Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta)

Abstract

We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.

Mitochondrial Genome Evolution in Pelagophyte Algae

“…A lateral transfer of a coxI group II intron was previously suggested to have occurred from diatoms to raphidophytes belonging to the genus Chattonella ( Kamikawa et al. 2009 ; Guillory et al. 2018 ); a similar lateral transfer may have occurred here, but with a group I intron in the coxI gene between green algae and Aureoc.…”

“…A group II intron was identified in the mitochondrial rnl gene of P. calceolata ; this intron encodes a reverse transcriptase/maturase. Similar group II introns have been identified in the mitochondrial genomes of various stramenopiles, including in the rnl gene of diatoms ( Guillory et al. 2018 ).…”

“…2015 ) and particularly common in coxI , as mentioned above, where they have been identified in red algae ( Yang et al. 2015 ), diatoms ( Guillory et al. 2018 ), and raphidophycean flagellates ( Chattonella spp.…”

“…That said, outside of green algae and fungi, an LHE homolog has thus far only been found in the mitochondrial coxI gene of the centrohelid Marophrys sp., the katablepharid Leucocryptos marina , and a few bacteria. Although group II introns have been identified in the mitochondrial coxI gene (as well as the rnl gene) of various stramenopiles, group I introns are relatively rare ( Guillory et al. 2018 ).…”

The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis

“…Fragilariopsis cylindrus (61 Mb) and Pseudo-nitzschia multistriata (59 Mb) ( Table 2). The genomic GC content (48%) is similar to other diatom nuclear genomes ( Table 2) and indicates that the exceptional decrease in GC content experienced by the plastid genome (Table 1) did not similarly affect the nuclear (Table 2) or mitochondrial [35] genomes. Bowler et al [37] Mock et al [38] Basu et al [39] This study 1 BUSCO analyses performed in protein mode against the eukaryota_odb9 database.…”