Comparative genomics of Chlamydomonas.

Rory J Craig,Ahmed R Hasan,Peter D Keightley,Rob W Ness

doi:10.1093/plcell/koab026

Rory J Craig, Ahmed R Hasan + Show 2 more

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https://doi.org/10.1093/plcell/koab026

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Abstract

Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: 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. schloesseri assemblies 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 (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and >260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system.

Highlights

With the rapid increase in genome sequencing over the past two decades, comparative genomics analyses have become a fundamental tool in biological research
(Herron et al, 2009), while the unicellular lineage leading to C. reinhardtii includes only two other confirmed species, C. incerta and C. schloesseri (Proschold et al, 2005, 2018)
Chlamydomonas schloesseri was recently described by Proschold et al (2018), with the three isolates currently maintained in culture originating from a single site in Kenya

Summary

Introduction

With the rapid increase in genome sequencing over the past two decades, comparative genomics analyses have become a fundamental tool in biological research. As additional genomes were sequenced, it became possible to produce whole-genome alignments (WGAs) across multiple species and to identify conserved elements (CEs) in noncoding regions for several of the most well-studied lineages (Siepel et al, 2005; Stark et al, 2007; Gerstein et al, 2010; LindbladToh et al, 2011). Many of these conserved noncoding sequences overlap regulatory elements and the identification of CEs has proven to be among the most accurate approaches for discovering functional genomic sequences.

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