Two CENH3 paralogs in the green alga Chlamydomonas reinhardtii have a redundantly essential function and associate with ZeppL‐LINE1 elements

The Plant Journal, Год журнала: 2025, Номер 122(2)

Опубликована: Апрель 1, 2025

SUMMARY Centromeres in eukaryotes are defined by the presence of histone H3 variant CENP‐A/CENH3. Chlamydomonas encodes two predicted CENH3 paralogs, CENH3.1 and CENH3.2, that have not been previously characterized. We generated peptide antibodies to unique N‐terminal epitopes for each paralogs as well an antibody against a shared epitope. All three recognized proteins expected size on immunoblots had punctate nuclear immunofluorescence staining patterns. These results consistent with both being expressed localized centromeres. CRISPR‐Cas9‐mediated insertional mutagenesis was used generate null mutations either or CENH3.2 . Single mutants were viable but cenh3.1 cenh3.2 double recovered, confirming function is essential. sequenced assembled chromosome‐scale genomes from strains CC‐400 UL‐1690 (a derivative CC‐1690) complete centromere sequences 17/17 14/17 chromosomes respectively, enabling us compare evolution across four isolates near assemblies. data revealed significant changes between homologous centromeres including mobility degeneration ZeppL‐LINE1 (ZeppL) transposons comprise major repeat sequence Chlamydomonas. cleavage under targets tagmentation (CUT&Tag) purify map CENH3‐bound genomic found enrichment CENH3‐binding almost exclusively at regions. An interesting exception chromosome 2 UL‐1690, which its genetically mapped region second, distal location, centered around single recently acquired ZeppL insertion. The regions 17 ranged 63.5 kb (average lower estimate) 175 upper estimate). relatively small suggests may be useful organism testing deploying artificial technologies.

Язык: Английский

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Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)

GigaScience, Год журнала: 2025, Номер 14

Опубликована: Янв. 1, 2025

Abstract Background Common bean is a significant grain legume in human diets. However, the lack of complete reference genome for common beans has hindered efforts to improve agronomic cultivars. Findings Herein, we present first telomere-to-telomere (T2T) assembly (Phaseolus vulgaris L., YP4) using PacBio High-Fidelity reads, ONT ultra-long sequencing, and Hi-C technologies. The resulted size 560.30 Mb with an N50 55.11 Mb, exhibiting high completeness accuracy (BUSCO score: 99.5%, quality value (QV): 54.86). sequences were anchored into 11 chromosomes, 20 22 telomeres identified, leading formation 9 T2T pseudomolecules. Furthermore, identified repetitive elements accounting 61.20% predicted 29,925 protein-coding genes. Phylogenetic analysis suggested estimated divergence time approximately 11.6 million years ago between P. Vigna angularis. Comparative revealed expanded gene families variations YP4 G19833 associated defense response. Conclusions genomic insights presented here are crucial future genetic studies not only but also other legumes.

Язык: Английский

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Chlamydomonas: Fast tracking from genomics

Journal of Phycology, Год журнала: 2023, Номер 59(4), С. 644 - 652

Опубликована: Июль 7, 2023

Abstract Elucidating biological processes has relied on the establishment of model organisms, many which offer advantageous features such as rapid axenic growth, extensive knowledge their physiological and gene content, ease with they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii been an exemplary that enabled scientific breakthroughs over decades, especially in fields photosynthesis, cilia function biogenesis, acclimation photosynthetic organisms to environment. Here, we discuss recent molecular/technological advances have applied C. how further fostered its development a “flagship” algal system. We also explore future promise this leveraging genomics, proteomics, imaging, synthetic biology for addressing critical issues.

Язык: Английский

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

PLoS ONE, Год журнала: 2024, Номер 19(2), С. e0297014 - e0297014

Опубликована: Фев. 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.

Язык: Английский

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Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Апрель 10, 2024

Centromeres play a crucial and conserved role in cell division, although their composition evolutionary history green algae, the ancestors of land plants, remains largely unknown.

Язык: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 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.

Язык: Английский

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Long-Read–Based Hybrid Genome Assembly and Annotation of Snow Algal Strain CCCryo 101-99 (cf. Sphaerocystis sp., Chlamydomonadales)

Genome Biology and Evolution, Год журнала: 2024, Номер 16(7)

Опубликована: Июнь 27, 2024

Abstract Polar regions harbor a diversity of cold-adapted (cryophilic) algae, which can be categorized into psychrophilic (obligate cryophilic) and cryotrophic (nonobligate snow algae. Both accumulate significant biomasses on glacier habitats play major roles in global climate dynamics. Despite their significance, genomic studies these organisms remain scarce, hindering our understanding evolutionary history adaptive mechanisms the face change. Here, we present draft genome assembly annotation algal strain CCCryo 101-99 (cf. Sphaerocystis sp.). The haploid is 122.5 Mb length represented by 664 contigs with an N50 0.86 Mb, Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness 92.9% (n = 1,519), maximum contig 5.3 guanine-cystosine (GC) content 53.1%. In total, 28.98% (35.5 Mb) contains repetitive elements. We identified 417 noncoding RNAs annotated chloroplast genome. predicted proteome comprises 14,805 genes BUSCO 97.8%. Our preliminary analyses reveal higher repeat compared mesophilic chlorophyte relatives, alongside enrichment gene families associated photosynthesis flagella functions. current data will facilitate future comparative studies, improving likely response polar algae to warming as well trajectories permanently cold environments.

Язык: Английский

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

Genome Research, Год журнала: 2023, Номер 33(9), С. 1582 - 1598

Опубликована: Авг. 14, 2023

Telomeres and subtelomeres, the genomic regions located at chromosome extremities, are essential for genome stability in eukaryotes. In absence of canonical maintenance mechanism provided by telomerase, telomere shortening induces instability. The landscape ensuing rearrangements is not accessible short-read sequencing. Here, we leverage Oxford Nanopore Technologies long-read sequencing to survey extensive repertoire telomerase mutants model green microalga

Язык: Английский

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Elevated accumulation of lutein and zeaxanthin in a novel high-biomass strain Dunaliella sp. ZP-1 through EMS mutagenesis

Research Square (Research Square), Год журнала: 2023, Номер unknown

Опубликована: Сен. 8, 2023

Abstract Background Dunaliella algae, such as salina rich in β-carotene and bardawil is lutein α-carotene, have been used aquaculture, supplements, cosmetics feed industries. The genus diverse secretive, so characterization of novel strains breeding new varieties through mutagenesis technology will promote natural carotenoid bioproduction. Results Salt stress test demonstrated microalgae strain ZP-1 was a halotolerant strain. Morphology observation phylogeny analysis indicated this unicellular green algae member the . Biomass RAM medium up to 2.45 g/L, showing an advantage over common terms yield. Furthermore, screen on ethyl methanesulfonate mutant library generated from high-biomass conducted improve productivity. A selected morphology combined with quantification by HPLC nominated turn yellow dunaliella 4 ( tyd4 ). displayed increased productivity 28.55% zeaxanthin 22.19%. promoted 17.40% continuous culture under red light. Application exogenous 1.0 µM melatonin lead cell density improved biomass. Conclusions results together support that EMS effective approach for improvement sp. ZP-1, which exhibiting potential some extent overcome bottleneck low biomass current commercial strains. had higher contents both zeaxanthin, whose yield could be further elevated light at lab-scale culture. Our study provided resources scientific research technical reference bioproduction carotenoids.

Язык: Английский

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Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 29, 2024

Background: Centromeres play a crucial and conserved role in cell division, although their composition evolutionary history green algae, the ancestors of land plants, remains largely unknown. Results: We constructed near telomere-to-telomere (T2T) assemblies for two Trebouxiophyceae species, Chlorella sorokiniana NS4-2 pyrenoidosa DBH, with chromosome numbers 12 13, genome sizes 58.11 Mb 53.41 Mb, respectively. identified validated centromere sequences using CENH3 ChIP-seq found that, similar to humans higher centromeric signals algae display pattern hypomethylation. Interestingly, centromeres both species comprised transposable elements, they differed significantly composition. Species within genus more diverse composition, major constituents including members LTR/Copia, LINE/L1, LINE/RTEX families. This is contrast Chlamydomonas reinhardtii, Coccomyxa subellipsoidea, Chromochloris zofingiensis, which instead has pronounced single-element Moreover, we observed significant differences structure among chromosomes strong collinearity genus, suggesting that sequence evolves rapidly than non-centromeric regions. Conclusions: study not only provides high-quality data comparative genomics but gives insight into early laying an important foundation further research on evolution.

Язык: Английский

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