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A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis.
Payne, Zachary L; Penny, Gervette M; Turner, Tychele N; Dutcher, Susan K.
Afiliación
  • Payne ZL; Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
  • Penny GM; Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
  • Turner TN; Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
  • Dutcher SK; Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA. Electronic address: dutcher@wustl.edu.
Plant Commun ; 4(2): 100493, 2023 03 13.
Article en En | MEDLINE | ID: mdl-36397679
Genomic assemblies of the unicellular green alga Chlamydomonas reinhardtii have provided important resources for researchers. However, assembly errors, large gaps, and unplaced scaffolds as well as strain-specific variants currently impede many types of analysis. By combining PacBio HiFi and Oxford Nanopore long-read technologies, we generated a de novo genome assembly for strain CC-5816, derived from crosses of strains CC-125 and CC-124. Multiple methods of evaluating genome completeness and base-pair error rate suggest that the final telomere-to-telomere assembly is highly accurate. The CC-5816 assembly enabled previously difficult analyses that include characterization of the 17 centromeres, rDNA arrays on three chromosomes, and 56 insertions of organellar DNA into the nuclear genome. Using Nanopore sequencing, we identified sites of cytosine (CpG) methylation, which are enriched at centromeres. We analyzed CRISPR-Cas9 insertional mutants in the PF23 gene. Two of the three alleles produced progeny that displayed patterns of meiotic inviability that suggested the presence of a chromosomal aberration. Mapping Nanopore reads from pf23-2 and pf23-3 onto the CC-5816 genome showed that these two strains each carry a translocation that was initiated at the PF23 gene locus on chromosome 11 and joined with chromosomes 5 or 3, respectively. The translocations were verified by demonstrating linkage between loci on the two translocated chromosomes in meiotic progeny. The three pf23 alleles display the expected short-cilia phenotype, and immunoblotting showed that pf23-2 lacks the PF23 protein. Our CC-5816 genome assembly will undoubtedly provide an important tool for the Chlamydomonas research community.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Chlamydomonas reinhardtii Tipo de estudio: Diagnostic_studies Idioma: En Revista: Plant Commun Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: China
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Chlamydomonas reinhardtii Tipo de estudio: Diagnostic_studies Idioma: En Revista: Plant Commun Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: China