Evaluation of genome skimming to detect and characterise human and livestock helminths

American mitogenome reference for the tropical brown dog tick, Rhipicephalus linnaei (Audouin, 1826)

“…2 ). Generating mitogenomes of ticks and other parasites is possible using genome skimming via next-generation sequencing ( Jia et al, 2020 ; Šlapeta et al, 2021 ; Papaiakovou et al, 2023 ). The cost of genome skimming for ticks is comparable to the cost of PCR amplification and bi-directional Sanger sequencing of three or more amplicons, yet it generates all mitochondrial full coding sequences as well as both 12S and 16S rDNA gene sequences compared to a partial amplicon ( Kneubehl et al, 2022 ; Šlapeta et al, 2022 , 2023 ).…”

Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates

“…Here I determined that just 0.01× coverage is sufficient to achieve high precision in global DNA methylation assessment in vertebrate genomes. Genome skimming has been used for diverse purposes, including plastid genome assembly, parasite identification, and evolutionary biology in extinct species, and is gaining software tools for phylogenetic analyses ( Grewe et al 2021 ; Ferrari et al 2022 ; Odago et al 2022 ; Reginato 2022 ; Papaiakovou et al 2023 ). Classical genome skimming focuses on mitochondrial genome recovery for species or individual identification but does not typically use the nuclear portion of the skimmed reads or their DNA methylation.…”

“…Genome skimming refers to unbiased low-pass sequencing below 0.05× coverage and is used to reconstruct mitochondrial genomes as well as identify species and parasites ( Twyford and Ness 2017 ; Papaiakovou et al 2023 ; Zhang et al 2023 ). Oxford Nanopore Technologies’ nanopore sequencers have been used for genome skimming to produce mitochondrial genomes with success, and at least one study used genome skimming to report DNA methylation ( Euskirchen et al 2017 ; De Vivo et al 2022 ).…”

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

“…Genome skimming has been used for diverse purposes including plastid genome assembly, parasite identification, evolutionary biology in extinct species, and is gaining software tools for phylogenetic analyses. 3,[19][20][21][22] Classical genome skimming focuses on mitochondrial genome recovery for species or individual identification but does not typically utilize the nuclear portion of the skimmed reads or their DNA methylation. There are only five reports of nanopore sequencing used for genome skimming in animals at the time of publication, none of which examine the epigenome.…”

“…Genome skimming refers to unbiased low-pass sequencing below 0.05X coverage and is used to reconstruct mitochondrial genomes as well as for species and parasite identification. [1][2][3] Oxford Nanopore Technologies' nanopore sequencers have been used for genome skimming to produce mitochondrial genomes with success, however no studies have used genome skimming to report DNA methylation. 4 An important biomarker, DNA methylation varies with age, tissue, species, and environmental exposures making it a useful measure from ecology to epidemiology.…”