Mitochondrial genome of tube-dwelling diatom Berkeleya fennica and new markers for benthic diatom diversity survey

Abstract

The Bacillariophyceae is the biggest class of the stramenopiles (> 9,600 species), and one of the most important and abundant primary producers of the aquatic ecosystem. Inspite of its importance in ecology, diversity and evolution, there was only one complete mitochondrial genome data available in the class, Phaeodactylum tricornutum. We determined a new mitochondrial genome of common tube-dwelling diatom, Berkeleya fennica TA424 (GenBank accession NC_026126), isolated from the Taean (36º 44 14.79N 126º 10 41.89E), west coast of Korea. Complete mitogenome (mtDNA) of Berkeleya fennica TA424 shows 35,509 bp circular genome with 29.7% GC content and shows typical bacillariophycean mitochondrial synteny. The mtDNA contains 63 genes, including of 36 protein-coding genes (i.e. 18 respiratory protein-coding genes, 16 ribosomal protein-coding genes, and 2 hypothetical protein-coding genes), two ribosomal RNA (rRNA) genes for large and small subunits, and 25 transfer RNA (tRNA) genes. We compared gene contents and synteny of newly determined mtDNAs with published three mtDNAs. The saturation tests for 31 shared CDS of four diatoms were performed using uncorrected (P) distance and corrected (K2P model) distance. Based on the sequencing test and statistical comparison, we suggest three new mitochondrial markers for diversity of diatoms, i.e. cob, nad5 and cox2. In present study, we determined 60 of cob, 45 of nad5, andas only one complete mitochondrial genome data available in the class, Phaeodactylum tricornutum. We determined a new mitochondrial genome of common tube-dwelling diatom, Berkeleya fennica TA424 (GenBank accession NC_026126), isolated from the Taean (36º 44 14.79N 126º 10 41.89E), west coast of Korea. Complete mitogenome (mtDNA) of Berkeleya fennica TA424 shows 35,509 bp circular genome with 29.7% GC content and shows typical bacillariophycean mitochondrial synteny. The mtDNA contains 63 genes, including of 36 protein-coding genes (i.e. 18 respiratory protein-coding genes, 16 ribosomal protein-coding genes, and 2 hypothetical protein-coding genes), two ribosomal RNA (rRNA) genes for large and small subunits, and 25 transfer RNA (tRNA) genes. We compared gene contents and synteny of newly determined mtDNAs with published three mtDNAs. The saturation tests for 31 shared CDS of four diatoms were performed using uncorrected (P) distance and corrected (K2P model) distance. Based on the sequencing test and statistical comparison, we suggest three new mitochondrial markers for diversity of diatoms, i.e. cob, nad5 and cox2. In present study, we determined 60 of cob, 45 of nad5, and