Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats.
The flat oyster (Ostrea edulis) is one of the most appreciated molluscs in Europe, but its production has been greatly reduced by the parasite Bonamia ostreae. Here, new generation genomic resources were used to analyse the repetitive fraction of the oyster genome, with the aim of developing molecular markers to face this main oyster production challenge. The resulting oyster database, consists of two sets of 10,318 and 7159 unique contigs (4.8 Mbp and 6.8 Mbp in total length) representing the oyster's genome (WG) and haemocyte transcriptome (HT), respectively. A total of 1083 sequences were identified as TE-derived, which corresponded to 4.0% of WG and 1.1% of HT. They were clustered into 142 homology groups, most of which were assigned to the Penelope order of retrotransposons, and to the Helitron and TIR DNA-transposons. Simple repeats and rRNA pseudogenes, also made a significant contribution to the oyster's genome (0.5% and 0.3% of WG and HT, respectively).The most frequent short tandem repeats identified in WG were tetranucleotide motifs while trinucleotide motifs were in HT. Forty identified microsatellite loci, 20 from each database, were selected for technical validation. Success was much lower among WG than HT microsatellites (15% vs 55%), which could reflect higher variation in anonymous regions interfering with primer annealing. All microsatellites developed adjusted to Hardy-Weinberg proportions and represent a useful tool to support future breeding programmes and to manage genetic resources of natural flat oyster beds.
Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain; Laboratori d'Ictiologia Genètica, Department de Biologia, Facultat de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain. Electronic address: manuel.vera@usc.es.
Manuel
M
Vera
Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain; Xenómica Comparada de Parásitos Humanos, IDIS, Santiago de Compostela, Galicia, Spain.
Xabier
X
Bello
Departamento de Matemática Aplicada, Facultad de Matemáticas, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
Jose-Antonio
JA
Álvarez-Dios
Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
Belen G
BG
Pardo
Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
Laura
L
Sánchez
School of Biology & Environmental Science, University College Dublin, Dublin, Ireland; School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, North Mall, Cork, Ireland.
Jens
J
Carlsson
School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, North Mall, Cork, Ireland.
Jeanette E L
JE
Carlsson
Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain; Xenómica Comparada de Parásitos Humanos, IDIS, Santiago de Compostela, Galicia, Spain.
Carolina
C
Bartolomé
Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain; Xenómica Comparada de Parásitos Humanos, IDIS, Santiago de Compostela, Galicia, Spain.
Xulio
X
Maside
Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
Paulino
P
Martinez
D000818:Animals; D004251:DNA Transposable Elements / Q000235:genetics*; D016678:Genome; D018895:Microsatellite Repeats / Q000235:genetics*; D049895:Ostrea / Q000235:genetics*
D004251:DNA Transposable Elements
Genome resources; Microsatellite validation; Ostrea edulis; Short tandem repeats; Transposable elements