Comparative genomics ofChlamydomonas

• DOI: 10.1101/2020.06.13.149070
• Publication Date: 2020-06-14T09:12:03Z
• Authors: Rory J. Craig; Ahmed R. Hasan; Rob W. Ness; Peter D. Keightley
• Keywords: 0301 basic medicine; Focus on the Biology of Plant Genomes; 0303 health sciences; Base Sequence; Centromere; Chlamydomonas; Molecular Sequence Annotation; Genomics; Genes, Plant; Introns; Evolution, Molecular; 03 medical and health sciences; Long Interspersed Nucleotide Elements; Genome Size; Chlamydomonas reinhardtii; Conserved Sequence; Genome, Plant; Phylogeny

AbstractDespite its fundamental role as a model organism in plant sciences, the green algaChlamydomonas reinhardtiientirely lacks genomic resources for any closely related species, obstructing its development as a study system in several fields. We present highly contiguous and well-annotated genome assemblies for the two closest known relatives of the species,Chlamydomonas incertaandChlamydomonas schloesseri, and a third more distantly related species,Edaphochlamys debaryana. We find the threeChlamydomonasgenomes to be highly syntenous with similar gene contents, although the 129.2 MbC. incertaand 130.2 MbC. schloesseriassemblies are more repeat-rich than the 111.1 MbC. reinhardtiigenome. We identify the major centromeric repeat inC. reinhardtiias an L1 LINE transposable element homologous to Zepp (the centromeric repeat inCoccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved inC. incertaandC. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating-type loci of theChlamydomonasspecies, potentially representing the early stages of mating-type haplotype reformation. We produce an 8-species whole-genome alignment of unicellular and multicellular volvocine algae and identify evolutionarily conserved elements in theC. reinhardtiigenome. We find that short introns (<~100 bp) are extensively overlapped by conserved elements, and likely represent an important functional class of regulatory sequence inC. reinhardtii. In summary, these novel resources enable comparative genomics analyses to be performed forC. reinhardtii, significantly developing the analytical toolkit for this important model system.