The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal...

Area of Science:

• Genomics
• Molecular Biology
• Algal Research

Background:

• The Chlamydomonas reinhardtii reference genome has undergone multiple revisions over 20 years.
• Previous versions contained significant misassemblies and annotation inaccuracies.

Purpose of the Study:

• To present version 6 of the Chlamydomonas reinhardtii reference genome with enhanced assembly quality and structural annotations.
• To provide chromosome-level assemblies for two key laboratory strains (CC-503 and CC-4532).

Main Methods:

• Utilized PacBio sequencing for chromosome-level assemblies.
• Employed Iso-Seq and deep RNA-sequencing for improved structural annotations.
• Conducted linkage analyses for assembly validation.

Main Results:

• Achieved a ten-fold increase in assembly contiguity with over 80% of filled gaps within genes.
• Identified genomic instability in strain CC-503, including a RECQ3 helicase deletion affecting >100 genes.
• Discovered unique structural mutations and retrotransposon proliferation in strain CC-4532.

Conclusions:

• Version 6 of the Chlamydomonas reinhardtii genome represents a significant advancement for algal genomics.
• Laboratory strains exhibit genomic instability, necessitating careful consideration during experimental data interpretation.
• The new genome assemblies provide a robust foundation for future research in this model organism.