Haematococcus lacustris: the makings of a giant-sized chloroplast genome

Abstract

Recent work on the chlamydomonadalean green alga Haematococcus lacustris uncovered the largest plastid genome on record: a whopping 1.35 Mb with >90 % non-coding DNA. A 500-word description of this genome was published in the journal Genome Announcements. But such a short report for such a large genome leaves many unanswered questions. For instance, the H. lacustris plastome was found to encode only 12 tRNAs, less than half that of a typical plastome, it appears to have a non-standard genetic code, and is one of only a few known plastid DNAs (ptDNAs), out of thousands of available sequences, not biased in adenine and thymine. Here, I take a closer look at the H. lacustris plastome, comparing its size, content and architecture to other large organelle DNAs, including those from close relatives in the Chlamydomonadales. I show that the H. lacustris plastid coding repertoire is not as unusual as initially thought, representing a standard set of rRNAs, tRNAs and protein-coding genes, where the canonical stop codon UGA appears to sometimes signify tryptophan. The intergenic spacers are dense with repeats, and it is within these regions where potential answers to the source of such extreme genomic expansion lie. By comparing ptDNA sequences of two closely related strains of H. lacustris, I argue that the mutation rate of the non-coding DNA is high and contributing to plastome inflation. Finally, by exploring publicly available RNA-sequencing data, I find that most of the intergenic ptDNA is transcriptionally active.

Keywords: Corynoplastis; Volvox; genome size; green algae; plastid genome.

Figure 1.

Known plastome size ranges within the Chlamydomonadales. Branching orders and clade names based on Nakada et al. (2008). Genome sizes based on published and/or GenBank data.

Figure 2.

Eukaryotic algae with giant plastomes. Clockwise from left: Haematococcus lacustris strain CCMP 3127, which is equivalent to UTEX 2505, the strain used for plastome sequencing (image: National Center for Marine Algae and Microbiota); the unicellular rhodellophycean red alga Corynoplastis japonica (image: Sergio Muñoz-Gómez); and the marine unicellular ulvophyte Acetabularia sp. (image: Albert Kok).