Characterization of the complete mitochondrial genome and phylogenetic analysis of Prototheca stagnorum (chlorellales: Chlorellaceae).

Prototheca stagnorum belongs to the genus Prototheca that are achloroplyllous algae with phylogenetic affinities to Chlorella sp. Microalgae of the genus Prototheca spp are associated with rare algal infections of invertebrates termed protothecosis. In this study, the complete nucleotide sequence of the circular mitochondrial (mt) DNA of the chlorophyte alga P. stagnorum has been determined (80,023 base-pairs, A + T content 13.77%). The genes identified encode three subunits of the cytochrome oxidase and apocytochrome b, eight subunits of the NADH dehydrogenase complex (nad1-7, nad4L), four ATPase subunits (atp1, atp4, atp6, atp8), three ribosomal RNAs (5 S (rrn5), small subunit (srn) and large subunit (lrn) RNA), 27 tRNAs, two succinate dehydrogenase and 10 ribosome proteins. The complete mitochondrial genome sequence will provide new molecular biology information to further understand the genetic diversity of the Prototheca sp. and to eliminate this population.

The Prototheca stagnorum belongs to the genus Prototheca within the family Chlorellaceae. The genus Prototheca, including P. Zopfii and P. wickethamii, are widely distributed in sewage wastewater, animal waste and the mucus secretion of some trees, and are involved in opportunistic infections of invertebrates termed protothecosis (Lassflörl and Mayr 2007; Seok et al. 2013). However, molecular studies about Prototheca sp. are limited, and only the mitochondrial genome of P. wickerhamii is available until now. Here, we assembled and characterized the complete mitochondrial genome of P. stagnorum.

The P. stagnorum sample was isolated from bottom sludge that obtained in Ohio, USA, and stored in Japan Collection of Microorganisms (ID: JCM 9641). Its total genomic DNA was extracted and sequenced using the Illumina HiSeq 2500 platform, and was stored in NCBI (Accession No. SAMD00028436). The sequencing reads were trimmed using Trimmomatic v0.36 (Bolger et al. 2014), and assembled with NOVOPlasty software v2.6.3 (Dierckxsens et al. 2017), then the 58 genes present in the genome were annotated using Mitofy (https://vcru.wisc.edu/cgi-bin/mitofy/mitofy.cgi) (Alverson et al. 2010). The complete mitochondrial genome of P. stagnorum is a double stranded, circular DNA 80,023 bp in total length (GenBank Accession No. MG833838.1), and includes a typical circle structure that contains 27 tRNA genes, 31 protein-coding genes and three rRNA genes. The percentage of coding region is 13.60%, and GC content is 44.33%. The Phylogenetic analysis of 11 mitochondrial genomes using MEGA 7 (Kumar et al. 2016) indicated that P. stagnorum and P. wickerhamii are the most closely related species (Figure 1). The mitogenome of P. stagnorum would contribute to the understanding of the phylogeny and evolution of Chlorellaceae.

Figure 1.

Neighbor-joining molecular phylogenetic tree of 11 species of Chlorellaceae based on the complete mitogenome sequences, with Dunaliella salina as outgroup. The asterisk indicates the individual sampled in this study. GenBank accession numbers are indicated in brackets.