An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyteChrysochromulinasp. NIES-1333

Abstract

Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames.

Rampant nuclear–mitochondrial–plastid phylogenomic discordance in globally distributed calcifying microalgae

“…2a) with two distinct 0.8–2.6 kb indels absent in the other Emiliania – Gephyrocapsa mitogenomes. One of them contains ORF584, also reported in Chrysochromulina (Nishimura et al ., 2014), and the other contains partially duplicated nad3 and cox2 genes. The mitogenome size and GC content are notably different between the two G. oceanica strains (RCC3711: 28.2 kb, 28.9%; RCC1296: 45.4 kb, 31.3%).…”

Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications

“…Among the known 18 mtDNAs of haptophyte species, nine were reported as complete sequences, and other nine were reported as partial sequences. Nine full-length mtDNAs all contain repeat regions of various lengths ranging from 1.9 to 20.7 kb (Puerta et al, 2004;Smith and Keeling, 2012;Hovde et al, 2014Hovde et al, , 2019Nishimura et al, 2014;Smith et al, 2014;Hulatt et al, 2020;Wideman et al, 2020). The mtDNA of the P. globosa strain CNS00066 had the longest repeat region among all constructed haptophyte mtDNAs.…”

Rappemonads are haptophyte phytoplankton

“…However, we failed to fill the gaps between the mitochondria-derived sequences, possibly because there are long repeated regions dispersed over the mitochondrial genomes of haptophyte species. 54…”