Abstract
BackgroundNucleomorphs, the remnant nuclei of photosynthetic algae that have become endosymbionts to other eukaryotes, represent a unique example of convergent reductive genome evolution in eukaryotes, having evolved independently on two separate occasions in chlorarachniophytes and cryptophytes. The nucleomorphs of the two groups have evolved in a remarkably convergent manner, with numerous very similar features. Chief among them is the extreme reduction and compaction of nucleomorph genomes, with very small chromosomes and extremely short or even completely absent intergenic spaces. These characteristics pose a number of intriguing questions regarding the mechanisms of transcription and gene regulation in such a crowded genomic context, in particular in terms of the functioning of the histone code, which is common to almost all eukaryotes and plays a central role in chromatin biology.ResultsThis study examines the sequences of nucleomorph histone proteins in order to address these issues. Remarkably, all classical transcription- and repression-related components of the histone code seem to be missing from chlorarachniophyte nucleomorphs. Cryptophyte nucleomorph histones are generally more similar to the conventional eukaryotic state; however, they also display significant deviations from the typical histone code. Based on the analysis of specific components of the code, we discuss the state of chromatin and the transcriptional machinery in these nuclei.ConclusionsThe results presented here shed new light on the mechanisms of nucleomorph transcription and gene regulation and provide a foundation for future studies of nucleomorph chromatin and transcriptional biology.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-016-0119-4) contains supplementary material, which is available to authorized users.
Highlights
Nucleomorphs, the remnant nuclei of photosynthetic algae that have become endosymbionts to other eukaryotes, represent a unique example of convergent reductive genome evolution in eukaryotes, having evolved independently on two separate occasions in chlorarachniophytes and cryptophytes
All cryptophyte nucleomorphs encode a version of H2B, implying that only H2A has been transferred to the host nucleus in this lineage
Overall, the observations presented here suggest that a substantial fraction of the epigenomic toolkit has been lost from nucleomorphs and much of whatever remains of it has been transferred to the nucleus, as has happened to many other genes previously resident in the nucleomorph genome
Summary
Nucleomorphs, the remnant nuclei of photosynthetic algae that have become endosymbionts to other eukaryotes, represent a unique example of convergent reductive genome evolution in eukaryotes, having evolved independently on two separate occasions in chlorarachniophytes and cryptophytes. Nucleomorph genomes are the smallest eukaryote genomes known, typically just a few hundred kilobases in size; in all known cases, they are organized into three AT-rich chromosomes, with arrays of ribosomal RNA genes in their subtelomeric regions; they are extremely compacted, with almost nonexistent intergenic spaces (sometimes genes overlap), and even the genes themselves are frequently shortened [8,9,10,11,12,13,14]. These generalizations can be made thanks to the availability of fully sequenced nucleomorph genomes from several species: the chlorarachniophytes Bigelowiella natans [13]
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