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Single gene circles in dinoflagellate chloroplast genomes : characterization and phylogeny Zhang, Zhaoduo

Abstract

Chloroplast DNA was isolated from the peridinean dinoflagellate Heterocapsa triquetra on CsCl gradients and used to construct three plasmid libraries. Complete sequencing of chloroplast 16S and 23S ribosomal RNA, and eight chloroplast protein genes revealed that each gene is located alone on a separate minicircle: "one gene - one circle". Each circle has an unusual tripartite non-coding 9G-9A-9G region (putative replicon origin), which is highly conserved among the ten circles. This organization is extremely different from the chloroplast genome (120-200 kb) in higher plants and algae. Five aberrant minicircles that have the tripartite 9G-9A-9G region were also sequenced. However, each aberrant circle consists of several short fragments from two or three of four chloroplast genes: psbA,psbC, 16S and 23S rRNA, instead of a complete chloroplast gene. Comparison of the sequences of the five circles indicated that all five circles are related, and could have evolved by differential deletions and duplications from four common ancestral unigenic circles. Probably the aberrant circles have no function, and are selfish DNA in the chloroplast of H. triquetra. In order to investigate the generality of the minicircular chloroplast genes, genomic DNA from fourteen other dinoflagellates of five orders were hybridized with chloroplast gene probes. Minicircles were detected in eight species. Chloroplast 23S rRNA and psbA genes were amplified from five species by PCR; sequencing the PCR products confirmed they are minicircles. Sequence comparison showed that the chloroplast genes are conserved among different species; the noncoding region of the circles is conserved within each species, but different between species. The presence of minicircles in five orders suggests that unigenic minicircles evolved in the ancestor of peridinean dinoflagellates. However, DNA blots and PCR amplification of chloroplast genes from several other dinoflagellates showed that chloroplast genes might be present in large DNA molecules outside the five orders. Phylogenetic analyses using sequences of ribosomal RNA genes, and sequences of individual proteins as well as seven concatenated protein sequences were carried out. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining and LogDet trees were constructed. Inter-site rate variation and invariant sites were allowed for quartet puzzling and neighbor joining. All psbA and 23 SrRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In protein trees they are related to those of chromists and red algae. In 23S rRNA trees dinoflagellates are the sisters of sporozoans (apicomplexans), suggesting that dinoflagellate chloroplasts may be related to sporozoan plastids. The branches of the dinoflagellates and sporozoans are very long, and the possibility of long-branch artifacts cannot be ruled out. All the trees fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis.

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