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The draft genome of Ruditapes philippinarum (the Manila clam), a promising model system for mitochondrial biology

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journal contribution
posted on 2017-06-28, 23:21 authored by Fabrizio GhiselliFabrizio Ghiselli, Aleksey Komissarov, Liliana MilaniLiliana Milani, Joseph P. Dunham, Sophie Breton, Sergey V. Nuzhdin, Marco PassamontiMarco Passamonti
The Class Bivalvia is a highly successful and ancient group including 20,000+ known species. They represent a good model for studying adaptation (anoxia/hypoxia, salinity, temperature, ...), and they are useful bioindicators for monitoring the concentration of pollutants 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. A striking feature of bivalves is the presence of an unusual mitochondrial inheritance system: the Doubly Uniparental Inheritance (DUI), so far detected in ~100 bivalve species. In DUI species, two mitochondrial genomes (mtDNAs) are present: one is transmitted through eggs (F-type), the other through sperm (M-type); the amino acid p-distance between conspecific M and F genomes ranges from 10% to over 50%. DUI provides a unique point of view for studying mitochondrial biology. In DUI systems: i) males are naturally heteroplasmic, with very divergent mtDNAs; ii) it is possible to study mitochondrial inheritance and bottleneck by following germ line mitochondria during development; iii) mitochondria are under selection for male functions. Here we present the draft genome of the DUI species Ruditapes philippinarum (the Manila clam). DNA from a male individual was sequenced with 40x Illumina HiSeq and 30x PacBio RSII. The best de novo assembly was obtained with Canu assembler, with contig N50=76kb (gVolante BUSCO stats: complete 85.79%, partial 4.6%, missing 9.61%). Here we report the results of the first analyses and the technical challenges we faced, especially in de novo assembly.


Italian Ministry of Education, University and Research MIUR - FIR Programme no. RBFR13T97A funded to FG; Italian Ministry of Education, University and Research MIUR - SIR Programme no. RBSI14G0P5 funded to LM; Canziani bequest funded to MP.


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