A1 Refereed original research article in a scientific journal
Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing
Authors: Mikhail Yu. Ozerov, Freed Ahmad, Riho Gross, Lilian Pukk, Siim Kahar, Veljo Kisand, Anti Vasemägi
Publisher: GENETICS SOCIETY AMERICA
Publication year: 2018
Journal: G3: genes, genomes, genetics
Journal name in source: G3-GENES GENOMES GENETICS
Journal acronym: G3-GENES GENOM GENET
Volume: 8
Issue: 12
First page : 3737
Last page: 3743
Number of pages: 7
ISSN: 2160-1836
eISSN: 2160-1836
DOI: https://doi.org/10.1534/g3.118.200768(external)
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/39178303(external)
The Eurasian perch (Perca fluviatilis) is the most common fish of the Percidae family and is widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries, and a promising freshwater aquaculture species in Europe. However, despite its high ecological, economical and societal importance, the available genomic resources for P. fluviatilis are rather limited. In this work, we report de novo assembly and annotation of the whole genome sequence of perch. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a draft perch genome approximate to 1.0 Gbp assembly (scaffold N-50 = 6.3 Mb; the longest individual scaffold of 29.3 Mb; BUSCO completeness of 88.0%), which included 281.6 Mb of putative repeated sequences. The perch genome assembly presented here, generated from small amount of starting material (0.75 ng) and a single linked-read library, is highly continuous and considerably more complete than the currently available draft of P. fluviatilis genome. A total of 23,397 protein-coding genes were predicted, 23,171 (99%) of which were annotated functionally from either sequence homology or protein signature searches. Linked-read technology enables fast, accurate and cost-effective de novo assembly of large non-model eukaryote genomes. The highly continuous assembly of the Eurasian perch genome presented in this study will be an invaluable resource for a range of genetic, ecological, physiological, ecotoxicological, functional and comparative genomic studies in perch and other fish species of the Percidae family.
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