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Analysis of the genomic DNA of the harmful dinoflagellate Prorocentrum minimum: a brief survey focused on the noncoding RNA gene sequences

Abstract

Dinoflagellate algae are considered some of the most complicated organisms owing to their unusual genomic characteristics and novel gene regulatory mechanisms. Here, we extracted information from the genomic sequences of the marine dinoflagellate Prorocentrum minimum using GS FLX pyrosequencing technology. We obtained 473 Mb of sequences from 1,379,588 reads, which generated 16,599 contigs after assembly. Among the annotated sequences (4902 contigs, 30 %), BLAST analyses showed that 28.95 % (4731 contigs) of the genome fragments were homologous with bacterial sequences and only 0.96 % (156 contigs) had eukaryotic origins. However, analysis of bacterial 16S/23S rDNA sequences in the P. minimum genome revealed that the organism likely acquired this genetic material from symbiotic bacteria, possibly through horizontal gene transfer, thus demonstrating a definitive association between bacteria and P. minimum. Moreover, a specific consensus pattern was defined for dinoflagellate spliced leader (SL) sequences, a well-known genetic marker of dinoflagellates. Further, comparisons of the various genomic proportions with respect to nuclear, mitochondrial, and chloroplast genes revealed unique genomic features that include clusters of noncoding RNA genes and tandem repeats. Taken together, this study details the salient features of noncoding RNA genes in P. minimum and provides further insights into the genome of this and other dinoflagellates.

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Acknowledgments

This work was supported by a National Research Foundation of Korea (NRF) grant funded by the Korea government (Nos. NRF-M1A5A1-2013-044476, and 2013R1A1A2013596), and a grant from the National Fisheries Research and Development (NFRDI) funded to J.-S. Ki.

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Correspondence to Jang-Seu Ki.

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Ponmani, T., Guo, R. & Ki, JS. Analysis of the genomic DNA of the harmful dinoflagellate Prorocentrum minimum: a brief survey focused on the noncoding RNA gene sequences. J Appl Phycol 28, 335–344 (2016). https://doi.org/10.1007/s10811-015-0570-0

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Keywords

  • Dinoflagellate
  • Prorocentrum minimum
  • Spliced leader
  • Genome
  • Noncoding RNA genes