27The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia 28 to Europe and North America, causing billions of dollars in damage and dramatically altering 29 invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for 30 Dreissena or related bivalves, with nearly 450 million years of divergence between zebra 31 mussels and its closest sequenced relative. Although the D. polymorpha genome is highly 32 repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to 33 generate the highest quality molluscan assembly to date. Through comparative analysis and 34 transcriptomics experiments we have gained insights into processes that likely control the 35 invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and 36 thermal tolerance. We identified multiple intact Steamer-Like Elements, a retrotransposon that 37 has been linked to transmissible cancer in marine clams. We also found that D. polymorpha 38 have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it 39 the largest observed in Eumetazoa. Together these findings create a rich resource for invasive 40 species research and control efforts.41 42 44 49 Laurentian Great Lakes region alone 6 , where Dreissena cause extensive damage to 50 hydropower, recreation and tourism industries, and lakefront property 7,8 . Dense infestations 51smother and outcompete native benthic species and remove large amounts of phytoplankton 52 from lakes and rivers, causing population declines and extinctions of native freshwater mussels 53 and other invertebrates, damage to fish populations 9-14 , and dramatic restructuring of aquatic 54 food webs [15][16][17] . The congener D. rostriformis (the quagga mussel), while far less widespread 55 than zebra mussels in inland waters, has ecologically replaced zebra mussels in much of the 56 Laurentian Great Lakes proper and in deep European lakes, and may cause even greater 57 ecological damage in those systems 18-20 . 58 The ongoing European and North American invasions (Fig. 1c-e) have spurred an explosion 59 in research effort on Dreissena, particularly focused on physiology, autecology, and ecosystem 60 impacts 21 . Aside from molecular systematic and population genetic studies 1,22-25 , comparatively 61 little genetic work has been accomplished, with transcriptomes from a few tissues 26,27 being the 62 only genomic resources.
63Bivalves are a diverse Class of Mollusca with over 10,000 described species in marine and 64 freshwater environments 28,29 . To date, complete genomes have been sequenced and analyzed 65 in only eight species-most of them marine organisms of commercial value (Fig. 1b,
66Supplemental Table 1). Yet 21 invasive bivalve species cause damage to aquatic and marine 67 ecosystems worldwide 30 and only the golden mussel, Limnoperna fortunei 31 has a published 68 genome available (the quagga mussel is also being sequenced at present 32 ). Moreover, the 69 divergence ti...