Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros

Abstract Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as “nois...

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Autores principales:	Daniele De Luca, Wiebe H. C. F. Kooistra, Diana Sarno, Elio Biffali, Roberta Piredda
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/12aff9d7bee74790bb59ff579459cb21
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spelling	oai:doaj.org-article:12aff9d7bee74790bb59ff579459cb212021-12-02T14:12:10ZEmpirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros10.1038/s41598-020-80829-62045-2322https://doaj.org/article/12aff9d7bee74790bb59ff579459cb212021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80829-6https://doaj.org/toc/2045-2322Abstract Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as “noise” in electropherograms and these variants have been characterised through cloning and sequencing of subsamples of amplified products. However, this approach limits the number of detectable variants and provides no information about the abundance of each variant. In this study, we investigated concerted evolution by using environmental time-series metabarcoding data, single strain high-throughput sequencing (HTS) and a collection of Sanger reference barcode sequences. We used six species of the marine planktonic diatom genus Chaetoceros as study system. Abundance plots obtained from environmental metabarcoding and single strain HTS showed the presence of a haplotype far more abundant than all the others (the “dominant” haplotype) and identical to the reference sequences of that species obtained with Sanger sequencing. This distribution fitted best with Zipf’s law among the rank abundance/ dominance models tested. Furthermore, in each strain 99% of reads showed a similarity of 99% with the dominant haplotype, confirming the efficiency of the homogenisation mechanism of concerted evolution. We also demonstrated that minor haplotypes found in the environmental samples are not only technical artefacts, but mostly intragenomic variation generated by incomplete homogenisation. Finally, we showed that concerted evolution can be visualised inferring phylogenetic networks from environmental data. In conclusion, our study provides an important contribution to the understanding of concerted evolution and to the interpretation of DNA barcoding and metabarcoding data based on multigene family markers.Daniele De LucaWiebe H. C. F. KooistraDiana SarnoElio BiffaliRoberta PireddaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Daniele De Luca Wiebe H. C. F. Kooistra Diana Sarno Elio Biffali Roberta Piredda Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros
description	Abstract Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as “noise” in electropherograms and these variants have been characterised through cloning and sequencing of subsamples of amplified products. However, this approach limits the number of detectable variants and provides no information about the abundance of each variant. In this study, we investigated concerted evolution by using environmental time-series metabarcoding data, single strain high-throughput sequencing (HTS) and a collection of Sanger reference barcode sequences. We used six species of the marine planktonic diatom genus Chaetoceros as study system. Abundance plots obtained from environmental metabarcoding and single strain HTS showed the presence of a haplotype far more abundant than all the others (the “dominant” haplotype) and identical to the reference sequences of that species obtained with Sanger sequencing. This distribution fitted best with Zipf’s law among the rank abundance/ dominance models tested. Furthermore, in each strain 99% of reads showed a similarity of 99% with the dominant haplotype, confirming the efficiency of the homogenisation mechanism of concerted evolution. We also demonstrated that minor haplotypes found in the environmental samples are not only technical artefacts, but mostly intragenomic variation generated by incomplete homogenisation. Finally, we showed that concerted evolution can be visualised inferring phylogenetic networks from environmental data. In conclusion, our study provides an important contribution to the understanding of concerted evolution and to the interpretation of DNA barcoding and metabarcoding data based on multigene family markers.
format	article
author	Daniele De Luca Wiebe H. C. F. Kooistra Diana Sarno Elio Biffali Roberta Piredda
author_facet	Daniele De Luca Wiebe H. C. F. Kooistra Diana Sarno Elio Biffali Roberta Piredda
author_sort	Daniele De Luca
title	Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros
title_short	Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros
title_full	Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros
title_fullStr	Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros
title_full_unstemmed	Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros
title_sort	empirical evidence for concerted evolution in the 18s rdna region of the planktonic diatom genus chaetoceros
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/12aff9d7bee74790bb59ff579459cb21
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Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros

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