Filling in the Gaps: Adopting Ultraconserved Elements Alongside COI to Strengthen Metabarcoding Studies

Abstract

Metabarcoding is rapidly gaining popularity as a means of conducting biodiversity studies. Using DNA barcodes to identify and catalog biodiversity has many advantages, and compares favorably with traditional methods based on morphological examination. Ease of use, taxonomic coverage, and increased efficiency are qualities that make metabarcoding a valuable ecological tool, particularly in light of the drastic anthropogenically induced ecosystem changes currently underway. However, limitations and challenges pertaining to existing barcodes create gaps from which inaccuracies can arise, contributing to skepticism regarding the value of metabarcoding based methods. Developing novel ways to address these limitations is crucial to improve metabarcoding methods and dispel doubt about their utility. Ultraconserved genomic elements (UCEs), genetic markers that have been used successfully in the field of phylogenomics, possess advantageous qualities that may be applied to fill in the gaps of existing metabarcoding methods. Here, I outline the strengths of UCEs and discuss their potential for complementing and strengthening existing metabarcoding methods based on the mitochondrial marker cytochrome oxidase I (COI).

Standardized nuclear markers improve and homogenize species delimitation in Metazoa

“…Besides COI , different markers have been used for metazoan DNA taxonomy: nuclear ribosomal RNA genes (rDNA, Chen et al, 2017; Krehenwinkel et al, 2019; Lebonah et al, 2014), restriction site associated DNA sequences (RADseq; Baird et al, 2008; Herrera & Shank, 2016; Pante et al, 2015), and ultra‐conserved elements (UCE; Bejerano et al, 2004; Faircloth et al, 2012), the latter typically including more variable flanking regions (Gueuning et al, 2020; Ješovnik et al, 2017; Prebus, 2021; Zarza et al, 2018). However, they can hardly be applied universally across animals, either because of insufficient infraspecific variation or a lack of homologous loci between distantly related taxa (Eberle et al, 2020; Pierce, 2019). Therefore, metazoan‐level universal single‐copy orthologs (metazoan USCOs) have been proposed as a core set of nuclear‐encoded protein‐coding genes for species delimitation in Metazoa (Eberle et al, 2020).…”

“…However, they can hardly be applied universally across animals, either because of insufficient infraspecific variation or a lack of homologous loci between distantly related taxa (Eberle et al, 2020;Pierce, 2019). Therefore, metazoan-level universal single-copy orthologs (metazoan USCOs) have been proposed as a core set of nuclear-encoded protein-coding genes for species delimitation in Metazoa (Eberle et al, 2020).…”

Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae)

“…The development of new primers and traceable databases, such as the BOLD platform, has been supporting its effectiveness and choice. However, the COI gene is still highly questioned in its application capacity, especially in highthroughput applications, which has been defended in recent years due to the choice of new primers and methodologies for this type of sequencing (see Andújar et al 2018, Pierce 2019.…”

Differential genetic variability at two mtDNA COI regions does not imply mismatches in Odonata molecular identification performances

“…In this context, species delimitation is best addressed considering different sources of information, such as morphology, ecology but also multiple independent molecular markers which may also have a phylogenetic utility (Roe & Sperling 2007;Bybee et al 2011;Cruaud et al 2017). In this sense, the development of standardised nuclear markers, such as universal single-copy orthologs and ultraconserved elements, seems promising in implementing the power of DNA barcoding to delimit and identify species (Eberle et al 2020;Gueuning et al 2020), and has great potential also for DNA metabarcoding studies (Pierce 2019).…”