FN Archimer Export Format
PT J
TI Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna
BT 
AF NIKOLIC, Natacha
   DUTHOY, Stephanie
   DESTOMBES, Antoine
   BODIN, Nathalie
   WEST, Wendy
   PUECH, Alexis
   BOURJEA, Jerome
AS 1:1;2:2;3:2;4:3;5:4;6:1;7:1;
FF 1:PDG-RBE-DOI;2:;3:;4:;5:;6:PDG-RBE-DOI;7:PDG-RBE-DOI;
C1 IFREMER, Inst Francais Rech Exploitat Mer, Delegat La Reunion, Le Port 97822, Reunion.
   GENOSCREEN, F-59000 Lille, France.
   IRD, UMR EME 212, Mahe, Seychelles.
   Dept Agr Forestry & Fisheries, ZA-8012 Cape Town, South Africa.
C2 IFREMER, FRANCE
   GENOSCREEN, FRANCE
   IRD, SEYCHELLES
   DEPT AGR FORESTRY & FISHERIES, SOUTH AFRICA
SI LA REUNION
SE PDG-RBE-DOI
UM MARBEC
IN WOS Ifremer jusqu'en 2018
   copubli-france
   copubli-p187
   copubli-int-hors-europe
   copubli-sud
IF 3.057
TC 3
UR https://archimer.ifremer.fr/doc/00293/40460/39151.pdf
LA English
DT Article
AB Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87–90%), and assignment index. ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24–27%), low assignment index and significant inbreeding. Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species—Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.
PY 2015
PD NOV
SO Plos One
SN 1932-6203
PU Public Library Science
VL 10
IS 11
UT 000364398700053
DI 10.1371/journal.pone.0141830
ID 40460
ER

EF