Plastid genome of Odontella aurita (Mediophyceae, Bacillariophyta) and evolution of acpP gene in diatoms.

Abstract

Odontella aurita (Lyngbye) C. Agardh is an oblong shaped diatom with long spines and is often observed forming chains. O. aurita is a ubiquitous marine planktonic species present from the temperate to arctic regions. This species has been subject to taxonomic and ecological studies. However, its chloroplast genome has not been determined yet. In present study, we collected the water sample from Sihwa-ho (37˚ 18 37.10 N 126˚ 36 19.0 E the west coast of Korea) using a plankton net (10 μm mash) and isolated Odontella aurita SH036. We have sequenced and annotated the chloroplast genome (ptDNA) of the strain by using NGS technology. The ptDNA length of O. aurita is 120.3 kb with 31.9% of GC and a pair of inverted repeats (IR 2 × 7,725 bp). The circular ptDNA contains 167 genes, including 129 protein-coding genes, 6 rRNAs, and 30 tRNAs. The ptDNA of O. aurita was compared to the ptDNA of Trieres chinensis (NC_001713 119.7 kb, 31.8% GC, a pair of IR (7,872 bp), and 129 protein-coding genes) previously known as Odontella sinensis. Two ptDNAs showed size differences in 23 CDS and intergenic regions, and in the number of ORFs. In order to understand the recent independent acquisition of acpP gene in diatoms, we searched almost all homologous genes from available organisms, i.e. bacteria and eukaryotes and studied the potential origins of acpP genes in diatoms. New ptDNA data may contribute to the better understandubject to taxonomic and ecological studies. However, its chloroplast genome has not been determined yet. In present study, we collected the water sample from Sihwa-ho (37˚ 18 37.10 N 126˚ 36 19.0 E the west coast of Korea) using a plankton net (10 μm mash) and isolated Odontella aurita SH036. We have sequenced and annotated the chloroplast genome (ptDNA) of the strain by using NGS technology. The ptDNA length of O. aurita is 120.3 kb with 31.9% of GC and a pair of inverted repeats (IR 2 × 7,725 bp). The circular ptDNA contains 167 genes, including 129 protein-coding genes, 6 rRNAs, and 30 tRNAs. The ptDNA of O. aurita was compared to the ptDNA of Trieres chinensis (NC_001713 119.7 kb, 31.8% GC, a pair of IR (7,872 bp), and 129 protein-coding genes) previously known as Odontella sinensis. Two ptDNAs showed size differences in 23 CDS and intergenic regions, and in the number of ORFs. In order to understand the recent independent acquisition of acpP gene in diatoms, we searched almost all homologous genes from available organisms, i.e. bacteria and eukaryotes and studied the potential origins of acpP genes in diatoms. New ptDNA data may contribute to the better understand