A5011003571- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Protist diversity and phylogeny
- Algal biology and biofuel production
- Microbial Community Ecology and Physiology
- Evolution and Genetic Dynamics
- Photosynthetic Processes and Mechanisms
- Metallurgy and Material Science
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- Diatoms and Algae Research
- CRISPR and Genetic Engineering
- Plant Virus Research Studies
- Physiological and biochemical adaptations
- Marine and coastal plant biology
- Marine and coastal ecosystems
- Genetic diversity and population structure
- Animal Behavior and Reproduction
- RNA regulation and disease
- Aquatic Ecosystems and Phytoplankton Dynamics
- Photoreceptor and optogenetics research
- Plant Molecular Biology Research
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Biocrusts and Microbial Ecology
- Genomics and Chromatin Dynamics
QB3
2022-2025
University of California, Berkeley
2022-2025
Max Planck Institute for Biology
2024
Max Planck Institute for Developmental Biology
2024
University of Edinburgh
2017-2023
University of Toronto
2019-2021
Joint Genome Institute
2021
United States Department of Energy
2021
Uppsala University
2017
In the study of transposable elements (TEs), generation a high confidence set consensus sequences that represent diversity TEs found in given genome is key step path to investigate these fascinating genomic elements. Many algorithms and pipelines are available automatically identify putative TE families present genome. Despite availability valuable resources, producing library high-quality full-length largely remains process manual curation. This know-how often passed on from...
Auxenochlorella are diploid oleaginous green algae that highly amenable to genetic transformation by homologous recombination, providing great potential for discovery research and bioengineering. Vegetatively organisms experience specific evolutionary phenomena, including allodiploid hybridization, mitotic loss-of-heterozygosity aneuploidy; however, studies of these forces have mostly focused on fungi. Here, we present a telomere-to-telomere phased genome assembly UTEX 250-A, revealing...
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...
Despite its role as a reference organism in the plant sciences, 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. relatives: incerta, schloesseri, more distantly Edaphochlamys debaryana. The genomes are syntenous with similar gene contents, although 129.2 Mb incerta 130.2 schloesseri repeat-rich than 111.1 genome. identify major centromeric repeat LINE...
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...
Polycistronic gene expression, common in prokaryotes, was thought to be extremely rare eukaryotes. The development of long-read sequencing full-length transcript isomers (Iso-Seq) has facilitated a reexamination that dogma. Using Iso-Seq, we discovered hundreds examples polycistronic expression nuclear genes two divergent species green algae: Chlamydomonas reinhardtii and Chromochloris zofingiensis Here, employ range independent approaches validate multiple proteins are translated from for...
RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, genome editing. Some these enzymes are components insertion sequences (IS) in IS200/IS605 IS607 transposon families. Both IS families encode a TnpA transposase TnpB nuclease, an enzyme ancestral to CRISPR-Cas12s. In eukaryotes, homologs occur as two distinct types, Fanzor1s Fanzor2s. We analyzed evolutionary relationships between prokaryotic TnpBs eukaryotic...
Marine algae are responsible for half of the world's primary productivity, but this critical carbon sink is often constrained by insufficient iron. One species marine algae, Dunaliella tertiolecta , remarkable its ability to maintain photosynthesis and thrive in low-iron environments. A related species, salina Bardawil, shares attribute an extremophile found hypersaline To elucidate how manage their iron requirements, we produced high-quality genome assemblies transcriptomes both serve as a...
Red seaweeds form part of an ancient lineage eukaryotes that were one the first to evolve multicellularity. Although they share a common evolutionary origin with modern-day plants and display complex multicellular development, we still lack comprehensive genome data from most highly-evolved groups red algae. Here, present chromosome-level assembly Bostrychia moritziana , species is classified into Rhodomelaceae family Ceramiales order, both which constitute largest diverse order algae,...
De novo mutations are central for evolution, since they provide the raw material natural selection by regenerating genetic variation. However, studying de is challenging and generally restricted to model species, so we have a limited understanding of evolution mutation rate spectrum between closely related species. Here, present accumulation (MA) experiment study in unicellular green alga Chlamydomonas incerta perform comparative analyses with its closest known relative, reinhardtii. Using...
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...
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 structure infer how they evolved. Here, we use recent genome assemblies Chlamydomonas reinhardtii based on long-read sequencing comprehensively describe subtelomere architecture 17 chromosomes this model...
The nature of population structure in microbial eukaryotes has long been debated. Competing models have argued that species are either ubiquitous, with high dispersal and low rates speciation, or for many gene flow between populations is limited, resulting evolutionary histories similar to those macroorganisms. However, genomic approaches seldom applied this question. Here, we analyse whole-genome resequencing data all 36 confirmed field isolates the green alga Chlamydomonas reinhardtii. At...
The distribution of fitness effects (DFE) for new mutations is fundamental many aspects population and quantitative genetics. In this study, we have inferred the DFE in single-celled alga Chlamydomonas reinhardtii by estimating changes frequencies 254 spontaneous under experimental evolution equating frequency linked with their selection coefficients. We generated seven populations recombinant haplotypes crossing independently derived mutation accumulation lines carrying an average 36...
Genetic variation originates from several types of spontaneous mutation, including single-nucleotide substitutions, short insertions and deletions (indels), larger structural changes. Structural mutations (SMs) drive genome evolution are thought to play major roles in evolutionary adaptation, speciation, genetic disease, cancers. Sequencing mutation accumulation (MA) lines has provided estimates rates spectra indel many species, yet the rate new SMs is largely unknown. Here, we use long-read...
Abstract It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes noncoding. However, since identification conserved elements ( CE s) has been restricted to limited number model organisms, dynamics and evolutionary character genomic landscape conserved, hence likely functional, poorly understood in most species. Moreover, analysis full suite are particularly important for understanding genetic basis trait loci identified genome...
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 canonical endonuclease (EN)+ PLEs encodes RT and C-terminal GIY–YIG EN that enables intrachromosomal integration, whereas EN− lack generally restricted to chromosome termini. EN+ have only been found in animals, except for one case horizontal transfer conifers, occur several kingdoms. Here, we report new,...
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,...
Abstract Despite its fundamental role as a model organism in plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources for any closely related species, obstructing development study system several fields. We present highly contiguous and well-annotated genome assemblies two closest known relatives of incerta schloesseri , third more distantly Edaphochlamys debaryana . find three genomes to be syntenous with similar gene contents, although 129.2 Mb C. 130.2 are...
Abstract Genetic variation originates from several types of spontaneous mutation, including single nucleotide substitutions, short insertions and deletions (INDELs), larger structural changes. Structural mutations (SMs) drive genome evolution are thought to play major roles in evolutionary adaptation, speciation genetic disease, cancers. Sequencing mutation accumulation (MA) lines has provided estimates rates spectra INDEL many species, yet the rate new SMs is largely unknown. Here, we use...
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....
Abstract Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, but little is known about the 3D architecture sex chromosomes within nucleus, how that impacts their role in determination. Here, we determine sex-specific organization model brown alga Ectocarpus at 2 kb resolution, by mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report interphase...
This protocol describes a method for extracting and sequencing high molecular weight DNA fromAuxenochlorella protothecoides (UTEX 250). The incorporates purification steps where RNA is degraded, larger fragments (>10 kb) are enriched, nicks repaired. Sequencing libraries prepared from the resulting using Ligation Kit (version 14 chemistry) sequenced Oxford Nanopore Technologies MinION (Mk1B model). POD5 files generated, bases called MinKnow’s built-in Dorado base caller. With just single...