ArticleScientific reports2019
Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- A Faroese perspective on decoding life for sustainable use of nature and protection of biodiversity.npj biodiversity · 2024Review
- Gap-free genome assembly of anadromous Coilia nasus.Scientific data · 2023Article
- CNVs with adaptive potential inLife science alliance · 2022Article
- Transcriptome characterization of BPG axis and expression profiles of ovarian steroidogenesis-related genes in the Japanese sardine.BMC genomics · 2020Article
- Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight.G3 (Bethesda, Md.) · 2020Article
- Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies.BMC genomics · 2020Article
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Authors and funding
6 authors.
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Abstract
Atlantic herring (Clupea harengus) is one of the most abundant fish species in the world. It is an important economical and nutritional resource, as well as a crucial part of the North Atlantic ecosystem. In 2016, a draft herring genome assembly was published. Being a species of such importance, we sought to independently verify and potentially improve the herring genome assembly. We sequenced the herring genome generating paired-end, mate-pair, linked and long reads. Three assembly versions of the herring genome were generated based on a de novo assembly (A1), which was scaffolded using linked and long reads (A2) and then merged with the previously published assembly (A3). The resulting assemblies were compared using parameters describing the size, fragmentation, correctness, and completeness of the assemblies. Results showed that the A2 assembly was less fragmented, more complete and more correct than A1. A3 showed improvement in fragmentation and correctness compared with A2 and the published assembly but was slightly less complete than the published assembly. Thus, we here confirmed the previously published herring assembly, and made improvements by further scaffolding the assembly and removing low-quality sequences using linked and long reads and merging of assemblies.
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