Draft genome of the American Eel (<i>Anguilla rostrata</i>)

Pavey, Scott A.; Laporte, Martin; Normandeau, Éric; Gaudin, Jérémy; Létourneau, Louis; Boisvert, Sébastien; Corbeil, Jacques; Audet, Céline; Bernatchez, Louis

doi:10.1111/1755-0998.12608

Cited by 24 publications

(31 citation statements)

References 46 publications

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“…Running the ABySS 2.0 assembly stage (abyss-bloom-dbg) led to a low False Positive Rate (<0.05%). The N50 for the contig assembly was 3.2Kb with 551,875 contigs (discarding contigs <1Kb, given that small contigs likely represent artefacts and provide little information for the overall genome assembly (Pavey et al 2016;Murgarella et al 2016, see Table 3). Once these were corrected and paired-end, matepairs and long read information were added, the scaffolds N50 increased to 5.5Kb, with 2.3% of nucleotides represented as "N" (see Table 3 for the summary statistics and Table 4 for overall genome assembly statistics acquired from QUAST analysis).…”

Section: Resultsmentioning

confidence: 99%

“…In addition, we predicted that, contrary to most other sequenced bivalve species, heterozygosity of V. ellipsiformis would be relatively low, given its history of genetic bottlenecks due to repeated glaciations events over its current geographical distribution (Zanatta & Harris 2013). Genomic resources are needed to help identifying genes essential for survival (and/or the genetic mechanisms that led to decline) and ultimately for developing monitoring tools for endangered biodiversity and plan sustainable recoveries (Pavey et al 2016;Savolainen et al 2013). In addition, a sequenced genome will help answer more fundamental questions of sex-determination (Breton et al 2011; and genome evolution through comparative genomics approaches (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach

Renaut

Guerra

Hoeh

et al. 2018

Preprint

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Freshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of Venustaconcha ellipsiformis, which will serve as a valuable genomic resource given the ecological value and unique “doubly uniparental inheritance” mode of mitochondrial DNA transmission of freshwater mussels. The genome described here was obtained by combining high coverage short reads (65X genome coverage of Illumina paired-end and 11X genome coverage of mate-pairs sequences) with low coverage Pacific Biosciences long reads (0.3X genome coverage). Briefly, the final scaffold assembly accounted for a total size of 1.54Gb (366,926 scaffolds, N50 = 6.5Kb, with 2.3% of “N” nucleotides), representing 86% of the predicted genome size of 1.80Gb, while over one third of the genome (37.5%) consisted of repeated elements and more than 85% of the core eukaryotic genes were recovered. Given the repeated genetic bottlenecks of V. ellipsiformis populations as a result of glaciations events, heterozygosity was also found to be remarkably low (0.6%), in contrast to most other sequenced bivalve species. Finally, we reassembled the full mitochondrial genome and found six polymorphic sites with respect to the previously published reference. This resource opens the way to comparative genomics studies to identify genes related to the unique adaptations of freshwater mussels and their distinctive mitochondrial inheritance mechanism.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach

Renaut

Guerra

Hoeh

et al. 2018

Preprint

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“…Except for the IGF‐1R sequence, which was obtained from the draft annotated American Eel genome (Pavey et al. ), the messenger RNA (mRNA) sequences for the reference and target genes were not available for American Eels in the GenBank databases. Therefore, oligonucleotide primers were designed using Primer‐BLAST (Basic Local Alignment Search Tool) for each reference and candidate gene of interest based on available mRNA sequences from genus Anguilla found in the National Center for Biotechnology Information (NCBI) database (http://www.ncbi.nlm.nih.gov/tools/primer-blast/ accessed November 23, 2015).…”

Section: Methodsmentioning

confidence: 99%

River‐Specific Gene Expression Patterns Associated with Habitat Selection for Key Hormone‐Coding Genes in Glass Eel‐Stage American Eels

et al. 2018

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The glass eel stage of the American Eel Anguilla rostrata marks the onset of the catadromous migration into estuarine or freshwater habitats, and the endocrine mechanisms underlying this habitat selection are still not well understood. Using a candidate genes approach, the aim of this study was to test for different patterns of gene expression related to (1) salinity preferences and/or (2) capture site to predict physiological differences between migratory behaviors. We performed analyses revealing the expression of genes coding for key hormonal factors or their receptors on glass eel‐stage American Eels collected at the mouths of three rivers on the east coast of Canada (Grande‐Rivière‐Blanche, St. Lawrence estuary; Rivière‐Saint‐Jean, Gaspé Peninsula; and the Mersey River, Nova Scotia); eels from the three systems displayed different salinity preferences (brackish water/salt water/freshwater) under laboratory conditions. Transcripts from genes coding for prolactin (PRL), thyroid‐stimulating hormone β subunit, type‐2 iodothyronine deiodinase (DIO‐2), thyroid hormone receptors αa and αb (THRαa and THRαb), growth hormone (GH), insulin‐like growth factor 1 (IGF‐1), and their respective receptors (GH‐R1 and IGF‐1R) were all detected in glass eels. No differences in the expression patterns were detected pertaining to salinity preference, but strong differences were found among rivers. Rivière‐Saint‐Jean glass eels, which were the longest and the least pigmented among the three rivers, were characterized by the highest expression of PRL, DIO‐2, and THRαb. Those from Grande‐Rivière‐Blanche showed an increase in IGF‐1R. Glass eels captured from these two rivers also exhibited the highest expression of GH and GH‐R1. Overall, these results confirm gene × environment interactions at the gene expression level when glass eels settle into their continental habitat. As such, our results also support the concept of the presence of different ecotypes in the Atlantic Canadian coast and in the estuary and Gulf of St. Lawrence.

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“…rostrata [66], as well as transcriptome shotgun assemblies (TSA) from A. anguilla [67][68][69] (Dasypus novemcinctus, Dn). All sequences are given in the Supplemental Information, where also the relevant database can be inferred according to the name/identity we have given the sequence.…”

Section: Collection Of Sequencesmentioning

confidence: 99%

Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

Mikalsen

Tausen

Kongsstovu³

2019

Preprint

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Background: Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). Results: The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. Conclusions: Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.

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Draft genome of the American Eel (Anguilla rostrata)

Cited by 24 publications

References 46 publications

Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach

Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach

River‐Specific Gene Expression Patterns Associated with Habitat Selection for Key Hormone‐Coding Genes in Glass Eel‐Stage American Eels

Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

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