Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes

Abstract

Plastids, similar to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations comes from studies of the primary plastids of green algae and land plants. To broaden our perspective, we obtained seven new ptDNA sequences from freshwater species of photosynthetic euglenids-a group that obtained secondary plastids, known to have dynamically evolving genome structure, via endosymbiosis with a green alga. Our analyses have demonstrated that the evolutionary history of euglenid plastid genome structure is exceptionally convoluted, with a patchy distribution of inverted ribosomal operon (rDNA) repeats, as well as several independent acquisitions of tandemly repeated rDNA copies. Moreover, we have shown that inverted repeats in euglenid ptDNA do not share their genome-stabilizing property documented in chlorophytes. We hypothesize that the degeneration of the quadripartite structure of euglenid plastid genomes is connected to the group II intron expansion. These findings challenge the current global paradigms of plastid genome architecture evolution and underscore the often-underestimated divergence between the functionality of shared traits in primary and complex plastid organelles.

Keywords: Euglenophyta; ancestral state reconstruction; euglenid; inverted repeat; plastid genome; secondary plastid.

Fig. 1.

Schematic representation of the three rDNA operon organization types in euglenid plastomes, with species investigated in this study listed as carrying the respective structures. Arrows represent rDNA copies and orientation; undirected sections represent protein-coding genes of the large single-copy region of the plastid genome (created with BioRender.com).

Fig. 2.

Plastid-based phylogenomic tree of Euglenophyta. Species names in bold indicate organisms whose ptDNA was first sequenced in this work. rDNA operon copy number (filled arrows denote complete operon copies; empty ones denote incomplete ones) and orientation are shown on the tree tips. Ancestral IR presence in euglenophytes is marked at the corresponding node; uncertain rDNA organization is marked at the node corresponding to the last common ancestor of Euglenaceae and Phacaceae. Full dots at the tree branches denote undisputed state transitions; striped dots at the tree branches denote hypothetical, mutually exclusive scenarios of only IR gains or only IR losses within Euglenaceae and Phacaceae. Bayesian posterior probability and bootstrap support values above 50 are shown at the nodes. Asterisks (*) denote absolute probability and support (>0.99/>95).

Fig. 3.

Ancestral state reconstruction of plastid genome organization in Euglenophyta, mapped onto the group's phylogeny (see fig. 2). State transition rate was preset as unequal (ARD model), and the transition rates were calculated based on empirical data. Pie charts at the nodes represent the calculated probabilities of the respective states.