Nuclear Genome Sequence Survey of the Dinoflagellate Heterocapsa triquetra

Abstract

Dinoflagellates have among the largest nuclear genomes known, but we know little about their contents or organisation. Given the interest in dinoflagellate ecology, cell biology, and evolutionary biology, there are many reasons to thoroughly investigate the contents of dinoflagellate genomes, but because of their large size the only thorough samples to date have relied on expressed sequence tag surveys to analyse cDNAs. To complement this, there are some studies of the physical properties of dinoflagellate chromosomes, but no direct survey of the nature of the sequences contained within them. To start to build a picture of the contents of these genomes, we have sequenced over 230,000 bp from the nuclear genome of Heterocapsa triquetra, which has been estimated to be 18-23 billion base pairs in total. The survey includes one putative gene with two relict spliced leaders, one putative pseudogene, and a small number of low-complexity repeats, transposons, and other putative selfish elements, all of which account for about 5% of the survey. Another 5% of the survey was long, complex repeats, some highly represented. By far the greatest fraction of the survey (89.5%) is made up of non-repeated sequence with no similarity to any other known sequence.

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

“…To accommodate 75,000 genes of 1 kbp with an average gene copy number of 30 within the 200-pg nuclear DNA (∼2 × 10 11 bp) we would have to assume a gene density of 1%. So far, the only report of a large genomic DNA fragment sequence (230 kb) is in Heterocapsa, and this indicates a gene density of only 0.2% (39). Furthermore, the size distribution of our sequences, biased toward short sequences (Fig.…”

Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates

“…Some of these are unique to one lineage and very different in the other. For example, dinoflagellates have among the largest nuclear genomes known, and these genomes have a very low gene density and permanently condensed chromosomes that lack nucleosomes (18). Kinetoplastid genomes, however, are relatively small, gene-dense, and remain uncondensed during the cell cycle (19).…”

Growth- and nutrient-dependent gene expression in the toxigenic marine dinoflagellate Alexandrium minutum

“…Dinoflagellates arguably contain the most unusual eukaryotic genetic machinery known. Their huge genomes (LaJeunesse et al, 2005) comprise both major proportions of apparently random, non-repetitive DNA with very little recognizable gene content (Jaeckisch et al, submitted for publication;McEwan et al, 2008) and unusually high numbers of transcribed genes (Moustafa et al, 2010). For example, Alexandrium tamarense, with about three times the nuclear DNA content of A. minutum, was shown to contain about 40,000 transcribed genes occurring in complex families (LaJeunesse et al, 2005).…”