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An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode.

ABSTRACT: Botryllids are colonial ascidians widely studied for their potential invasiveness and as model organisms, however the morphological description and discrimination of these species is very problematic, leading to frequent specimen misidentifications. To facilitate species discrimination and detection of cryptic/new species, we developed new barcoding primers for the amplification of a COI fragment of about 860 bp (860-COI), which is an extension of the common Folmer's barcode region. Our 860-COI was successfully amplified in 177 worldwide-sampled botryllid colonies. Combined with morphological analyses, 860-COI allowed not only discriminating known species, but also identifying undescribed and cryptic species, resurrecting old species currently in synonymy, and proposing the assignment of clade D of the model organism Botryllus schlosseri to Botryllus renierii. Importantly, within clade A of B. schlosseri, 860-COI recognized at least two candidate species against only one recognized by the Folmer's fragment, underlining the need of further genetic investigations on this clade. This result also suggests that the 860-COI could have a greater ability to diagnose cryptic/new species than the Folmer's fragment at very short evolutionary distances, such as those observed within clade A. Finally, our new primers simplify the amplification of 860-COI even in non-botryllid ascidians, suggesting their wider usefulness in ascidians.

SUBMITTER: Salonna M

PROVIDER: S-EPMC7892571 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode.

Salonna Marika M Gasparini Fabio F Huchon Dorothée D Montesanto Federica F Haddas-Sasson Michal M Ekins Merrick M McNamara Marissa M Mastrototaro Francesco F Gissi Carmela C

Scientific reports 20210218 1

Botryllids are colonial ascidians widely studied for their potential invasiveness and as model organisms, however the morphological description and discrimination of these species is very problematic, leading to frequent specimen misidentifications. To facilitate species discrimination and detection of cryptic/new species, we developed new barcoding primers for the amplification of a COI fragment of about 860 bp (860-COI), which is an extension of the common Folmer's barcode region. Our 860-COI ...[more]

PMID: 33603059

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Project description:BackgroundThe Palearctic region supports relatively few avian species, yet recent molecular studies have revealed that cryptic lineages likely still persist unrecognized. A broad survey of cytochrome c oxidase I (COI) sequences, or DNA barcodes, can aid on this front by providing molecular diagnostics for species assignment. Barcodes have already been extensively surveyed in the Nearctic, which provides an interesting comparison to this region; faunal interchange between these regions has been very dynamic. We explored COI sequence divergence within and between species of Palearctic birds, including samples from Russia, Kazakhstan, and Mongolia. As of yet, there is no consensus on the best method to analyze barcode data. We used this opportunity to compare and contrast three different methods routinely employed in barcoding studies: clustering-based, distance-based, and character-based methods.ResultsWe produced COI sequences from 1,674 specimens representing 398 Palearctic species. These were merged with published COI sequences from North American congeners, creating a final dataset of 2,523 sequences for 599 species. Ninety-six percent of the species analyzed could be accurately identified using one or a combination of the methods employed. Most species could be rapidly assigned using the cluster-based or distance-based approach alone. For a few select groups of species, the character-based method offered an additional level of resolution. Of the five groups of indistinguishable species, most were pairs, save for a larger group comprising the herring gull complex. Up to 44 species exhibited deep intraspecific divergences, many of which corresponded to previously described phylogeographic patterns and endemism hotspots.ConclusionCOI sequence divergence within eastern Palearctic birds is largely consistent with that observed in birds from other temperate regions. Sequence variation is primarily congruent with taxonomic boundaries; deviations from this trend reveal overlooked biological patterns, and in some cases, overlooked species. More research is needed to further refine the taxonomic status of some Palearctic birds, but large genetic surveys such as this may facilitate this effort. DNA barcodes are a practical means for rapid species assignment, although efficient analytical methods will likely require a two-tiered approach to differentiate closely related pairs of species.

Dataset Information

An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode.

Publications

An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode.

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