The draft genome of Ruditapes philippinarum (the Manila clam), a promising model system for mitochondrial biology
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Abstract
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 (86% complete, 5% fragmented, and 9% missing metazoan orthologs according to BUSCO). Here we report the results of the first analyses and the technical challenges we faced, especially with the de novo assembly.
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2017. The draft genome of Ruditapes philippinarum (the Manila clam), a promising model system for mitochondrial biology. PeerJ Preprints 5:e3096v1 https://doi.org/10.7287/peerj.preprints.3096v1Author comment
Poster presentation for the Open Symposium of SMBE 2017.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Fabrizio Ghiselli conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Aleksey Komissarov analyzed the data, reviewed drafts of the paper.
Liliana Milani conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.
Joseph P Dunham conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.
Sophie Breton reviewed drafts of the paper.
Sergey V Nuzhdin conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Marco Passamonti contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
The raw data and the genome assembly will be made publicly available when all the analyses will be completed.
Funding
This study was supported by the Italian Ministry of Education, University and Research (MIUR) FIR Programme no. RBFR13T97A funded to FG, MIUR SIR Programme no. RBSI14G0P5 funded to LM, Zumberge Foundation to SVN, and by the Canziani bequest funded to MP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.