Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants

Abstract

Background: The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. Results: We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms.

Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta)

“…, Lee et al. ). The 18 complete mitochondrial genomes (6 for Gracilariopsis , 11 for Gracilaria , and 1 for Melanthalia ) are highly conserved except in two regions that include variations in tRNA genes and inserted PDS (Fig.…”

“…, , Lee et al. ,b). The aa matrices were aligned using MAFFT version 7 (Katoh and Standley ) as implemented in Geneious 9.1.8.…”

Plasmid‐Associated Organelle Genome Evolution In Red Algae

“…As a consequence, Rhodophyta (red algae) contains the largest number of plastid genes but the smallest mitochondrial gene inventory is found among Archaeplastida (Lee et al. 2016a, Qiu et al. ).…”

Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta)

“…Red algae have the largest plastid (cp) genomes among the groups of algae, ranging from 149,987 nt in length in Cyanidioschyzon merolae (Cyanidiophyceae) to 259,000 nt in Porphyridium sordidum (Porphyridiophyceae), but with narrow ranges (175,000–194,000 nt) in the Florideophyceae (Lee et al. ). However, much larger cp genomes have been recently described (Muñoz‐Gómez et al.…”

“…The number of coding genes in red algae is also the highest among the groups of algae (184–235; Lee et al. ). Red algal cp genomes not only have the highest gene content among eukaryotes with primary cp (Archaeplastida), but their genomes are also the most conserved (Janouškovec et al.…”