
IS  - 1758-2229 (Linking)
VI  - 7
IP  - 4
DP  - 2015 Aug
TI  - Mining environmental high-throughput sequence data sets to identify divergent 
      amplicon clusters for phylogenetic reconstruction and morphotype visualization.
PG  - 679-86
LID - 10.1111/1758-2229.12307 [doi]
AB  - Environmental high-throughput sequencing (envHTS) 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 rDNA 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 envHTS 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.
CI  - (c) 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.
FAU - Gimmler, Anna
AU  - Gimmler A
AD  - Department of Ecology, University of Kaiserslautern, Erwin-Schrodinger-Strasse 14, 
      Kaiserslautern, D-67633, Germany.
FAU - Stoeck, Thorsten
AU  - Stoeck T
AD  - Department of Ecology, University of Kaiserslautern, Erwin-Schrodinger-Strasse 14, 
      Kaiserslautern, D-67633, Germany.
LA  - eng
SI  - GENBANK/KR028987
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Environ Microbiol Rep
JT  - Environmental microbiology reports
JID - 101499207
RN  - 0 (DNA Primers)
RN  - 0 (DNA, Protozoan)
RN  - 0 (DNA, Ribosomal)
RN  - 0 (RNA, Ribosomal, 18S)
SB  - IM
MH  - *Biodiversity
MH  - Cluster Analysis
MH  - *Computational Biology
MH  - DNA Primers/genetics
MH  - DNA, Protozoan/chemistry/genetics
MH  - DNA, Ribosomal/chemistry/genetics
MH  - *Environmental Microbiology
MH  - High-Throughput Nucleotide Sequencing
MH  - In Situ Hybridization, Fluorescence
MH  - Molecular Sequence Data
MH  - *Phylogeography
MH  - Polymerase Chain Reaction
MH  - RNA, Ribosomal, 18S/genetics
MH  - Sequence Analysis, DNA
EDAT- 2015/06/11 06:00
MHDA- 2016/04/15 06:00
CRDT- 2015/06/11 06:00
PHST- 2015/04/04 00:00 [received]
PHST- 2015/06/03 00:00 [accepted]
PHST- 2015/06/11 06:00 [entrez]
PHST- 2015/06/11 06:00 [pubmed]
PHST- 2016/04/15 06:00 [medline]
AID - 10.1111/1758-2229.12307 [doi]
PST - ppublish
SO  - Environ Microbiol Rep. 2015 Aug;7(4):679-86. doi: 10.1111/1758-2229.12307.