The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type <i>plus</i> and <i>minus</i> strains reveal extensive structural mutation in the laboratory

Craig, Rory J.; Gallaher, Sean D.; Shu, Shengqiang; Salomé, Patrice A.; Jenkins, Jerry; Blaby-Haas, Crysten E.; Purvine, Samuel O.; O’Donnell, Samuel; Barry, Kerrie; Grimwood, Jane; Strenkert, Daniela; Kropat, Janette; Daum, Chris; Yoshinaga, Yuko; Goodstein, David; Vallon, Olivier; Schmutz, Jeremy; Merchant, Sabeeha

doi:10.1093/plcell/koac347

Cited by 52 publications

(44 citation statements)

References 166 publications

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“…This satellite, MSAT-11_cRei , consists of a ∼1.9-kb monomer and does not feature any characteristics typical of a TE. We have recently observed mobile insertions of MSAT-11_cRei in other C. reinhardtii strains (CC-1690 and CC-4532) ( Craig et al 2022 ). Although the mechanisms mediating satellite dissemination are not well understood, the phenomenon has been observed in other species and may be an important mechanism of satellite evolution ( Ruiz-Ruano et al 2016 ).…”

Section: Resultsmentioning

confidence: 99%

“…Approximately 22% of TRMs occurred in microsatellites (defined as tandem repeats with monomers <10 bp), and most of the remainder occurred in satellite DNA. The C. reinhardtii genome contains many introns featuring tandem repeats ( Craig et al 2022 ), and 30.3% and 64.7% of satellite and microsatellite TRMs, respectively, were located in genic sequences. It is important to note that the rate of TRMs per site per generation is several times higher than the genome-wide rate displayed in Figure 2 B, because TRMs can only occur within the ∼12% of the genome that features tandem repeats, effectively resulting in a smaller “callable” genome.…”

Section: Resultsmentioning

confidence: 99%

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Rates and spectra of de novo structural mutations inChlamydomonas reinhardtii

et al. 2022

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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 algaChlamydomonas 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% and CC-2931 38% of SMs). In CC-2931, a Crypton and a previously undescribed type of DNA element caused 71% of chromosomal rearrangements, whereas in CC-1952 a Dualen LINE was associated with 87% of duplications. Other SMs, notably large duplications in CC-2931, were likely products of various double-strand break repair pathways. Our results demonstrate that diverse types of SMs occur at substantial rates and support prominent roles for SMs and TEs in evolution.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Rates and spectra of de novo structural mutations inChlamydomonas reinhardtii

et al. 2022

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“…1C, outer circles) indicated a partial duplication of chromosome 1 in CC-4533 not present in previous sequencing 50 , suggesting that a duplicated mini-chromosome 1 emerged during the long-term culture in our laboratory, a phenomenon that is quite common since similar duplications were observed in other laboratory strains 51 . The copy number variation (CNV) on chromosome 15 and 16 were due to frequently misassembled regions known to contain repeated sequences 52 . No other chromosome-scale difference was found between CC-4533 and CC-1690 (Fig.…”

Section: Resultsmentioning

confidence: 99%

Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements inChlamydomonas reinhardtii

Chaux-Jukic

Agier

Garrido

et al. 2023

Preprint

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Telomeres and subtelomeres, the genomic regions located at chromosome extremities, are essential for genome stability in eukaryotes. In the absence of the canonical maintenance mechanism provided by telomerase, telomere shortening induces genome instability. The landscape of the ensuing genome rearrangements is not accessible by short-read sequencing. Here, we leverage Oxford Nanopore Technologies long-read sequencing to survey the extensive repertoire of genome rearrangements in telomerase mutants of the model green microalga Chlamydomonas reinhardtii. In telomerase mutant strains grown for ~700 generations, most chromosome extremities were capped by short telomere sequences that were either recruited de novo from other loci or maintained in a telomerase-independent manner. Other extremities did not end with telomeres but only with repeated subtelomeric sequences. The subtelomeric elements, including rDNA, were massively rearranged and involved in breakage-fusion-bridge cycles, translocations, recombinations and chromosome circularization. These events were established progressively over time and displayed heterogeneity at the subpopulation level. New telomere-capped extremities composed of sequences originating from more internal genomic regions were associated with high DNA methylation, suggesting that de novo heterochromatin formation contributes to restore chromosome end stability in C. reinhardtii. The diversity of alternative strategies to maintain chromosome integrity and the variety of rearrangements found in telomerase mutants are remarkable and illustrate genome plasticity at short timescales.

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“…The C. priscuii genome (Zhang et al ., 2021; BUSCO score of 85%) and transcriptome (Cvetkovska et al ., 2022) were recently sequenced. These datasets were screened for the presence of photoreceptor genes using previously identified sequences from C. reinhardtii and conserved photoreceptor domains (Greiner et al ., 2017) obtained from Phytozome (v6.1) as queries (Merchant et al ., 2007; Craig et al ., 2022). Photoreceptor genes in C. priscuii were identified through a tBLASTn search (e-value<e -10 , bit-score>100) and manually inspected for redundant sequences and to ensure correct gene structure annotation.…”

Section: Methodsmentioning

confidence: 99%

Aberrant light sensing and motility in the green algaChlamydomonas priscuiifrom the ice-covered Antarctic Lake Bonney

Poirier

Osmers

Wilkins

et al. 2023

Preprint

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The Antarctic green algaChlamydomonas priscuiiis an obligate psychrophile and an emerging model for photosynthetic adaptation to extreme conditions. Endemic to the ice-covered Lake Bonney, this alga thrives at highly unusual light conditions characterized by very low light irradiance (<15 μmol m-2s-1), a narrow wavelength spectrum enriched in blue light, and an extreme photoperiod. Genome sequencing ofC. priscuiiexposed an unusually large genome, with hundreds of highly similar gene duplicates and expanded gene families, some of which could be aiding its survival in extreme conditions. In contrast to the described expansion in the genetic repertoire inC. priscuii, here we suggest that the gene family encoding for photoreceptors is reduced when compared to related green algae. This alga also possesses a very small eyespot and exhibits an aberrant phototactic response, compared to the modelChlamydomonas reinhardtii. We also investigated the genome and behaviour of the closely related psychrophilic algaChlamydomonassp. ICE that is found throughout the photic zone of Lake Bonney and is naturally exposed to higher light levels. Our analyses revealed a photoreceptor gene family and a robust phototactic response similar to those in the modelChlamydomonas reinhardtii. These results suggest that the aberrant phototactic response inC. priscuiiis a result of life under extreme shading rather than a common feature of all psychrophilic algae. We discuss the implications of these results on the evolution and survival of shade adapted polar algae.

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The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory

Cited by 52 publications

References 166 publications

Rates and spectra of de novo structural mutations inChlamydomonas reinhardtii

Rates and spectra of de novo structural mutations inChlamydomonas reinhardtii

Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements inChlamydomonas reinhardtii

Aberrant light sensing and motility in the green algaChlamydomonas priscuiifrom the ice-covered Antarctic Lake Bonney

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