Next-generation sequencing of Dreissena polymorpha transcriptome sheds light on its mitochondrial DNA

Soroкa, Мarianna; Rymaszewska, Anna; Sanko, Tomasz Janusz; Przyłucka, Aleksandra; Lubośny, Marek; Śmietanka, Beata; Burzyński, Artur

doi:10.1007/s10750-017-3088-4

Cited by 9 publications

(13 citation statements)

References 58 publications

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“…GC content plots (blue) based on 40 bp sliding window. Annotations based on sequence similarity to previously published partial mitochondrial genome 26 . Coding regions are in green and red, and the three large repeat blocks are colored turquoise, blue, and purple.…”

Section: Resultsmentioning

confidence: 99%

“…In the initial assembly we recovered a single contig containing the D. polymorpha mitochondrial genome (Figure 2b). A partial D. polymorpha mitogenome sequence was previously published 26 , but contained a gap which short-read sequencing and targeted PCR were unable to resolve. PacBio and Oxford Nanopore sequencing (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…5). Eumetazoan mitogenomes, with few exceptions, generally lack length variation and non-coding DNA content 26 . Among these few exceptions are the long enigmatic mitogenomes of scallops 50 , but unlike scallops the coding genes of D. polymorpha remain contiguous, instead of being interrupted by interspersed repeats.…”

Section: Resultsmentioning

confidence: 99%

“…This assembly was polished for indels via Pilon using Illumina reads as with the nuclear genome, and a single substitution error in the coding region was manually edited (c.14475 C>A, G184W) based on strong support from Illumina reads (data not shown). The mitochondrial genome was annotated based a previously published partial mitochondrial sequence 26 in Geneious using the “Annotate from Database” function with a 98% similarity cutoff. The origin point was set to place the tRNA-Val annotation at base 48, matching the previously published sequence.…”

Section: Methodsmentioning

confidence: 99%

“…1c-e) have spurred an explosion in research effort on Dreissena , particularly focused on physiology, autecology, and ecosystem impacts 21 . Aside from molecular systematic and population genetic studies 1,22–25 , comparatively little genetic work has been accomplished, with transcriptomes from a few tissues 26,27 being the only genomic resources.…”

Section: Introductionmentioning

confidence: 99%

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The Genome of the Zebra Mussel,Dreissena polymorpha: A Resource for Invasive Species Research

McCartney

Auch

Kono

et al. 2019

Preprint

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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...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The Genome of the Zebra Mussel,Dreissena polymorpha: A Resource for Invasive Species Research

McCartney

Auch

Kono

et al. 2019

Preprint

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Conservation of freshwater bivalves at the global scale: diversity, threats and research needs

et al. 2018

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Bivalves are ubiquitous members of freshwater ecosystems and responsible for important functions and services. The present paper revises freshwater bivalve diversity, conservation status and threats at the global scale and discusses future research needs and management actions. The diversity patterns are uneven across the globe with hotspots in the interior basin in the United States of America (USA), Central America, Indian subcontinent and Southeast Asia. Freshwater bivalves are affected by multiple threats that vary across the globe; however, pollution and natural system (habitat) modifications being consistently found as the most impacting. Freshwater bivalves are among the most threatened groups in the world with 40% of the species being near threatened, threatened or extinct, and among them the order Unionida is the most endangered. We suggest that global cooperation between scientists, managers, politicians and general public, and application of new technologies (new generation sequencing and remote sensing, among others) will strengthen the quality of studies on the natural history and conservation of freshwater bivalves. Finally, we introduce

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mtDNA analysis of Mytilopsis (Bivalvia, Dreissenidae) invasion in Brazil reveals the existence of two species

et al. 2018

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Next-generation sequencing of Dreissena polymorpha transcriptome sheds light on its mitochondrial DNA

Cited by 9 publications

References 58 publications

The Genome of the Zebra Mussel,Dreissena polymorpha: A Resource for Invasive Species Research

The Genome of the Zebra Mussel,Dreissena polymorpha: A Resource for Invasive Species Research

Conservation of freshwater bivalves at the global scale: diversity, threats and research needs

mtDNA analysis of Mytilopsis (Bivalvia, Dreissenidae) invasion in Brazil reveals the existence of two species

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