2016
DOI: 10.1111/1755-0998.12608
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Draft genome of the American Eel (Anguilla rostrata)

Abstract: Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American eel. This ge… Show more

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Cited by 24 publications
(31 citation statements)
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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%
See 1 more Smart Citation
“…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%
“…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%
“…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%