Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known - PubMed (original) (raw)

Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

Mikhail I Schelkunov et al. PeerJ. 2019.

Abstract

Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

Keywords: AT content; Chloroplast genomes; GC content; Heterotrophic plants; Parasitic plants; Plastid genomes.

© 2019 Schelkunov et al.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1

Figure 1. Map of the Rhopalocnemis phalloides plastid genome showing various features.

The circular-mapping plastid genome is represented linearly for convenience. Green arrows are rRNA-coding genes, red arrows are ribosomal protein-coding genes and blue arrows are genes coding proteins with other functions. Gray arcs represent splicing. Blue columns show non-coding regions.

Figure 2

Figure 2. AT content and lengths of the plastid genomes of Embryophyta.

Red dots denote completely heterotrophic plants and black dots mixotrophic and completely autotrophic.

Figure 3

Figure 3. Amino acid frequencies in the plastid proteins of Rhopalocnemis phalloides and Balanophora reflexa are affected by the high AT content.

Figure 4

Figure 4. The radial cladogram of rrn16 from Embryophyta and SAR.

Branches with bootstrap support below 70 are collapsed. The group of SAR with Balanophoraceae is colored orange, while Embryophyta without Balanophoraceae are colored green. The placement of Balanophoraceae within SAR is indicated by pink.

Figure 5

Figure 5. Evolutionary parameters of the phylogeny of Santalales.

Arabidopsis thaliana, used as the outgroup, is not shown. The total length of the alignment, used for the analysis, was 3,363 bp after removal of poorly aligned regions by Gblocks. * dN/dS on this branch cannot be calculated owing to a very small dS value.

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Grants and funding

The work was funded by a Russian Foundation for Basic Research grant (No. 16-34-01003) and a budgetary subsidy to the Institute for Information Transmission Problems (No. 0053-2019-0005). The work of Maxim Segreevich Nuraliev was carried out in accordance with a Government order for the Lomonosov Moscow State University (project No. AAAA-A16-116021660105-3). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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