Beyond DNA barcoding: The unrealised potential of genome skim data in sample identification

Bohmann, Kristine; Mirarab, Siavash; Bafna, Vineet; Gilbert, Tom

doi:10.22541/au.158274776.61753752

Cited by 2 publications

(2 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, genome skimming has increasingly been used to help build DNA barcode reference databases for applications such as environmental DNA (eDNA) sequencing (Zeng et al, 2018; Hoban et al, 2022; Zhang et al, 2023). This method’s potential, however, for other applications remains unrealized, as typically more than 99% of the sequence data produced by skimming is not used (Bohmann et al, 2020). Low-coverage genome skims could readily be used to bioinformatically pull out ultraconserved elements (UCEs), exons, and other genes of interest.…”

Section: Introductionmentioning

confidence: 99%

Skimming genomes for systematics and DNA barcodes of corals

Quattrini,

McCartin,

Easton

et al. 2023

Preprint

View full text Add to dashboard Cite

1: Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage whole genome sequencing) remains a low-cost, promising method to not only extract high-copy loci, but also 100s to 1000s of phylogenetically informative single-copy nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and historical museum samples. The subphylum Anthozoa, which includes important ecosystem engineers (e.g., stony corals, black corals, anemones and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. 2: Genome skimming was conducted on 242 hexacorals and octocorals collected from 1890 to 2022. Using previously developed target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. We also extracted partial to whole mitogenomes and nuclear rRNA genes from the skim data. 3: The mean number of UCE and exon loci extracted from the genome skimming data was 1,837 ± 662 SD for octocorals and 1,422 ± 720 loci for hexacorals; phylogenetic relationships were well resolved within each class. A mean of 1,422 ± 720 loci were obtained from the historical museum specimens, with 1,253 loci recovered from the oldest specimen collected in 1886 and 1,336 loci recovered from a holotype. The nuclear rRNA genes and the majority of mitochondrial genes were successfully obtained from >95% of samples. Out of 99 circularized mitogenomes, 88% were recovered in samples from which we obtained >15M paired-end (PE) reads (>30M total reads); there was more variability in whether mitogenomes were circularized or not in samples with <15M PE reads. 4: Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.

show abstract

Section: Introductionmentioning

confidence: 99%

Skimming genomes for systematics and DNA barcodes of corals

Quattrini,

McCartin,

Easton

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…The idea of a barcoding zone where species could distinguish life forms from one another was quickly adopted. Later, barcoding studies expanded with the idea that other organelle regions, markers and associated primer sets could also be used for barcoding [3].…”

Section: Introductionmentioning

confidence: 99%

DNA Barcoding of Commercial Cockroaches in Turkey

Berk

PEKTAŞ

2023

Cumhuriyet Science Journal

View full text Add to dashboard Cite

Accurate species identification has become a precondition for accomplished biodiversity administration and further genetic research. Species acquaintance technics require molecular tools such as DNA barcoding as well as morphological identification for accurate identification. Particularly, the application of subunit I of the mitochondrial cytochrome c oxidase (COI) gene for DNA barcoding for insects has approved to be very useful in species acquaintance. The main aim of this study is to generate the first reference library of DNA barcode for cockroaches in Turkey using previously published data. As a result of the literature research, it has been observed that no study has been carried out on the DNA barcode of Turkish cockroaches. Therefore, in this study, we evaluated the advantage of DNA barcoding applied to two cockroach samples from Turkey for the first time. Our working samples implicated 10 DNA barcodes grounded on sequences created from our present study and 109 other DNA barcodes from BOLD. Various molecular analyzes including genetic distance-origin assessment (NeighborJoining and Maximum Likelihood trees) has been applied to accurately identify and describe species. In addition, Blaptica dubia (B. dubia) (Serville, 1838) and Nauphoeta cinerea (N. cinerea) (Olivier, 1789) have been reported as the first country records. It has been observed that reference libraries like BOLD are not yet sufficiently populated with COI sequences of Turkish cockroach species. In order for Turkish cockroach bio-assessment and biodiversity studies to benefit from the advantages of DNA barcoding, it is of great importance that cockroach inventories and taxonomic studies include DNA barcodes.

show abstract

Beyond DNA barcoding: The unrealised potential of genome skim data in sample identification

Cited by 2 publications

References 0 publications

Skimming genomes for systematics and DNA barcodes of corals

Skimming genomes for systematics and DNA barcodes of corals

DNA Barcoding of Commercial Cockroaches in Turkey

Contact Info

Product

Resources

About