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, Journal Year: 2022, Volume and Issue: 35(2), P. 644 - 672

Published: Dec. 23, 2022

Abstract Five versions of the Chlamydomonas reinhardtii reference genome have been produced over last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for laboratory strains, CC-503 CC-4532, provide resources plus minus mating-type alleles. We corrected major misassemblies previous validated our via linkage analyses. Contiguity increased ten-fold >80% filled gaps are within genes. used Iso-Seq deep RNA-seq datasets to improve annotations, updated gene symbols textual annotation functionally characterized genes extensive manual curation. discovered that cell wall-less classical strain exhibits genomic instability potentially caused by deletion helicase RECQ3, with mutations identified affect >100 therefore CC-4532 as primary reference, although this also carries unique is experiencing rapid proliferation a Gypsy retrotransposon. expect all strains harbor gene-disrupting mutations, which should be considered when interpreting comparing experimental results. Collectively, presented here herald new era genomics will foundation continued research important organism.

Language: Английский

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Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(9)

Published: Feb. 26, 2025

Advances in sequencing technology have unveiled examples of nucleus-encoded polycistrons, once considered rare. Exclusively polycistronic transcripts are prevalent green algae, although the mechanism by which multiple polypeptides translated from a single transcript is unknown. Here, we used bioinformatic and vivo mutational analyses to evaluate competing mechanistic models for translation bicistronic mRNAs algae. High-confidence manually curated datasets loci two divergent Chlamydomonas reinhardtii Auxenochlorella protothecoides , revealed preference weak Kozak-like sequences ORF 1 an underrepresentation potential initiation codons before 2 start codon, suitable conditions leaky ribosome scanning allow translation. We analysis A. test mechanism. In manipulation sequence codon altered reporter expression at 2, with weaker enhancing stronger one diminishing it. A synthetic dual demonstrated inversely adjustable activity fluorescent protein expressed luciferase depending on strength sequence. Our findings demonstrate that ORFs algal consistent episodic 2. This work has implications functionality upstream open reading frames (uORFs) found across eukaryotic genomes transgene biology applications.

Language: Английский

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Blessing or curse: how the epigenetic resolution of host-transposable element conflicts shapes their evolutionary dynamics

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2020)

Published: April 9, 2024

Transposable elements (TEs) are selfish genetic whose antagonistic interactions with hosts represent a common conflict in eukaryotes. To resolve this conflict, have widely adopted epigenetic silencing that deposits repressive marks at TEs. However, mechanism is imperfect and fails to fully halt TE replication. Furthermore, can inadvertently spread adjacent functional sequences, phenomenon considered 'curse' of resolution. Here, we used forward simulations explore how its harmful side effects shape the evolutionary dynamics TEs their hosts. Our findings reveal allows stably coexist under wide range conditions, because underlying molecular mechanisms give rise copy-number dependency strength silencing. Interestingly, contrary intuitive expectations should evolve be as strong possible, found selective benefit for modifier alleles weaken biologically feasible conditions. These results dual nature silencing, both positive negative effects, complicates trajectory makes it challenging determine whether 'blessing' or 'curse'.

Language: Английский

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Cryptic infection of a giant virus in a unicellular green alga

Science, Journal Year: 2025, Volume and Issue: unknown

Published: April 10, 2025

Latency is a common strategy in wide range of viral lineages, but its prevalence giant viruses remains unknown. Here we describe 617 kbp integrated element the model green alga Chlamydomonas reinhardtii . We resolve genome using long-read sequencing, identify putative polinton-like integrase, and show that particles accumulate primarily during stationary growth phase. A diverse array viral-encoded selfish genetic elements expressed activity, including several Fanzor nuclease-encoding transposable elements. In addition, field isolates sp. harbor signatures endogenous related to C. virus exhibit similar infection dynamics, suggesting latency prevalent natural host communities. Our work describes an unusually large temperate unicellular eukaryote, substantially expanding scope cryptic infections virosphere.

Language: Английский

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Replitrons: A major group of eukaryotic transposons encoding HUH endonuclease

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(25)

Published: June 12, 2023

HUH endonucleases of the Rep (replication protein) class mediate replication highly diverse plasmids and viral genomes across all domains life. transposases have independently evolved from Reps, giving rise to three major transposable element groups: prokaryotic insertion sequences IS 200 /IS 605 91 CR , eukaryotic Helitrons. Here, I present Replitrons, a second group transposons encoding endonuclease. Replitron feature domain with one catalytic Tyr (Y1) an adjacent that may function in oligomerization, contrasting Helitron two (Y2) fused helicase (i.e., RepHel). Protein clustering found no link between described transposases, instead recovered weak association Reps circular Rep-encoding single-stranded (CRESS) DNA viruses their related (pCRESS). The predicted tertiary structure transposase Replitron-1 founding member is active green alga Chlamydomonas reinhardtii closely resembles CRESS-DNA other endonucleases. Replitrons are at least supergroups reach high copy numbers nonseed plant genomes. short direct repeats at, or potentially near, termini. Finally, characterize -and- paste de novo insertions using long-read sequencing C. experimental lines. These results support ancient evolutionarily independent origin line groups transposons. This work expands known diversity both eukaryotes.

Language: Английский

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Genome editing in the green alga Chlamydomonas: past, present practice and future prospects

The Plant Journal, Journal Year: 2025, Volume and Issue: 122(1)

Published: April 1, 2025

SUMMARY The green alga Chlamydomonas is an important and versatile model organism for research topics ranging from photosynthesis metabolism, cilia, basal bodies to cellular communication the cycle of significant interest bioengineering processes. genome in this unicellular contained 17 haploid chromosomes codes 16 883 protein coding genes. Functional genomics, as well biotechnological applications, rely on ability remove, add, change these genes a controlled efficient manner. In review, history gene editing put context wider developments genetics demonstrate how many key engineer algae follow global trends availability technology. Building background, overview state art engineering given, focusing primarily practical aspects while giving examples recent applications. Commonly encountered ‐specific challenges, developments, community resources are presented, finally, comprehensive discussion emergence evolution CRISPR/Cas‐based precision given. An outline possible future paths based current genetic tools presented.

Language: Английский

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Intragenomic mutational heterogeneity: structural and functional insights from gene evolution

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Language: Английский

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Extraction and selection of high-molecular-weight DNA for long-read sequencing from Chlamydomonas reinhardtii

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(2), P. e0297014 - e0297014

Published: Feb. 8, 2024

Recent advances in long-read sequencing technologies have enabled the complete assembly of eukaryotic genomes from telomere to by allowing repeated regions be fully sequenced and assembled, thus filling gaps left previous short-read methods. Furthermore, can also help characterizing structural variants, with applications fields genome evolution or cancer genomics. For many organisms, main bottleneck sequence long reads remains lack robust methods obtain high-molecular-weight (HMW) DNA. this purpose, we developed an optimized protocol extract DNA suitable for unicellular green alga Chlamydomonas reinhardtii , based on CTAB/phenol extraction followed a size selection step molecules. We provide validation results protocol, as well statistics obtained Oxford Nanopore Technologies sequencing.

Language: Английский

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Latent infection of an active giant endogenous virus in a unicellular green alga

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 3, 2024

Abstract Latency is a common strategy in wide range of viral lineages, but its prevalence giant viruses remains unknown. Here we describe the activity and production from 617 kbp integrated element model green alga Chlamydomonas reinhardtii . We resolve region using long-read sequencing show that particles are produced released otherwise healthy cultures. A diverse array viral-encoded selfish genetic elements expressed during GEVE reactivation produce proteins packaged virions. In addition, field isolates sp. harbor latent related to C. exhibit similar infection dynamics, demonstrating virus latency prevalent natural host communities. Our work reports largest temperate documented date first active identified unicellular eukaryote, substantially expanding known limits latency.

Language: Английский

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The effects of de novo mutation on gene expression and the consequences for fitness in Chlamydomonas reinhardtii

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(3)

Published: Feb. 16, 2024

Abstract Mutation is the ultimate source of genetic variation, bedrock evolution. Yet, predicting consequences new mutations remains a challenge in biology. Gene expression provides potential link between genotype and its phenotype. But variation gene created by de novo mutation fitness mutational changes to remain relatively unexplored. Here, we investigate effects >2,600 on across transcriptome 28 accumulation lines derived from 2 independent wild-type genotypes green algae Chlamydomonas reinhardtii. We observed that amount variance (Vm) was similar generates typical polygenic phenotypic traits approximately 15-fold seen limited species where Vm has been estimated. Despite clear effect expression, did not observe simple additive change, with no linear correlation total change count individual MA lines. therefore inferred distribution connect number differentially expressed genes (DEGs). Our DEE highly L-shaped 95% causing 0-1 DEG while remaining 5% are spread over long tail large cause multiple expression. The consistent many cis-acting targets affect only 1 target trans-acting have tens or hundreds genes. Further evidence for can be overabundance near Supporting comes 15:1 ratio DEGs clusters co-expression network, indicative shared regulatory architecture. Lastly, show there negative extent divergence ancestor fitness, providing direct deleterious perturbing

Language: Английский

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