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Open Access Research article

Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae

Goro Tanifuji12, Naoko T Onodera1, Matthew W Brown3, Bruce A Curtis1, Andrew J Roger1, Gane Ka-Shu Wong456, Michael Melkonian7 and John M Archibald1*

Author Affiliations

1 Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada

2 Faculty of life and environmental sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan

3 Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762, USA

4 Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada

5 Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada

6 BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China

7 Department of Botany, Cologne Biocenter, University of Cologne, Cologne 50674, Germany

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BMC Genomics 2014, 15:374  doi:10.1186/1471-2164-15-374

Published: 15 May 2014

Abstract

Background

Nucleomorphs are residual nuclei derived from eukaryotic endosymbionts in chlorarachniophyte and cryptophyte algae. The endosymbionts that gave rise to nucleomorphs and plastids in these two algal groups were green and red algae, respectively. Despite their independent origin, the chlorarachniophyte and cryptophyte nucleomorph genomes share similar genomic features such as extreme size reduction and a three-chromosome architecture. This suggests that similar reductive evolutionary forces have acted to shape the nucleomorph genomes in the two groups. Thus far, however, only a single chlorarachniophyte nucleomorph and plastid genome has been sequenced, making broad evolutionary inferences within the chlorarachniophytes and between chlorarachniophytes and cryptophytes difficult. We have sequenced the nucleomorph and plastid genomes of the chlorarachniophyte Lotharella oceanica in order to gain insight into nucleomorph and plastid genome diversity and evolution.

Results

The L. oceanica nucleomorph genome was found to consist of three linear chromosomes totaling ~610 kilobase pairs (kbp), much larger than the 373 kbp nucleomorph genome of the model chlorarachniophyte Bigelowiella natans. The L. oceanica plastid genome is 71 kbp in size, similar to that of B. natans. Unexpectedly long (~35 kbp) sub-telomeric repeat regions were identified in the L. oceanica nucleomorph genome; internal multi-copy regions were also detected. Gene content analyses revealed that nucleomorph house-keeping genes and spliceosomal intron positions are well conserved between the L. oceanica and B. natans nucleomorph genomes. More broadly, gene retention patterns were found to be similar between nucleomorph genomes in chlorarachniophytes and cryptophytes. Chlorarachniophyte plastid genomes showed near identical protein coding gene complements as well as a high level of synteny.

Conclusions

We have provided insight into the process of nucleomorph genome evolution by elucidating the fine-scale dynamics of sub-telomeric repeat regions. Homologous recombination at the chromosome ends appears to be frequent, serving to expand and contract nucleomorph genome size. The main factor influencing nucleomorph genome size variation between different chlorarachniophyte species appears to be expansion-contraction of these telomere-associated repeats rather than changes in the number of unique protein coding genes. The dynamic nature of chlorarachniophyte nucleomorph genomes lies in stark contrast to their plastid genomes, which appear to be highly stable in terms of gene content and synteny.

Keywords:
Nucleomorph; Genome reduction; Chlorarachniophytes; Cryptophytes; Endosymbiosis; Phylogenomics