2019/02/22 by Duckhyun Lhee, Ji-San Ha, Sunju Kim +3 · 2 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Protist diversity and phylogeny #Microbial Community Ecology and Physiology #Genomics and Phylogenetic Studies #Biology #Plastid #Endosymbiosis #GC-content #Genome #Chromatophore #Evolutionary biology #Lineage (genetic) #Gene #Phylogenetics #Genetics #Chloroplast
paper · pdf · doi:10.1038/s41598-019-38621-8
openalex publication_date 2019/02/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
The thecate amoeba Paulinella is a valuable model for understanding plastid organellogenesis because this lineage has independently gained plastids (termed chromatophores) of alpha-cyanobacterial provenance. Plastid primary endosymbiosis in Paulinella occurred relatively recently (90-140 million years ago, Mya), whereas the origin of the canonical Archaeplastida plastid occurred >1,500 Mya. Therefore, these two events provide independent perspectives on plastid formation on vastly different timescales. Here we generated the complete chromatophore genome sequence from P. longichromatophora (979,356 bp, GC-content = 38.8%, 915 predicted genes) and P. micropora NZ27 (977,190 bp, GC-content = 39.9%, 911 predicted genes) and compared these data to that from existing chromatophore genomes. Our analysis suggests that when a basal split occurred among photosynthetic Paulinella species ca. 60 Mya, only 35% of the ancestral orthologous gene families from the cyanobacterial endosymbiont remained in chromatophore DNA. Following major gene losses during the early stages of endosymbiosis, this process slowed down significantly, resulting in a conserved gene content across extant taxa. Chromatophore genes faced relaxed selection when compared to homologs in free-living alpha-cyanobacteria, likely reflecting the homogeneous intracellular environment of the Paulinella host. Comparison of nucleotide substitution and insertion/deletion events among different P. micropora strains demonstrates that increases in AT-content and genome reduction are ongoing and dynamic processes in chromatophore evolution.