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

Abstract

Diatoms are the most diverse lineage of algae, but the diversity of their chloroplast genomes, particularly within a genus, has not been well documented. Herein, we present three chloroplast genomes from the genus Halamphora ( H . americana , H . calidilacuna , and H . coffeaeformis ), the first pennate diatom genus to be represented by more than one species. Halamphora chloroplast genomes ranged in size from ~120 to 150 kb, representing a 24% size difference within the genus. Differences in genome size were due to changes in the length of the inverted repeat region, length of intergenic regions, and the variable presence of ORFs that appear to encode as-yet-undescribed proteins. All three species shared a set of 161 core features but differed in the presence of two genes, serC and tyrC of foreign and unknown origin, respectively. A comparison of these data to three previously published chloroplast genomes in the non-pennate genus Cyclotella (Thalassiosirales) revealed that Halamphora has undergone extensive chloroplast genome rearrangement compared to other genera, as well as containing variation within the genus. Finally, a comparison of Halamphora chloroplast genomes to those of land plants indicates diatom chloroplast genomes within this genus may be evolving at least ~4–7 times faster than those of land plants. Studies such as these provide deeper insights into diatom chloroplast evolution and important genetic resources for future analyses.

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

“…This intron resides within petB at the same location as a similar intron found in the raphid Halamphora calidilacuna (Hamsher et al. 2019 ).…”

“…The N. shiloi chloroplast genome features a single intron, a group II intron encoding a putative reverse transcriptase/maturase. This intron resides within petB at the same location as a similar intron found in the raphid Halamphora calidilacuna (Hamsher et al 2019).…”

Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses

“…This finding further suggests that the 35S rDNAs are more cost-effective super-barcodes than plastomes since the former is approximately 13 times shorter than the latter in the cypresses (Table 1). www.nature.com/scientificreports/ Plastomic rearrangements between congeneric species, albeit rare in seed plants, have been documented in some lineages, such as Pelargonium and Hypseocharis 40 , Podocarpus 41 , Juniperus 26 , Calocedrus 28 , and Halamphora 42 . Recently, plastomic rearrangements were found in conspecific individuals of yews, likely due to recurrent shifts between predominant and substoichiometric isomeric plastomes 24 .…”

“…Plastomic rearrangements between congeneric species, albeit rare in seed plants, have been documented in some lineages, such as Pelargonium and Hypseocharis 40 , Podocarpus 41 , Juniperus 26 , Calocedrus 28 , and Halamphora 42 . Recently, plastomic rearrangements were found in conspecific individuals of yews, likely due to recurrent shifts between predominant and substoichiometric isomeric plastomes 24 .…”

It's what's inside that matters: physiological adaptations of high‐latitude marine microalgae to environmental change

“…However, there is a need to understand how these compensatory mechanisms impact cell fitness and metabolic profiles, and how this ultimately impacts ecology and biogeochemical cycles. Considering the high rate of evolution of diatom chloroplast genes compared to land plants (Hamsher et al, 2019), and the strong selective pressure in polar environments, highlatitude diatoms are ideal candidates with which to study photosynthetic adaptations to a changing climate.…”