TY - JOUR
T1 - Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture
AU - Boutet, Isabelle
AU - Alves Monteiro, Homère J.
AU - Baudry, Lyam
AU - Takeuchi, Takeshi
AU - Bonnivard, Eric
AU - Billoud, Bernard
AU - Farhat, Sarah
AU - Gonzales-Araya, Ricardo
AU - Salaun, Benoit
AU - Andersen, Ann C.
AU - Toullec, Jean Yves
AU - Lallier, François H.
AU - Flot, Jean François
AU - Guiglielmoni, Nadège
AU - Guo, Ximing
AU - Li, Cui
AU - Allam, Bassem
AU - Pales-Espinosa, Emmanuelle
AU - Hemmer-Hansen, Jakob
AU - Moreau, Pierrick
AU - Marbouty, Martial
AU - Koszul, Romain
AU - Tanguy, Arnaud
N1 - Publisher Copyright:
© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.
PY - 2022/11
Y1 - 2022/11
N2 - The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species in the foreshore, obtaining a reference genome becomes essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio, Illumina, 10X linked, and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein-coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.
AB - The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species in the foreshore, obtaining a reference genome becomes essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio, Illumina, 10X linked, and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein-coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.
KW - Martelia
KW - aquaculture
KW - flat oyster
KW - genome
KW - transposable elements
UR - https://www.scopus.com/pages/publications/85135886394
U2 - 10.1111/eva.13462
DO - 10.1111/eva.13462
M3 - Article
AN - SCOPUS:85135886394
SN - 1752-4563
VL - 15
SP - 1730
EP - 1748
JO - Evolutionary Applications
JF - Evolutionary Applications
IS - 11
ER -