DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

Abstract DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jordan M. Casey, Emma Ransome, Allen G. Collins, Angka Mahardini, Eka M. Kurniasih, Andrianus Sembiring, Nina M. D. Schiettekatte, Ni Kadek Dita Cahyani, Aji Wahyu Anggoro, Mikaela Moore, Abby Uehling, Mahdi Belcaid, Paul H. Barber, Jonathan B. Geller, Christopher P. Meyer
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	18S rDNA coral reefs cryptic diversity cytochrome c oxidase subunit I high‐throughput sequencing taxonomy Environmental sciences GE1-350 Microbial ecology QR100-130
Acceso en línea:	https://doaj.org/article/2545296e4bb94568923cc4bfb5b4330b
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:2545296e4bb94568923cc4bfb5b4330b
record_format	dspace
spelling	oai:doaj.org-article:2545296e4bb94568923cc4bfb5b4330b2021-11-23T16:15:25ZDNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity2637-494310.1002/edn3.245https://doaj.org/article/2545296e4bb94568923cc4bfb5b4330b2021-11-01T00:00:00Zhttps://doi.org/10.1002/edn3.245https://doaj.org/toc/2637-4943Abstract DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macroeukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world's most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image‐based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multimarker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice.Jordan M. CaseyEmma RansomeAllen G. CollinsAngka MahardiniEka M. KurniasihAndrianus SembiringNina M. D. SchiettekatteNi Kadek Dita CahyaniAji Wahyu AnggoroMikaela MooreAbby UehlingMahdi BelcaidPaul H. BarberJonathan B. GellerChristopher P. MeyerWileyarticle18S rDNAcoral reefscryptic diversitycytochrome c oxidase subunit Ihigh‐throughput sequencingtaxonomyEnvironmental sciencesGE1-350Microbial ecologyQR100-130ENEnvironmental DNA, Vol 3, Iss 6, Pp 1229-1246 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	18S rDNA coral reefs cryptic diversity cytochrome c oxidase subunit I high‐throughput sequencing taxonomy Environmental sciences GE1-350 Microbial ecology QR100-130
spellingShingle	18S rDNA coral reefs cryptic diversity cytochrome c oxidase subunit I high‐throughput sequencing taxonomy Environmental sciences GE1-350 Microbial ecology QR100-130 Jordan M. Casey Emma Ransome Allen G. Collins Angka Mahardini Eka M. Kurniasih Andrianus Sembiring Nina M. D. Schiettekatte Ni Kadek Dita Cahyani Aji Wahyu Anggoro Mikaela Moore Abby Uehling Mahdi Belcaid Paul H. Barber Jonathan B. Geller Christopher P. Meyer DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
description	Abstract DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macroeukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world's most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image‐based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multimarker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice.
format	article
author	Jordan M. Casey Emma Ransome Allen G. Collins Angka Mahardini Eka M. Kurniasih Andrianus Sembiring Nina M. D. Schiettekatte Ni Kadek Dita Cahyani Aji Wahyu Anggoro Mikaela Moore Abby Uehling Mahdi Belcaid Paul H. Barber Jonathan B. Geller Christopher P. Meyer
author_facet	Jordan M. Casey Emma Ransome Allen G. Collins Angka Mahardini Eka M. Kurniasih Andrianus Sembiring Nina M. D. Schiettekatte Ni Kadek Dita Cahyani Aji Wahyu Anggoro Mikaela Moore Abby Uehling Mahdi Belcaid Paul H. Barber Jonathan B. Geller Christopher P. Meyer
author_sort	Jordan M. Casey
title	DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
title_short	DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
title_full	DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
title_fullStr	DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
title_full_unstemmed	DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
title_sort	dna metabarcoding marker choice skews perception of marine eukaryotic biodiversity
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/2545296e4bb94568923cc4bfb5b4330b
work_keys_str_mv	AT jordanmcasey dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT emmaransome dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT allengcollins dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT angkamahardini dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT ekamkurniasih dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT andrianussembiring dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT ninamdschiettekatte dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT nikadekditacahyani dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT ajiwahyuanggoro dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT mikaelamoore dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT abbyuehling dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT mahdibelcaid dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT paulhbarber dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT jonathanbgeller dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity AT christopherpmeyer dnametabarcodingmarkerchoiceskewsperceptionofmarineeukaryoticbiodiversity
_version_	1718416199322173440

DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

Ejemplares similares