Repeat region absent in mitochondrial genome of tube-dwelling diatom Berkeleya fennica (Naviculales, Bacillariophyceae)

Abstract

The complete mitochondrial DNA of tube-dwelling diatom, Berkeleya fennica was sequenced and characterized. The circular mitogenome contains 63 genes in 35,509 bp (29.7% GC), including 36 protein-coding, 25 tRNA, 2 rRNA genes. Most of the protein-coding (27) genes have usual ATG start codon, except 9 genes such as ATA for rps8; ATC for rps14; ATT for rps12 and orf51; GTG for nad5; TTA for cox3, nad4 and orf147; and TTG for cob. The nad11 and rrs are the only interrupted genes in the mitogenome. Gene content and synteny of B. fennica are very similar to Phaeodactylum tricoruntum (NC_016739). Absence of repeat region in B. fennica resulted in mitogenome size difference to P. tricoruntum. A new mitogenome will provide useful information for mitochondrial genome diversity and evolution of the diatoms.

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

“…It is possible that this region plays a role in chromosome replication and/or gene expression but it is not essential for mitochondrial function in all diatoms since it is absent from some (An et al. ,b, Pogoda et al. ).…”

“…Mitochondrial genomes (chondriomes) are relatively small and useful for phylogenetic comparisons because of their relatively low rate of polymorphisms (Pogoda et al 2018). Nearly 20 diatom chondriomes have been sequenced (Armbrust et al 2004, Bowler et al 2008, Ravin et al 2010, Imanian et al 2012, An et al 2016a,b, 2017, Tang and Bi 2016, Villain et al 2017, Pogoda et al 2018. They have a conserved set of 33 genes and so far all but one is described as circular (Kamikawa et al 2018).…”

Phylogeny and species delineation in the marine diatomPseudo‐nitzschia(Bacillariophyta) usingcox1,LSU, andITS2rRNAgenes: A perspective in character evolution

“…The complete sequence length of cox1 in diatoms varies from ~1,000 to 6,500 bp (e.g., Berkeleya fennica [1,434 bp; An et al. ], Thalassiosira pseudonana [3,838 bp; Armbrust et al. ], Phaeodactylum tricornutum [6,295 bp; Outdot‐Le Secq and Green ], Synedra acus [6,468 bp; Ravin et al.…”

“…The complete sequence length of cox1 in diatoms varies from~1,000 to 6,500 bp (e.g., Berkeleya fennica [1,434 bp; An et al 2016], Thalassiosira pseudonana [3,838 bp; Armbrust et al 2004], Phaeodactylum tricornutum [6,295 bp; Outdot-Le Secq and Green 2011], Synedra acus [6,468 bp; Ravin et al 2010], and Pseudo-nitzschia multiseries [6,111 bp;Cao et al 2016]. Similarly, the number and length of introns in cox1 varies among different species.…”

Complete mitochondrial genome of biraphid benthic diatom, Navicula ramosissima (Naviculales, Bacillariophyceae)

“…In the present study, we determined novel mitogenome of N. ramosissima TA439 isolated from the Geunsoman, Taean (36 44 0 12.06 00 N 126 10 0 47.52 00 E), Korea (strain available upon request). We followed next-generation sequencing strategy as described in An et al (2016) and Yang et al (2015).…”