Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage short reads sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement
The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA...
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Veröffentlicht in: | Gene 2023-10, p.147939 |
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Format: | Artikel |
Sprache: | eng |
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Zusammenfassung: | The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon and mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is in line with the assembly length but slightly below the genome size of other representatives of the family Carcharhinidae. Using a k-mer analysis, approx. 64-71% of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this remarkable large coastal shark. |
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ISSN: | 1879-0038 1879-0038 |
DOI: | 10.1016/j.gene.2023.147939 |