TY - JOUR

T1 - Transcriptome of the bivalve Limecola balthica L. from Western Pacific: A new resource for studies of European populations

AU - Юрченко, Антон Алексеевич

AU - Katolikova, N.

AU - Polev, D.

AU - Shcherbakova, I.

AU - Strelkov, P.

PY - 2018/7/1

Y1 - 2018/7/1

N2 - The Baltic clam Limecola balthica L. (Tellinidae) is broadly used in ecophysiological, toxicological, evolutionary and environmental monitoring studies. However, it is poorly studied in respect of genome and gene functions. We obtained a transcriptome of Limecola b. balthica from Kamchatka (Western Pacific) generated with the use of Illumina high-throughput sequencing. We annotated 11,374 proteins, including 53 from the oxidative phosphorylation pathway and a number of pollution-stress biomarkers, recovered 254,540 single nucleotide variants within two annotated transcriptomes including 25,330 scorable in the previously published European data. Our results confirmed the available allozyme data indicating that nuclear genomes of the clams from the Baltic Sea were intermediate in their genetic composition between the Pacific (L. b. balthica) and the Atlantic (L. b. rubra) subspecies. At the same time, the mitochondrial genomes of Limecola from Kamchatka were nearly identical to the single published genome from the Baltic. The genomic diversity in Limecola was found to be high and comparable with that of other marine mollusks (0.0138 and 0.0142 heterozygous positions in the two studied transcriptomes). The data obtained in our study are a valuable resource for further development of genomic markers for evolutionary genetic and ecophysiological studies of L. balthica complex.

AB - The Baltic clam Limecola balthica L. (Tellinidae) is broadly used in ecophysiological, toxicological, evolutionary and environmental monitoring studies. However, it is poorly studied in respect of genome and gene functions. We obtained a transcriptome of Limecola b. balthica from Kamchatka (Western Pacific) generated with the use of Illumina high-throughput sequencing. We annotated 11,374 proteins, including 53 from the oxidative phosphorylation pathway and a number of pollution-stress biomarkers, recovered 254,540 single nucleotide variants within two annotated transcriptomes including 25,330 scorable in the previously published European data. Our results confirmed the available allozyme data indicating that nuclear genomes of the clams from the Baltic Sea were intermediate in their genetic composition between the Pacific (L. b. balthica) and the Atlantic (L. b. rubra) subspecies. At the same time, the mitochondrial genomes of Limecola from Kamchatka were nearly identical to the single published genome from the Baltic. The genomic diversity in Limecola was found to be high and comparable with that of other marine mollusks (0.0138 and 0.0142 heterozygous positions in the two studied transcriptomes). The data obtained in our study are a valuable resource for further development of genomic markers for evolutionary genetic and ecophysiological studies of L. balthica complex.

KW - Assembly

KW - Hybridization

KW - Limecola balthica

KW - Macoma balthica

KW - Marine biomarkers

KW - Transcriptome

KW - EVOLUTIONARY

KW - READ ALIGNMENT

KW - MACOMA-BALTHICA

KW - MYTILUS-EDULIS

KW - GENE ONTOLOGY

KW - BIOMARKERS

KW - HYBRID SWARM

KW - BALTIC SEA

KW - GENERATION

KW - TOOL

UR - http://www.scopus.com/inward/record.url?scp=85045193567&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/transcriptome-bivalve-limecola-balthica-l-western-pacific-new-resource-studies-european-populations

U2 - 10.1016/j.margen.2018.03.007

DO - 10.1016/j.margen.2018.03.007

M3 - Article

VL - 40

SP - 58

EP - 63

JO - Marine Genomics

JF - Marine Genomics

SN - 1874-7787

ER -