Cas9-based enrichment for targeted long-read metabarcoding DOI Creative Commons
Lucia Nikolaeva-Reynolds, Christopher Cammies, Rosemary Crichton

и другие.

Royal Society Open Science, Год журнала: 2025, Номер 12(4)

Опубликована: Апрель 1, 2025

Metabarcoding is a valuable tool for characterizing the communities that underpin functioning of ecosystems. However, current methods often rely on polymerase chain reaction (PCR) amplification enrichment marker genes. PCR can introduce significant biases affect quantification and typically restricted to one target loci at time, limiting diversity be captured in single reaction. Here, we address these issues by using Cas9 enrich genes long-read nanopore sequencing directly from DNA sample, removing need PCR. We show this approach effectively isolate 4.5 kb region covering partial 18S 28S rRNA ITS mixed nematode community, further adapt our diverse microbial community. demonstrate ability Cas9-based support multiplexed targeting several different regions simultaneously, enabling optimal gene selection clades interest within sample. also find strong correlation between input concentrations output read proportions mixed-species samples, demonstrating relative species abundance. This study lays foundation targeted more fully capture organisms present complex environments.

Язык: Английский

Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy‐Relevant Biodiversity Research DOI Open Access
Tyler R. Kartzinel, Hannah K. Hoff, Timothy J. Divoll

и другие.

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Фев. 28, 2025

ABSTRACT Genetic technologies such as DNA barcoding make it easier and less expensive to monitor biodiversity its associated ecosystem services, particularly in hotspots where traditional assessments are challenging. Successful use of these data‐driven technologies, however, requires access appropriate reference data. We reviewed the >373,584 plant barcodes public repositories found that they cumulatively cover a remarkable quarter ~435,000 extant land species (Embryophyta). Nevertheless, coverage gaps tropical reflect well‐documented biases science – most specimens originated Global North. Currently, at least 17% families lack any barcode data whatsoever, affecting temperate regions alike. Investigators often emphasise importance marker choice need ensure protocols technically capable detecting identifying broad range taxa. Yet persistent geographic taxonomic datasets show rely upon risk undermining all downstream applications strategy, ranging from basic monitoring policy‐relevant objectives forensic authentication materials illegal trade. Future networks investigators could work strategically improve coverage, which will be essential global efforts conserve while advancing more fair equitable benefits arising genetic resources.

Язык: Английский

Процитировано

0
Cas9-based enrichment for targeted long-read metabarcoding DOI Creative Commons
Lucia Nikolaeva-Reynolds, Christopher Cammies, Rosemary Crichton

и другие.

Royal Society Open Science, Год журнала: 2025, Номер 12(4)

Опубликована: Апрель 1, 2025

Metabarcoding is a valuable tool for characterizing the communities that underpin functioning of ecosystems. However, current methods often rely on polymerase chain reaction (PCR) amplification enrichment marker genes. PCR can introduce significant biases affect quantification and typically restricted to one target loci at time, limiting diversity be captured in single reaction. Here, we address these issues by using Cas9 enrich genes long-read nanopore sequencing directly from DNA sample, removing need PCR. We show this approach effectively isolate 4.5 kb region covering partial 18S 28S rRNA ITS mixed nematode community, further adapt our diverse microbial community. demonstrate ability Cas9-based support multiplexed targeting several different regions simultaneously, enabling optimal gene selection clades interest within sample. also find strong correlation between input concentrations output read proportions mixed-species samples, demonstrating relative species abundance. This study lays foundation targeted more fully capture organisms present complex environments.

Язык: Английский

Процитировано

0