The Draft Genome of Ruditapes philippinarum (the Manila clam)

Bivalve molluscs are a highly successful and ancient Class, including over 20,000 known species, and they are an interesting group for evolutionary and biodiversity studies. Bivalves represent a good model for studying adaptation to anoxia/hypoxia, salinity, and temperature, and they are useful bioindicators for monitoring the concentration of pollutants and heavy metals in the water. They also make up an important source of food all over the world, with a production corresponding to ~20% of the global aquaculture yield; clams are first in production, followed by oysters, mussels, and scallops. A striking feature of bivalves—and the main reason behind this project—is the presence of an unusual mitochondrial inheritance system: the Doubly Uniparental Inheritance (DUI), so far detected in ~50 bivalve species, belonging to seven families. In DUI species, two mitochondrial genomes (mtDNAs) are present: one is transmitted through eggs (F-type, for female-inherited), the other through sperm (M-type, for male-inherited), and the amino acid p-distance between conspecific M and F genomes ranges from 10% to over 50%. DUI provides a unique and privileged point of view for studying several fundamental aspects of eukaryote biology. In DUI systems: i) males are naturally heteroplasmic, with two very divergent mtDNAs; ii) it is possible to follow germ line mitochondria during development (to study mitochondrial inheritance and bottleneck); iii) mitochondria are under selection for male functions (e.g.: spermatogenesis, sperm swimming); iv) there are two coexisting mitochondrial genomes in the same nuclear background (coevolution, conflicts). All these interesting biological features are in sharp contrast with the lack of genomic resources about bivalve molluscs.Here we present the draft genome of the DUI species Ruditapes philippinarum (the Manila clam). DNA from a male individual was sequenced with x40 Illumina HiSeq and with x30 PacBio RSII. We have tried to assembly this dataset with all available hybrid or PacBio only assembly pipelines. The best results were obtained with PacBio reads assembled by Canu assembler with contig N50 76 kb, and 39.92% completed and 74.60% partial genes according to CEGMA. We annotated families of tandem and dispersed repeats, we found a new highly repeated dispersed element, and characterised the major families of satellite DNA. We report the results of the first analyses as well as the technical challenges we faced, especially during the phase of de novo assembly.