1
|
Sandler G, Agrawal AF, Wright SI. Population Genomics of the Facultatively Sexual Liverwort Marchantia polymorpha. Genome Biol Evol 2023; 15:evad196. [PMID: 37883717 PMCID: PMC10667032 DOI: 10.1093/gbe/evad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
The population genomics of facultatively sexual organisms are understudied compared with their abundance across the tree of life. We explore patterns of genetic diversity in two subspecies of the facultatively sexual liverwort Marchantia polymorpha using samples from across Southern Ontario, Canada. Despite the ease with which M. polymorpha should be able to propagate asexually, we find no evidence of strictly clonal descent among our samples and little to no signal of isolation by distance. Patterns of identity-by-descent tract sharing further showed evidence of recent recombination and close relatedness between geographically distant isolates, suggesting long distance gene flow and at least a modest frequency of sexual reproduction. However, the M. polymorpha genome contains overall very low levels of nucleotide diversity and signs of inefficient selection evidenced by a relatively high fraction of segregating deleterious variants. We interpret these patterns as possible evidence of the action of linked selection and a small effective population size due to past generations of asexual propagation. Overall, the M. polymorpha genome harbors signals of a complex history of both sexual and asexual reproduction.
Collapse
Affiliation(s)
- George Sandler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
2
|
Craig RJ, Gallaher SD, Shu S, Salomé PA, Jenkins JW, Blaby-Haas CE, Purvine SO, O’Donnell S, Barry K, Grimwood J, Strenkert D, Kropat J, Daum C, Yoshinaga Y, Goodstein DM, Vallon O, Schmutz J, Merchant SS. The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory. THE PLANT CELL 2023; 35:644-672. [PMID: 36562730 PMCID: PMC9940879 DOI: 10.1093/plcell/koac347] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 10/12/2022] [Accepted: 12/16/2022] [Indexed: 05/20/2023]
Abstract
Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating-type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.
Collapse
Affiliation(s)
- Rory J Craig
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean D Gallaher
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Shengqiang Shu
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
| | - Jerry W Jenkins
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Crysten E Blaby-Haas
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Samuel O’Donnell
- Laboratory of Computational and Quantitative Biology, UMR 7238, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris 75005, France
| | - Kerrie Barry
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Daniela Strenkert
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Chris Daum
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - David M Goodstein
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Olivier Vallon
- Unité Mixte de Recherche 7141, CNRS, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris 75005, France
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
3
|
Bafort Q, Prost L, Aydogdu E, Van de Vloet A, Casteleyn G, Van de Peer Y, De Clerck O. Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas. Methods Mol Biol 2023; 2545:351-372. [PMID: 36720822 DOI: 10.1007/978-1-0716-2561-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this chapter, we present the use of Chlamydomonas reinhardtii in experiments designed to study the evolutionary impacts of whole genome duplication. We shortly introduce the algal species and depict why it is an excellent model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related Chlamydomonas experiment. These steps include strain selection, ploidy determination, different methods of making diplo- and polyploid Chlamydomonas cells, replication, culturing conditions, preservation, and the ways to quantify phenotypic and genotypic change.
Collapse
Affiliation(s)
- Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Lucas Prost
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Eylem Aydogdu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Antoine Van de Vloet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Griet Casteleyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | |
Collapse
|
4
|
Ford SA, Craig RJ, Ness RW. A novel method for identifying Chlamydomonas reinhardtii (Chlorophyta) and closely related species from nature. JOURNAL OF PHYCOLOGY 2023; 59:281-288. [PMID: 36453860 DOI: 10.1111/jpy.13306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Here, we introduce a new method for efficiently sampling Chlamydomonas reinhardtii and closely related species using a colony PCR-based screen with novel primer sets designed to specifically detect these important model microalgae. To demonstrate the utility of our new method, we collected 130 soil samples from a wide range of habitats in Ontario, Canada and identified 33 candidate algae, which were barcoded by sequencing a region of the rbcL plastid gene. For select isolates, 18S rRNA gene and YPT4 nuclear markers were also sequenced. Based on phylogenetic and haplotype network analyses of these three loci, seven novel isolates were identified as C. reinhardtii, and one additional isolate appeared to be more closely related to C. reinhardtii than any other known species. All seven new C. reinhardtii strains were interfertile with previously collected C. reinhardtii field isolates, validating the effectiveness of our molecular screen.
Collapse
Affiliation(s)
- Scott A Ford
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, M5S 3G5, Canada
| | - Rory J Craig
- California Institute for Quantitative Biosciences, University of California, Berkeley, 174 Stanley Hall, Berkeley, California, 94720-3220, USA
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, M5S 3G5, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
| |
Collapse
|
5
|
López-Cortegano E, Craig RJ, Chebib J, Balogun EJ, Keightley PD. Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii. Genome Res 2023; 33:45-60. [PMID: 36617667 PMCID: PMC9977147 DOI: 10.1101/gr.276957.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Genetic variation originates from several types of spontaneous mutation, including single-nucleotide substitutions, short insertions and deletions (indels), and larger structural changes. Structural mutations (SMs) drive genome evolution and are thought to play major roles in evolutionary adaptation, speciation, and genetic disease, including cancers. Sequencing of mutation accumulation (MA) lines has provided estimates of rates and spectra of single-nucleotide and indel mutations in many species, yet the rate of new SMs is largely unknown. Here, we use long-read sequencing to determine the full mutation spectrum in MA lines derived from two strains (CC-1952 and CC-2931) of the green alga Chlamydomonas reinhardtii The SM rate is highly variable between strains and between MA lines, and SMs represent a substantial proportion of all mutations in both strains (CC-1952 6%; CC-2931 12%). The SM spectra differ considerably between the two strains, with almost all inversions and translocations occurring in CC-2931 MA lines. This variation is associated with heterogeneity in the number and type of active transposable elements (TEs), which comprise major proportions of SMs in both strains (CC-1952 22%; CC-2931 38%). In CC-2931, a Crypton and a previously undescribed type of DNA element have caused 71% of chromosomal rearrangements, whereas in CC-1952, a Dualen LINE is associated with 87% of duplications. Other SMs, notably large duplications in CC-2931, are likely products of various double-strand break repair pathways. Our results show that diverse types of SMs occur at substantial rates, and support prominent roles for SMs and TEs in evolution.
Collapse
Affiliation(s)
- Eugenio López-Cortegano
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Rory J. Craig
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;,California Institute for Quantitative Biosciences, UC Berkeley, Berkeley, California 94720, USA
| | - Jobran Chebib
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Eniolaye J. Balogun
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario ON M5S 3B2, Canada;,Department of Biology, University of Toronto Mississauga, Mississauga ON L5L 1C6, Canada
| | - Peter D. Keightley
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| |
Collapse
|
6
|
Le Gac M, Mary L, Metegnier G, Quéré J, Siano R, Rodríguez F, Destombe C, Sourisseau M. Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta-transcriptome samples. Environ Microbiol 2022; 24:5966-5983. [PMID: 36302091 DOI: 10.1111/1462-2920.16257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic frequency directly from population wide samples, without any isolation step, offers an interesting alternative. Here, we validate the use of meta-transcriptome environmental samples to determine the population genetic structure of the dinoflagellate Alexandrium minutum. Strain and meta-transcriptome based results both indicated a strong genetic structure for A. minutum in Western Europe, to the level expected between cryptic species. The presence of numerous private alleles, and even fixed polymorphism, would indicate ancient divergence and absence of gene flow between populations. Single nucleotide polymorphisms (SNPs) displaying strong allele frequency differences were distributed throughout the genome, which might indicate pervasive selection from standing genetic variation (soft selective sweeps). However, a few genomic regions displayed extremely low diversity that could result from the fixation of adaptive de novo mutations (hard selective sweeps) within the populations.
Collapse
Affiliation(s)
| | - Lou Mary
- Ifremer, Dyneco, Plouzané, France
| | | | | | | | | | | | | |
Collapse
|
7
|
Moniruzzaman M, Erazo-Garcia MP, Aylward FO. Endogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii. Virus Evol 2022; 8:veac102. [PMID: 36447475 PMCID: PMC9693826 DOI: 10.1093/ve/veac102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/05/2022] [Accepted: 10/20/2022] [Indexed: 11/14/2023] Open
Abstract
Chlamydomonas reinhardtii is a unicellular eukaryotic alga that has been studied as a model organism for decades. Despite an extensive history as a model system, phylogenetic and genetic characteristics of viruses infecting this alga have remained elusive. We analyzed high-throughput genome sequence data of C. reinhardtii field isolates, and in six we discovered sequences belonging to endogenous giant viruses that reach up to several 100 kb in length. In addition, we have also discovered the entire genome of a closely related giant virus that is endogenized within the genome of Chlamydomonas incerta, the closest sequenced relative of C. reinhardtii. Endogenous giant viruses add hundreds of new gene families to the host strains, highlighting their contribution to the pangenome dynamics and interstrain genomic variability of C. reinhardtii. Our findings suggest that the endogenization of giant viruses may have important implications for structuring the population dynamics and ecology of protists in the environment.
Collapse
Affiliation(s)
- Mohammad Moniruzzaman
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Maria P Erazo-Garcia
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, 981 Kraft Dr, Room 2036, Blacksburg, VA 24060, USA
| |
Collapse
|
8
|
Hasan AR, Lachapelle J, El-Shawa SA, Potjewyd R, Ford SA, Ness RW. Salt stress alters the spectrum of de novo mutation available to selection during experimental adaptation of Chlamydomonas reinhardtii. Evolution 2022; 76:2450-2463. [PMID: 36036481 DOI: 10.1111/evo.14604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/12/2022] [Indexed: 01/22/2023]
Abstract
The genetic basis of adaptation is driven by both selection and the spectrum of available mutations. Given that the rate of mutation is not uniformly distributed across the genome and varies depending on the environment, understanding the signatures of selection across the genome is aided by first establishing what the expectations of genetic change are from mutation. To determine the interaction between salt stress, selection, and mutation across the genome, we compared mutations observed in a selection experiment for salt tolerance in Chlamydomonas reinhardtii to those observed in mutation accumulation (MA) experiments with and without salt exposure. MA lines evolved under salt stress had a single-nucleotide mutation rate of 1.1 × 10 - 9 $1.1 \times 10^{-9}$ , similar to that of MA lines under standard conditions ( 9.6 × 10 - 10 $9.6 \times 10^{-10}$ ). However, we found that salt stress led to an increased rate of indel mutations, but that many of these mutations were removed under selection. Finally, lines adapted to salt also showed excess clustering of mutations in the genome and the co-expression network, suggesting a role for positive selection in retaining mutations in particular compartments of the genome during the evolution of salt tolerance. Our study shows that characterizing mutation rates and spectra expected under stress helps disentangle the effects of environment and selection during adaptation.
Collapse
Affiliation(s)
- Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Josianne Lachapelle
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Sara A El-Shawa
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.,Department of Mathematical and Computational Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Roman Potjewyd
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Scott A Ford
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Rob W Ness
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| |
Collapse
|
9
|
Böndel KB, Samuels T, Craig RJ, Ness RW, Colegrave N, Keightley PD. The distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii inferred using frequency changes under experimental evolution. PLoS Genet 2022; 18:e1009840. [PMID: 35704655 PMCID: PMC9239454 DOI: 10.1371/journal.pgen.1009840] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 06/28/2022] [Accepted: 04/13/2022] [Indexed: 12/23/2022] Open
Abstract
The distribution of fitness effects (DFE) for new mutations is fundamental for many aspects of population and quantitative genetics. In this study, we have inferred the DFE in the single-celled alga Chlamydomonas reinhardtii by estimating changes in the frequencies of 254 spontaneous mutations under experimental evolution and equating the frequency changes of linked mutations with their selection coefficients. We generated seven populations of recombinant haplotypes by crossing seven independently derived mutation accumulation lines carrying an average of 36 mutations in the haploid state to a mutation-free strain of the same genotype. We then allowed the populations to evolve under natural selection in the laboratory by serial transfer in liquid culture. We observed substantial and repeatable changes in the frequencies of many groups of linked mutations, and, surprisingly, as many mutations were observed to increase as decrease in frequency. Mutation frequencies were highly repeatable among replicates, suggesting that selection was the cause of the observed allele frequency changes. We developed a Bayesian Monte Carlo Markov Chain method to infer the DFE. This computes the likelihood of the observed distribution of changes of frequency, and obtains the posterior distribution of the selective effects of individual mutations, while assuming a two-sided gamma distribution of effects. We infer that the DFE is a highly leptokurtic distribution, and that approximately equal proportions of mutations have positive and negative effects on fitness. This result is consistent with what we have observed in previous work on a different C. reinhardtii strain, and suggests that a high fraction of new spontaneously arisen mutations are advantageous in a simple laboratory environment.
Collapse
Affiliation(s)
- Katharina B. Böndel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Toby Samuels
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rory J. Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rob W. Ness
- Department of Biology, William G. Davis Building, University of Toronto, Mississauga, Canada
| | - Nick Colegrave
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter D. Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| |
Collapse
|
10
|
Sandell L, Sharp NP. Fitness Effects of Mutations: An Assessment of PROVEAN Predictions Using Mutation Accumulation Data. Genome Biol Evol 2022; 14:evac004. [PMID: 35038732 PMCID: PMC8790079 DOI: 10.1093/gbe/evac004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2021] [Indexed: 11/14/2022] Open
Abstract
Predicting fitness in natural populations is a major challenge in biology. It may be possible to leverage fast-accumulating genomic data sets to infer the fitness effects of mutant alleles, allowing evolutionary questions to be addressed in any organism. In this paper, we investigate the utility of one such tool, called PROVEAN. This program compares a query sequence with existing data to provide an alignment-based score for any protein variant, with scores categorized as neutral or deleterious based on a pre-set threshold. PROVEAN has been used widely in evolutionary studies, for example, to estimate mutation load in natural populations, but has not been formally tested as a predictor of aggregate mutational effects on fitness. Using three large published data sets on the genome sequences of laboratory mutation accumulation lines, we assessed how well PROVEAN predicted the actual fitness patterns observed, relative to other metrics. In most cases, we find that a simple count of the total number of mutant proteins is a better predictor of fitness than the number of proteins with variants scored as deleterious by PROVEAN. We also find that the sum of all mutant protein scores explains variation in fitness better than the number of mutant proteins in one of the data sets. We discuss the implications of these results for studies of populations in the wild.
Collapse
Affiliation(s)
- Linnea Sandell
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Systematic Biology, Department of Organismal Biology, Uppsala University, Sweden
| | | |
Collapse
|
11
|
Chaux-Jukic F, O'Donnell S, Craig RJ, Eberhard S, Vallon O, Xu Z. Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii. Nucleic Acids Res 2021; 49:7571-7587. [PMID: 34165564 PMCID: PMC8287924 DOI: 10.1093/nar/gkab534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.
Collapse
Affiliation(s)
- Frédéric Chaux-Jukic
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Samuel O'Donnell
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Rory J Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, Edinburgh, UK
| | - Stephan Eberhard
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Olivier Vallon
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Zhou Xu
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| |
Collapse
|
12
|
Craig RJ, Yushenova IA, Rodriguez F, Arkhipova IR. An ancient clade of Penelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genomes. Mol Biol Evol 2021; 38:5005-5020. [PMID: 34320655 PMCID: PMC8557442 DOI: 10.1093/molbev/msab225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Penelope-like elements (PLEs) are an enigmatic clade of retrotransposons whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical endonuclease (EN)+ PLEs encodes RT and a C-terminal GIY–YIG EN that enables intrachromosomal integration, whereas EN− PLEs lack EN and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, whereas EN− PLEs occur in several kingdoms. Here, we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY–YIG EN is linked to a C-terminal RT by a short domain with a characteristic CxC motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune, and Nematis clades, and show insertion bias for microsatellites, but lack canonical hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiads, found in numerous invertebrate phyla, can reach tens of thousands of copies per genome. In spiders and clams, Naiads independently evolved to encode selenoproteins containing multiple selenocysteines. Chlamys, which lack the CCHH motif universal to PLE ENs, occur in green algae, spike mosses (targeting ribosomal DNA), and slime molds. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain (IFD), strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, taxonomic distribution, and abundance are comparable with non-LTR and LTR-retrotransposons.
Collapse
Affiliation(s)
- Rory J Craig
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| |
Collapse
|
13
|
Hasan AR, Ness RW. Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii. Genome Biol Evol 2021; 12:370-380. [PMID: 32181819 PMCID: PMC7186780 DOI: 10.1093/gbe/evaa057] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.
Collapse
Affiliation(s)
- Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Ontario, Canada
| | - Rob W Ness
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Ontario, Canada
| |
Collapse
|
14
|
Craig RJ, Hasan AR, Ness RW, Keightley PD. Comparative genomics of Chlamydomonas. THE PLANT CELL 2021; 33:1016-1041. [PMID: 33793842 PMCID: PMC8226300 DOI: 10.1093/plcell/koab026] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/22/2021] [Indexed: 05/06/2023]
Abstract
Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas incerta, Chlamydomonas schloesseri, and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and >260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system.
Collapse
Affiliation(s)
| | - Ahmed R Hasan
- Department of Biology, University of Toronto Mississauga, Mississauga, Onatrio, Canada L5L 1C6
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, Onatrio, Canada L5L 1C6
| | - Peter D Keightley
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, UK
| |
Collapse
|
15
|
Sleith RS, Katz LA. Ubiquity or not ubiquity: That is the question. Mol Ecol 2020; 28:4842-4844. [PMID: 31746076 DOI: 10.1111/mec.15297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/24/2019] [Accepted: 10/28/2019] [Indexed: 02/05/2023]
Abstract
The nature of population structure in eukaryotic microbes has been the subject of intense debate, but until recently the tools to test these hypotheses were either problematic (e.g., allozymes that cannot detect all genetic changes) or beyond financial and technological limits of most laboratories (e.g., high throughput sequencing). In a recent issue of Molecular Ecology, Craig et al. (2019) use a genomic approach to investigate the population structure of a model alga, the chlorophyte Chlamydomonas reinhardtii (Figure 1). Using high throughput sequencing, read mapping, and variant calling, they detected strong signals of differentiation at a continental scale, while local patterns of admixture were complex. Population genomic techniques such as these have not been used extensively in studies of microbial eukaryotes and the fields of conservation genetics and evolution stand to benefit vastly from the adoption of these techniques to studies of diverse protist lineages.
Collapse
Affiliation(s)
- Robin S Sleith
- Department of Biological Sciences, Smith College, Northampton, MA, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, USA.,Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, USA
| |
Collapse
|