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An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids

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An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids

Kelsey R Moore et al. Front Microbiol.

Abstract

The phylum Cyanobacteria includes free-living bacteria and plastids, the descendants of cyanobacteria that were engulfed by the ancestral lineage of the major photosynthetic eukaryotic group Archaeplastida. Endosymbiotic events that followed this primary endosymbiosis spread plastids across diverse eukaryotic groups. The remnants of the ancestral cyanobacterial genome present in all modern plastids, enable the placement of plastids within Cyanobacteria using sequence-based phylogenetic analyses. To date, such phylogenetic studies have produced conflicting results and two competing hypotheses: (1) plastids diverge relatively recently in cyanobacterial evolution and are most closely related to nitrogen-fixing cyanobacteria, or (2) plastids diverge early in the evolutionary history of cyanobacteria, before the divergence of most cyanobacterial lineages. Here, we use phylogenetic analysis of ribosomal proteins from an expanded data set of cyanobacterial and representative plastid genomes to infer a deep placement for the divergence of the plastid ancestor lineage. We recover plastids as sister to Gloeomargarita and show that the group diverges from other cyanobacterial groups before Pseudanabaena, a previously unreported placement. The tree topologies and phylogenetic distances in our study have implications for future molecular clock studies that aim to model accurate divergence times, especially with respect to groups containing fossil calibrations. The newly sequenced cyanobacterial groups included here will also enable the use of novel cyanobacterial microfossil calibrations.

Keywords: Archaeplastida; chloroplast; cyanobacteria; evolution; phylogenetic tree.

Figures

FIGURE 1
FIGURE 1
A maximum likelihood (ML) phylogenetic tree made using a concatenation of 30 large and small subunit ribosomal proteins (Table 2) and RAxML. This tree supports a deep placement of the plastid clade with high bootstrap support. Bootstrap values are denoted for major divergences of cyanobacterial and plastid clades. All internal nodes have bootstrap values of >90.
FIGURE 2
FIGURE 2
A ML phylogenetic tree made without the inclusion of Pseudanabaena using RAxML. The placement of plastids in this tree is consistent with Figure 1, but with lower bootstrap support values. Additionally, the placement of clade 4 is shifted to be more recently branching in this tree than in trees that contain Pseudanabaena.
FIGURE 3
FIGURE 3
A ML phylogenetic tree that does not include any newly sequenced genomes, made using RAxML. This tree recovers a topology consistent with Figure 1, but with lower bootstrap support values.

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