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 “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.

Diversity and biogeography of planktonic diatoms in Svalbard fjords: The role of dispersal and Arctic endemism in phytoplankton community structuring

“…This finding was most notable within the L. minimus clade, but also within other clades such as C. contortus, A. cornucervis or the new strain from the Cymatosiraceae family. This high diversity of ASVs may indicate high intragenomic haplotype diversity of the 18S rRNA gene, as was shown in environmental metabarcoding data from the genus Chaetoceros (Gaonkar et al, 2020) and within clonal strains of the genus Chaetoceros (De Luca et al, 2021), where dominant haplotype is accompanied with peripheral haplotypes with order of magnitude lower read numbers. High intragenomic haplotype diversity was also reported for the genus Skeletonema (Alverson and Kolnick, 2005).…”

Diversity and Distribution of Harmful Algal Bloom Species from Seamount to Coastal Waters in the South China Sea

“…The sampling locations were visualized using a grid-based mapping program Surfer 16.0 (Golden Software). In addition to analyzing the relative abundance of phytoplankton at the species level, we also analyzed the richness indexes and relative abundance of these samples at the division and the class level using R. The phylogenetic haplotype networks were constructed using the statistical parsimony algorithm implemented in the TCS network ( 63 ). Haplotype networks were visualized in PopART v1.7 ( 64 ).…”

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

“…One exception is the nuclear ribosomal RNA gene repeats (rDNAs) such as the internal transcribed spacer (ITS) and the external transcribed spacer (ETS) (Baldwin et al, 1995; Baldwin and Markos, 1998), which have dozens to thousands of genomic copies. These sequences, therefore, are commonly used in the phylogenetic reconstruction; however, their typically short lengths with fewer than 1,000 bp and incomplete concerted evolution among copies have limited the phylogenetic resolution using these markers (De Luca et al, 2021; Wang et al, 2023a). Single‐copy/low‐copy nuclear genes can be effective in phylogenetic studies due to their simple evolutionary history, conservation, and high phylogenetic resolution (Álvarez et al, 2008; Zimmer and Wen, 2012, 2015) and their comprehensive use can provide a relatively complete and clear evolutionary history (Zimmer and Wen, 2015; Li et al, 2017).…”