The Chlamydomonas genome project: a decade on

Abstract

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes.

Keywords: Chlamydomonas; Phytozome; algae; annotation; gene symbols; nomenclature.

Figure 1

Refinement of the NRAMP4 gene model. Black and red boxes represent genome sequence and gaps respectively on portions of scaffolds or chromosomes (coordinates in bp indicated at the edges), for genome assembly versions as labelled on the left. Gene models are depicted as filled boxes (exons) along horizontal lines (introns). Box fill color indicates the first assembly version an exon was predicted in (green is v3, mauve is v4, orange is v5); wide and narrow sections represent coding sequence and untranslated regions respectively) and an arrowhead indicates the direction of transcription. Shading between dotted lines represents identical nucleic acid sequence between genome assemblies. (A) Comparing assembly v3 to v4, note the amount of gap sequence (red) that was filled, allowing more accurate gene loci to be predicted. The sequence from contig_128 and contig_129 from scaffold 6 were placed on chromosome 5, as was all of scaffold 289. The gap between contig_128 and contig_129 was filled (by addition of 17bp) in v4, while the gap in scaffold 289 was partially filled (by addition of a further 1178bp). (B) The gap in v4 was filled in the v5 assembly (899bp), which is near-finished quality, allowing the extension of exon 12 and prediction of a new exon (both represented by orange boxes) and a gene model that is completely consistent with assembled 454 EST evidence (lilac track at the bottom).