THE DRAFT GENOME OF Ruditapes philippinarum (THE MANILA CLAM) Ruditapes philippinarum (Bivalvia Veneridae) Synonyms: Venerupis philippinarum, Tapes philippinarum, Venerupis japonica, Tapes japonica. Common Names: Japanese littleneck, Manila clam C-value = 1.97 pg (Genome Size = 1.93 Gb) Sequencing 1.PacBio RSII P6-C4 Chemistry, 10-50 Kb BluePippin size selected libraries, 54 SMRTcells. Coverage ~30x. 2. Illumina HiSeq 2500, 2x250 bp, 1 short insert library (450-500bp) + 1 long insert library (1500-1700bp). Coverage ~40x. UCI Genomics University of California, Irvine Why R. philippinarum? 1. BIVALVIA is a highly successful and ancient Class (20,000+ known species). Important group for EVOLUTIONARY and BIODIVERSITY studies. 2. FOOD: Bivalve aquaculture production: 13.2+ million metric tons (20% of the global aquaculture production). Clams are first in production (5 million tons), followed by oysters (4.7 million tons), mussels (1.8 million tons), and scallops (1.6 million tons). 3. GOOD MODEL FOR STUDYING ADAPTATION: anoxia and hypoxia (intertidal zones, buried in sediment); salinity and temperature (same species, different environments). 3. BIOINDICATORS: they filter water to get food and oxygen accumulating heavy metals and pollutants. 4. EXCEPTIONAL MODEL FOR STUDYING MITOCHONDRIAL INHERITANCE AND EVOLUTION: THE DOUBLY UNIPARENTAL INHERITANCE (DUI) UPC Genome Core University of Southern California, Los Angeles [email protected] www.mozoolab.unibo.it Follow on Twitter Download the Poster Fabrizio Ghiselli, Aleksey Komissarov, Liliana Milani, Joseph P. Dunham, Sophie Breton, Sergey V. Nuzhdin, Marco Passamonti a. Natural heteroplasmy b. Coevolution, conflicts c. Mitochondria under selection for male functions d. Mitochondrial inheritance and bottleneck e. Role of mitochondria in germ line development f. Mitochondrial recombination R. philippinarum Complete 99 40% 1,967 Mb 30X + 40X R. philippinarum Partial 185 75% [Modified from: Murgarella et al. 2016 PLoS ONE 15;11(3):e0151561] De novo assembly We have tried to assembly the data with all available hybrid or PacBio-only assembly pipelines. The best results were obtained with PacBio reads assembled with Canu. Major problems: 1. High heterozygosity 2. Large number of tandem repeats 3. Many repeats larger than PacBio reads 4. Correction and scaffolding of PacBio reads Now what? Right now we are working on PacBio correction, and on scaffolding of PacBio reads using Illumina super-reads.