A New Insight Into Amicula, a Genus of Tiny Marine Benthic Diatoms With the Description of Two New Tropical Species and the Largest Mitogenome Known for a Stramenopile

Abstract

The current article focuses on the morphological and molecular characterization of the often inconspicuous genus Amicula. This recently erected genus from brackish and marine sediments was monotypic but here we describe two new tropical species: Amicula micronesica sp. nov. and Amicula vermiculata sp. nov. Once considered an incertae sedis genus regarding its higher rank taxonomy, its position among the family Diploneidaceae is proposed here by molecular phylogenetics. The complete plastid and mitochondrial genomes of Amicula micronesica sp. nov. are also presented here. It appears that the 177614-bp long mitogenome is the biggest yet recorded among stramenopiles, due to its invasion by 57 introns. Moreover, it utilizes the genetic code 4 for translation instead of the code 1 usually found among diatoms.

Phylogeny and Evolution of Cocconeiopsis (Cocconeidaceae) as Revealed by Complete Chloroplast and Mitochondrial Genomes

“…The tsf is a translation factor gene, which is also missing in other naviculoid species [ 13 ], while in Phaeodactylum tricornutum , this gene is presented in both the nuclear and plastid genomes, indicating an ongoing process of endosymbiotic gene transfer [ 9 ]. Moreover, the bas1 , syfB , thiG , and thiS were annotated in the C. kantsiensis plastid genome, and are often absent or present as pseudogenes in other diatoms [ 25 ].…”

“…It encoded a total of 66 genes, including 33 PCGs that included the two conserved subunits of Nad11 in diatoms, 6 ORFs, 2 rRNA genes, and 25 tRNA genes. In these 33 PCGs, the TTA is the most common start codon (25) and is followed by the CTA (3), ATG (3), ATT (1), and TCA (1) codons. Two introns were found in the C. kantsiensis mitochondrial genome: one located in the trnY-GUG genes with 1387 bp, the other one being a group II intron of 3270 bp in length which classically interrupts the cox1 [18], with two intronic orf (orf168 and orf710).…”

Description of Navicula vanseea sp. nov. (Naviculales, Naviculaceae), a new species of diatom from the highly alkaline Lake Van (Republic of Türkiye) with complete characterisation of its organellar genomes and multigene phylogeny

“…Reads were assembled with a k-mer parameter of 125 using SPAdes 3.15.0 ( Bankevich et al 2012 ). Contigs of interest were retrieved by customised command-line BLASTn analyses as previously described ( Dąbek et al 2022 ; Gastineau et al 2022 ). Consed ( Gordon and Green 2013 ) was used to merge the different subunits of the plastome and when trying to circularise the mitogenome.…”

“…Consed ( Gordon and Green 2013 ) was used to merge the different subunits of the plastome and when trying to circularise the mitogenome. Annotations were performed using the same tools as described in Gastineau et al (2022) . The maps of the organellar genomes were obtained from the OGDRAW online portal ( Lohse et al 2013 ).…”

Contributions to the Diatom Flora of the Aegean Sea and the Mediterranean Sea from the Turkish Coasts with Remarks on Rare Taxa

“…So far, There was only one previous record of A. specululum from the Eastern Mediterranean Sea (Schmidt et al, 2018), where however it was misidentified as Diploneis sp. (Gastineau et al, 2022). We hypothesize that it is common species for this area, yet very easy to omit during LM analysis, due to its small size.…”