Dataset Information

Complete chloroplast genome of the tiny marine diatom Nanofrustulum shiloi (Bacillariophyta) from the Adriatic Sea.

ABSTRACT: We report the chloroplast genome sequence of Nanofrustulum shiloi, a tiny araphid pennate diatom collected from the Adriatic Sea. The 160,994-bp N. shiloi genome displays a quadripartite structure and its gene repertoire resembles those of other diatom chloroplast genomes. Besides the genes located in the inverted repeat, psbY is duplicated. A gene-poor region in the large single-copy region contains multiple ORFs sharing sequence similarities with plasmids and chloroplast ORFs found in other diatom species. The genome features a single intron, a group II intron in petB. Phylogenomic analysis identified N. shiloi at a basal position within the araphid 2 clade.

SUBMITTER: Li C

PROVIDER: S-EPMC7707228 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Complete chloroplast genome of the tiny marine diatom Nanofrustulum shiloi (Bacillariophyta) from the Adriatic Sea.

Li Chunlian C Gastineau Romain R Turmel Monique M Witkowski Andrzej A Otis Christian C Car Ana A Lemieux Claude C

Mitochondrial DNA. Part B, Resources 20191004 2

We report the chloroplast genome sequence of Nanofrustulum shiloi, a tiny araphid pennate diatom collected from the Adriatic Sea. The 160,994-bp N. shiloi genome displays a quadripartite structure and its gene repertoire resembles those of other diatom chloroplast genomes. Besides the genes located in the inverted repeat, psbY is duplicated. A gene-poor region in the large single-copy region contains multiple ORFs sharing sequence similarities with plasmids and chloro ...[more]

PMID: 33366000

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Project description:BACKGROUND:Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions. RESULTS:All isolates from the more regionally-localized population (population 2) possessed 1.94 +/- 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1). The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history. CONCLUSIONS:The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is consistent with a recent divergence between the populations, which are likely cryptic species. Genome size variation is known to occur in other diatom genera; we hypothesize that genome duplication may be an active and important mechanism of genetic and physiological diversification and speciation in diatoms.

Dataset Information

Complete chloroplast genome of the tiny marine diatom Nanofrustulum shiloi (Bacillariophyta) from the Adriatic Sea.

Publications

Complete chloroplast genome of the tiny marine diatom <i>Nanofrustulum shiloi</i> (Bacillariophyta) from the Adriatic Sea.

Similar Datasets

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