Comparative genomics of chlamydomonas

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. We present highly contiguous and well-annotated genome assemblies for three unicellular relatives of the species, Chlamydomonas incerta, Chlamydomonas schloesseri and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseriassemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (thecentromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations andstructure are likely conserved in C. incerta and C. schloesseri. We report extensive re-arrangements, but limited gene turnover, between the minus mating-type loci of the Chlamydomonas species. We produce an 8-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtiiannotation and >260,000 evolutionary conserved elements in the C. reinhardtii genome. In summary, these novel resources enable comparative genomics analyses to be performed for C. reinhardtii, significantly developing the analytical toolkit for this important model system.