Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents

Gollnisch, Raphael LU ; Ahrén, Dag LU orcid and Rengefors, Karin LU (2024) In The Isme Journal 18(1).
Abstract

The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears to be expanding in Europe, whereas similar trends are not observed in the USA. Our aim was to investigate if populations of Gonyostomum semen in Europe and in the USA are genetically differentiated, if there is population genetic structure within the continents, and what the potential drivers of differentiation are. To this end, we used a... (More)

The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears to be expanding in Europe, whereas similar trends are not observed in the USA. Our aim was to investigate if populations of Gonyostomum semen in Europe and in the USA are genetically differentiated, if there is population genetic structure within the continents, and what the potential drivers of differentiation are. To this end, we used a novel method based on single-amplified genomes combined with Restriction-site Associated DNA sequencing that allows de novo genotyping of natural single-cell isolates without the need for culturing. We amplified over 900 single-cell genomes from 25 lake populations across Europe and the USA and identified two distinct population clusters, one in Europe and another in the USA. Low genetic diversity in European populations supports the hypothesized recent expansion of Gonyostomum semen on this continent. Geographic population structure within each continent was associated with differences in environmental variables that may have led to ecological divergence of population clusters. Overall, our results show that single-amplified genomes combined with Restriction-site Associated DNA sequencing can be used to analyze microalgal population structure and differentiation based on single-cell isolates from natural, uncultured samples.

(Less)
Please use this url to cite or link to this publication:
author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
adaptation, dispersal, ecological divergence, Gonyostomum semen, restriction-site associated DNA (RAD) sequencing, single-cell whole-genome amplification (WGA)
in
The Isme Journal
volume
18
issue
1
article number
wrae045
pages
13 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:85192114412
  • pmid:38489771
ISSN
1751-7362
DOI
10.1093/ismejo/wrae045
language
English
LU publication?
yes
id
2cc43a19-faf3-4f52-a186-410988691397
date added to LUP
2024-05-16 08:51:57
date last changed
2024-06-13 11:37:49
@article{2cc43a19-faf3-4f52-a186-410988691397,
  abstract     = {{<p>The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears to be expanding in Europe, whereas similar trends are not observed in the USA. Our aim was to investigate if populations of Gonyostomum semen in Europe and in the USA are genetically differentiated, if there is population genetic structure within the continents, and what the potential drivers of differentiation are. To this end, we used a novel method based on single-amplified genomes combined with Restriction-site Associated DNA sequencing that allows de novo genotyping of natural single-cell isolates without the need for culturing. We amplified over 900 single-cell genomes from 25 lake populations across Europe and the USA and identified two distinct population clusters, one in Europe and another in the USA. Low genetic diversity in European populations supports the hypothesized recent expansion of Gonyostomum semen on this continent. Geographic population structure within each continent was associated with differences in environmental variables that may have led to ecological divergence of population clusters. Overall, our results show that single-amplified genomes combined with Restriction-site Associated DNA sequencing can be used to analyze microalgal population structure and differentiation based on single-cell isolates from natural, uncultured samples.</p>}},
  author       = {{Gollnisch, Raphael and Ahrén, Dag and Rengefors, Karin}},
  issn         = {{1751-7362}},
  keywords     = {{adaptation; dispersal; ecological divergence; Gonyostomum semen; restriction-site associated DNA (RAD) sequencing; single-cell whole-genome amplification (WGA)}},
  language     = {{eng}},
  month        = {{01}},
  number       = {{1}},
  publisher    = {{Nature Publishing Group}},
  series       = {{The Isme Journal}},
  title        = {{Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents}},
  url          = {{http://dx.doi.org/10.1093/ismejo/wrae045}},
  doi          = {{10.1093/ismejo/wrae045}},
  volume       = {{18}},
  year         = {{2024}},
}