Diversity of transcripts and transcript processing forms in plastids of the dinoflagellate alga Karenia mikimotoi.

Richard G Dorrell,George A Hinksman,Christopher J Howe

doi:10.1007/s11103-015-0408-9

Richard G Dorrell, George A Hinksman + Show 1 more

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https://doi.org/10.1007/s11103-015-0408-9

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Abstract

Plastids produce a vast diversity of transcripts. These include mature transcripts containing coding sequences, and their processing precursors, as well as transcripts that lack direct coding functions, such as antisense transcripts. Although plastid transcriptomes have been characterised for many plant species, less is known about the transcripts produced in other plastid lineages. We characterised the transcripts produced in the fucoxanthin-containing plastids of the dinoflagellate alga Karenia mikimotoi. This plastid lineage, acquired through tertiary endosymbiosis, utilises transcript processing pathways that are very different from those found in plants and green algae, including 3′ poly(U) tail addition, and extensive substitutional editing of transcript sequences. We have sequenced the plastid transcriptome of K. mikimotoi, and have detected evidence for divergent evolution of fucoxanthin plastid genomes. We have additionally characterised polycistronic and monocistronic transcripts from two plastid loci, psbD-tRNAMet-ycf4 and rpl36-rps13-rps11. We find evidence for a range of transcripts produced from each locus that differ in terms of editing state, 5′ end cleavage position, and poly(U) tail addition. Finally, we identify antisense transcripts in K. mikimotoi, which appear to undergo different processing events from the corresponding sense transcripts. Overall, our study provides insights into the diversity of transcripts and processing intermediates found in plastid lineages across the eukaryotes.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-015-0408-9) contains supplementary material, which is available to authorized users.

Highlights

As a consequence of their endosymbiotic origin, chloroplasts and other plastid lineages retain their own genomes, which encode proteins and other factors essential for their function (Dorrell and Howe 2015; Green 2011)
To characterise the diversity of polyuridylylated transcripts produced in plastids of the fucoxanthin-containing dinoflagellate Karenia mikimotoi, double stranded cDNA was generated from Karenia mikimotoi total cellular RNA using an oligo-d(A) cDNA synthesis primer, which anneals to dinoflagellate plastid poly(U) tails (Barbrook et al 2012; Dorrell and Howe 2012)
This is broadly similar to the situation for the Karlodinium veneficum plastid genome, which retains 73 protein-coding genes, but far fewer than the 110–115 protein-coding genes found in the plastid genomes of free living haptophytes (Gabrielsen et al 2011; Puerta et al 2005) (Fig. 1, genes in green circle)

Summary

Introduction

As a consequence of their endosymbiotic origin, chloroplasts and other plastid lineages retain their own genomes, which encode proteins and other factors essential for their function (Dorrell and Howe 2015; Green 2011). Understanding how these genomes are transcribed, and expressed, is fundamental to understanding plastid physiology. In addition to coding transcripts, plant plastids produce noncoding transcripts These include antisense transcripts, which are transcribed from promoters located on the template strand of plastid genes (Georg et al 2010; Sharwood et al 2011; Zghidi-Abouzid et al 2011).

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