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http://cibnor.repositorioinstitucional.mx/jspui/handle/1001/2771| Are we there yet? Benchmarking low- coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis | |
| Juan Antonio Baeza FRANCISCO JAVIER GARCIA DE LEON | |
| Acceso Abierto | |
| Atribución-NoComercial-SinDerivadas | |
| DOI: https://doi.org/10.1186/s12864-022-08482-z URL: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08482-z ISSN: 14712164 | |
| Long-read sequencing, Nanopore, Elasmobranch | |
| "Background: Whole mitochondrial genomes are quickly becoming markers of choice for the exploration of within- species genealogical and among-species phylogenetic relationships. Most often, ‘primer walking’ or ‘long PCR’ strategies plus Sanger sequencing or low-pass whole genome sequencing using Illumina short reads are used for the assembling of mitochondrial chromosomes. In this study, we frst confrmed that mitochondrial genomes can be sequenced from long reads using nanopore sequencing data exclusively. Next, we examined the accuracy of the long-reads assembled mitochondrial chromosomes when comparing them to a ‘gold’ standard reference mitochon‐ drial chromosome assembled using Illumina short-reads sequencing. Results: Using a specialized bioinformatics tool, we frst produced a short-reads mitochondrial genome assembly for the silky shark C. falciformis with an average base coverage of 9.8x. The complete mitochondrial genome of C. falciformis was 16,705bp in length and 934bp shorter than a previously assembled genome (17,639bp in length) that used bioinformatics tools not specialized for the assembly of mitochondrial chromosomes. Next, low-pass whole genome sequencing using a MinION ONT pocket-sized platform plus customized de-novo and reference-based work‐ fows assembled and circularized a highly accurate mitochondrial genome in the silky shark Carcharhinus falciformis. Indels at the fanks of homopolymer regions explained most of the dissimilarities observed between the ‘gold’ stand‐ ard reference mitochondrial genome (assembled using Illumina short reads) and each of the long-reads mitochon‐ drial genome assemblies. Although not completely accurate, mitophylogenomics and barcoding analyses (using entire mitogenomes and the D-Loop/Control Region, respectively) suggest that long-reads assembled mitocondrial genomes are reliable for identifying a sequenced individual, such as C. falciformis, and separating the same individual from others belonging to closely related congeneric species. Conclusions: This study confrms that mitochondrial genomes can be sequenced from long-reads nanopore sequencing data exclusively. With further development, nanopore technology can be used to quickly test in situ mislabeling in the shark fn fshing industry and thus, improve surveillance protocols, law enforcement, and the regulation of this fshery..." | |
| BioMed Central Ltd. | |
| 2022 | |
| Artículo | |
| BMC Genomics | |
| Inglés | |
| Baeza, J.A., García-De León, F.J. Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis. BMC Genomics 23, 320 (2022). https://doi.org/10.1186/s12864-022-08482-z | |
| GENÉTICA ANIMAL | |
| Versión publicada | |
| publishedVersion - Versión publicada | |
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