New mitochondrial markers for diatom diversity survey in the tidal mudflat, the west coast of Korea

Abstract

Diatom is one of the most important primary producers of the aquatic ecosystem, from polar to tropical waters. Diverse diatoms are occurred in inter-tidal mudflats of the west coast of Korea, the West Sea. In spite of ecological importance of the phytoplankton community, there are a little number of molecular markers have been developed, such as nuclear encoded 18S rRNA and plastid encoded rbcL. In present study, we determined a new mitochondrial genome of common tube-dwelling diatom, Berkeleya fennica TA424 (GenBank accession KM886611), isolated from the Taean mudflat (36º4414.79N 126º1041.89E) in order to develop new molecular marker for diatom survey. Complete mitogenome of B. fennica TA424 indicates a 35,509 bp circular genome with 29.7% GC content overall and shows typical bacillariophycean mitochondrial synteny. It 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 subunit, and 25 transfer RNA (tRNA) genes. All CDS of mtDNA aligned with previous data such as Phaeodactylum tricoruntum (NC_016739), Synedra acus (NC_013710), and Thalassiosira pseudonana (NC_007405). 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 of the phytoplankton community, there are a little number of molecular markers have been developed, such as nuclear encoded 18S rRNA and plastid encoded rbcL. In present study, we determined a new mitochondrial genome of common tube-dwelling diatom, Berkeleya fennica TA424 (GenBank accession KM886611), isolated from the Taean mudflat (36º4414.79N 126º1041.89E) in order to develop new molecular marker for diatom survey. Complete mitogenome of B. fennica TA424 indicates a 35,509 bp circular genome with 29.7% GC content overall and shows typical bacillariophycean mitochondrial synteny. It 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 subunit, and 25 transfer RNA (tRNA) genes. All CDS of mtDNA aligned with previous data such as Phaeodactylum tricoruntum (NC_016739), Synedra acus (NC_013710), and Thalassiosira pseudonana (NC_007405). 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