CHAPTER CONTENTS INTRODUCTION THE CHLAMYDOMONAS REFERENCE GENOME A. Versions 1-5: improvements of a draft genome B. Version 6: Long reads, misassembly corrections and a new reference strain STRUCTURAL ANNOTATIONS AND GENE ORGANIZATION A. Versions 3-5: The history of gene model annotation in Chlamydomonas B. Version 6 structural annotations C. Gene IDs D. Gene structure and organization E. Intron abundance and lengths F. Alternative splicing G. Polycistronic gene expression H. Non-coding RNA genes GENOME ARCHITECTURE A. Centromeres B. Telomeres and subtelomeres C. Transposable elements D. Genome-wide patterns of methylation E. Base composition, mutation, recombination and codon usage F. The mating-type locus GENOME EVOLUTION A Genomic variation among laboratory strains B. Population & species-level genomic variation C. Comparative genomics in the Reinhardtinia clade ONLINE RESOURCES FOR THE CHLAMYDOMONAS GENOME FUTURE PERSPECTIVES