Complete Chloroplast Genome Sequence of Freshwater Araphid Pennate Diatom Alga Synedra acus from Lake Baikal

Abstract

Complete chloroplast genome of diatom alga Synedra acus possesses canonical quadripartite structure with two inverted repeats containing ribosomal RNA gene loci that separate small and large single-copy regions. Chloroplast genome maps as a circular molecule of 116 251 bp. It encodes 27 tRNAs, three rRNAs, two small RNA genes, and 128 protein-coding genes. Comparison of the genic features across diatom chloroplast genomes reveals the absence of an overlap between atpD and atpF gene coding sequences that is present in other plastid genomes of diatom origin. This feature is a clear synapomorphy of S. acus plastid genome that is likely a result of either relaxed constraints or extensive selection forces acting upon atpF gene. We also characterized nuclear-encoded acyl-carrier protein gene with chloroplastic targeting in S. acus. The transfer of acpp gene into the nuclear host genome is hypothesized to have occurred independently in several lineages of diatoms.

Chloroplast genome of Sargassum horneri (Sargassaceae, Phaeophyceae): comparative chloroplast genomics of brown algae

“…The S. horneri cpDNA contains 16 SIRs and 9 TRs (Table 2), representing 1.02 and 0.32 % of the S. horneri genome, respectively, which is similar to those of three other brown algal cpDNAs. The total repeat number found in brown algal cpDNAs (18-25) is similar to that in diatoms (Oudot-Le Secq et al 2007;Galachyants et al 2012), more than that in Pelagophyceae (Ong et al 2010), and less than that in Raphidophyceae (Cattolico et al 2008).…”

“…The overlaps of psbC-psbD (53 bp) and rpl23-rpl4 (8 bp) are highly conserved among the four brown algal cpDNAs. These two overlapping regions are also observed in diatom plastid genomes (e.g., Oudot-Le Secq et al 2007;Tanaka et al 2011;Galachyants et al 2012).…”

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

“…To date, a few dozen diatom chloroplast genomes (plastomes) have been sequenced (Kowallik et al 1995, Oudot-Le Secq et al 2007, Tanaka et al 2011, Galachyants et al 2012, Brembu et al 2014, Ruck et al 2014, Yu et al 2018. They are circular chromosomes with a quadripartite structure and two inverted repeats (IR) separating small (SSC) and large singlecopy (LSC) regions.…”

Sequencing of the complete genome of an araphid pennate diatom Synedra acus subsp. radians from Lake Baikal

“…from Lake Baikal. First, we deciphered mitochondrial [4] and chloro plast [5] genome sequences of Synedra acus subsp. radians in collaboration with the Center "Bioengi neering," Russian Academy of Sciences.…”

“…radians via horizontal gene transfer and a region of diatom mtDNAs with intensive gene rearrangements as opposed to the rest of mitochondrial DNA sequence where the order of genes is conserved [4]. It was shown that the gene order in chloroplast DNA could be used for phyloge netic analysis [5].…”