The Genome of the Steller Sea Lion (Eumetopias jubatus)

Abstract

The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabases. As a measure of completeness, 95.1% of 4104 highly conserved mammalian genes were found to be complete within the assembly. Further annotation identified 19,668 protein coding genes. The assembled genome sequence and underlying sequence data can be found at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA475770.

Nanopore sequencing technology, bioinformatics and applications

“…The increasing yield, read length and accuracy of ONT data enable much more time-and cost-efficient genome assembly of all sizes of genomes, from bacteria of several megabases 109 , fruit fly 139,156 , fish 143,144,157 , blood clam 158 , banana 159 , cabbage 159 and walnut 160,161 , all of whose genomes are in the hundreds of megabases, as well as the Komodo dragon 146 , Steller sea lion 162 , lettuce (https://nanoporetech. com/resource-centre/tip-iceberg-sequencing-lettuce-genome) and giant sequoia 163 , with genomes of a few gigabases, to coast redwood (https://www.savetheredwoods.org/project/redwoodgenome-project/) and tulip (https://nanoporetech.com/resourcecentre/beauty-and-beast), with genomes of 27-34 Gb.…”

High-quality carnivore genomes from roadkill samples enable species delimitation in aardwolf and bat-eared fox

“…The use of less GC-biased long reads of single DNA molecules and ultra-long reads spanning repeated genomic regions provides a powerful solution for obtaining assemblies with high contiguity and completeness, although long-read sequencing has limited accuracy (10-20% errors). Long reads can indeed be used alone at a high depth of coverage permitting autocorrection (Koren et al, 2017; Shafin et al, 2020) or in combination with short reads for (1) scaffolding short-read contigs (Armstrong et al, 2020; Kwan et al, 2019), (2) using short reads to polish long-read contigs (Batra et al, 2019b; Datema et al, 2016; Jansen et al, 2017; Michael et al, 2018), or (3) optimizing the assembly process by using information from both long and short reads (Díaz-Viraqué et al, 2019; Gan et al, 2019; Jiang et al, 2019; Kadobianskyi et al, 2019; Tan et al, 2018; Wang et al, 2020; Zimin et al, 2017). Given the previously demonstrated efficiency of the MaSuRCA tool for the assembly of large genomes (Scott et al, 2020; Wang et al, 2020; Zimin et al, 2017), we decided to rely on hybrid sequencing data combining the advantages of Illumina short-read and Nanopore long-read sequencing technologies.…”

“…Furthermore, it is possible to correct errors in ONT long reads by combining them with Illumina short reads, either to polish de novo long read-based genome assemblies (Batra et al, 2019a; Jain et al, 2018; Nicholls et al, 2019; Walker et al, 2014) or to construct hybrid assemblies (Di Genova et al, 2018; Gan et al, 2019; Tan et al, 2018; Zimin et al, 2013). In hybrid assembly approaches, the accuracy of short reads with high depth of coverage (50-100x) allows the use of long reads at lower depth of coverage (10-30x) essentially for scaffolding (Armstrong et al, 2020; Kwan et al, 2019). A promising hybrid assembly approach combining short and long read sequencing data has been implemented in MaSuRCA software (Zimin et al, 2017, 2013).…”

High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox

“…Furthermore, it is possible to correct errors in ONT long reads by combining them with Illumina short reads, either to polish de novo long-read-based genome assemblies ( Batra et al, 2019 ; Jain et al, 2018 ; Nicholls et al, 2019 ; Walker et al, 2014 ) or to construct hybrid assemblies ( Di Genova et al, 2018 ; Gan et al, 2019 ; Tan et al, 2018 ; Zimin et al, 2013 ). In hybrid assembly approaches, the accuracy of short reads with high depth-of-coverage (50–100x) allows the use of long reads at lower depths of coverage (10–30x) essentially for scaffolding ( Armstrong et al, 2020 ; Kwan et al, 2019 ). A promising hybrid assembly approach, combining short- and long-read sequencing data has been implemented in MaSuRCA software ( Zimin et al, 2017 ; Zimin et al, 2013 ).…”