The complete chloroplast and mitochondrial genomes of the diatomNitzschia palea(Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotomDurinskia baltica

Abstract

Nitzschia palea is a common freshwater diatom used as a bioindicator because of its tolerance of polluted waterways. There is also evidence it may be the tertiary endosymbiont within the “dinotom” dinoflagellate Durinskia baltica. A putative strain of N. palea was collected from a pond on the University of Virginia's College at Wise campus and cultured. For initial identification, three markers were sequenced—nuclear 18S rDNA, the chloroplast 23S rDNA, and rbcL. Morphological characteristics were determined using light and scanning electron microscopy; based on these observations the cells were identified as N. palea and named strain “Wise.” DNA from N. palea was deep sequenced and the chloroplast and mitochondrial genomes assembled. Single gene phylogenies grouped N. palea—Wise within a clearly defined N. palea clade and showed it was most closely related to the strain “SpainA3.” The chloroplast genome of N. palea is 119,447 bp with a quadripartite structure, 135 protein‐coding, 28 tRNA, and 3 rRNA genes. The mitochondrial genome is 37,754 bp with a single repeat region as found in other diatom chondriomes, 37 protein‐coding, 23 tRNA, and 2 rRNA genes. The chloroplast genomes of N. palea and D. baltica have identical gene content, synteny, and a 92.7% pair‐wise sequence similarity with most differences occurring in intergenic regions. The N. palea mitochondrial genome and D. baltica's endosymbiont mitochondrial genome also have identical gene content and order with a sequence similarity of 90.7%. Genome‐based phylogenies demonstrated that D. baltica is more similar to N. palea than any other diatom sequence currently available. These data provide the genome sequences of two organelles for a widespread diatom and show they are very similar to those of Durinskia baltica's endosymbiont.

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

“…The circular N. inconspicua mitochondrial genome is larger than many other pennate diatoms due to a 19,055 nt intragenic spacer (Fig. 5 A), consistent with the observation of intragenic spacers of widely varying sizes in mitochondrial genomes from other diatoms 35 . In addition to small and large mitochondrial rRNA subunits (rrnS, rrnL), the mitochondrial genome encodes ATP synthase complex components (atp 6 and 9), cytochrome B, cytochrome oxidase subunits (cox 1–3), NADH dehydrogenase subunits (nad 1–7, 9, and 11), large and small ribosomal subunit proteins (rpl 2, 5, 7, 14, and 16, plus rps 2, 3, 4, 7, 8, 10, 11, 13, 14, and 19), a tatC transporter, and 24 tRNA genes.…”

Diploid Genomic Architecture of Nitzschia Hildebrandi, An Elite Biomass Production Diatom

“…The circular N. hildebrandi mitochondrial genome is larger than many other pennate diatoms due to a 19,055 nt intragenic spacer (Figure 5A), consistent with the observation of intragenic spacers of widely varying sizes in mitochondrial genomes from other diatoms (Crowell et al 2019). In addition to small and large mitochondrial rRNA subunits (rrnS, rrnL), the mitochondrial genome encodes ATP synthase complex components (atp 6 and 9), cytochrome B, cytochrome oxidase subunits (cox 1-3), NADH dehydrogenase subunits (nad 1-7, 9, and 11), large and small ribosomal subunit proteins (rpl 2, 5, 7, 14, and 16, plus rps 2, 3, 4, 7, 8, 10, 11, 13, 14, and 19), a tatC transporter, and 24 tRNA genes.…”

Extensive chloroplast genome rearrangement amongst three closely related Halamphora spp. (Bacillariophyceae), and evidence for rapid evolution as compared to land plants

“…Numerous studies have compared gene content and genome rearrangement among diatom chloroplast genomes (e.g., [15,16,17,32,55,56,57,58,59,60,61,62]), but this is the first to compare multiple genomes within a genus of biraphid pennate diatoms and several surprising patterns were identified. In regard to the phylogenetic position of Halamphora and the relationship between Halamphora species, our 20-gene phylogeny supported similar relationships to those revealed in other studies [13,14].…”