FN Archimer Export Format
PT J
TI Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach
BT 
AF NANJAPPA, Deepak
   AUDIC, Stephane
   ROMAC, Sarah
   KOOISTRA, Wiebe H. C. F.
   ZINGONE, Adriana
AS 1:1;2:2;3:2;4:1;5:1;
FF 1:;2:;3:;4:;5:;
C1 Stn Zool Anton Dohrn, Naples, Italy.
   Univ Sorbonne, UPMC, CNRS, EPEP,UMR,Stn Biol Roscoff, Roscoff, France.
C2 STN ZOOL ANTON DOHRN, ITALY
   UNIV PARIS 06, FRANCE
IN DOAJ
IF 3.234
TC 34
UR https://archimer.ifremer.fr/doc/00374/48494/48846.pdf
   https://archimer.ifremer.fr/doc/00374/48494/48847.eps
   https://archimer.ifremer.fr/doc/00374/48494/48848.eps
   https://archimer.ifremer.fr/doc/00374/48494/48849.eps
   https://archimer.ifremer.fr/doc/00374/48494/48850.eps
   https://archimer.ifremer.fr/doc/00374/48494/48851.eps
   https://archimer.ifremer.fr/doc/00374/48494/48852.eps
   https://archimer.ifremer.fr/doc/00374/48494/48853.eps
   https://archimer.ifremer.fr/doc/00374/48494/48854.eps
   https://archimer.ifremer.fr/doc/00374/48494/48855.xlsx
   https://archimer.ifremer.fr/doc/00374/48494/48856.pdf
LA English
DT Article
BO Neomysis
AB Background: Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family. Methodology/Principal Findings: We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay. Conclusions/Significance: Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the diversity of this ancient diatom family appears to be low, at least at the level of the marker used in this study.
PY 2014
PD AUG
SO Plos One
SN 1932-6203
PU Public Library Science
VL 9
IS 8
UT 000341302700017
DI 10.1371/journal.pone.0103810
ID 48494
ER

EF