Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis.

ABSTRACT:

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 first confirmed 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 mitochondrial chromosome assembled using Illumina short-reads sequencing.

Results

Using a specialized bioinformatics tool, we first produc

SUBMITTER: Baeza JA 

PROVIDER: S-EPMC9027416 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature