Complete mitochondrial genome of a DHA-rich protist Schizochytrium sp. TIO1101

Abstract

Schizochytrium sp. TIO1101 is a crucial commercial alga used to produce docosahexaenoic acid (DHA), a long-chain polyunsaturated fatty acid that is beneficial for human health. In this study, we sequenced the mitochondrial genome (mitogenome) of Schizochytrium sp. TIO1101 for the first time using an Illumina HiSeq 2500 system (Illumina Inc., San Deigo, CA). The assembled mitogenome was 31 494 bp long with 33.92% GC content. The mitogenome contains 56 genes, including 33 protein-coding genes, 21 transfer RNA genes and two ribosomal RNA genes. Maximum-likelihood phylogenetic analysis of Schizochytrium sp. TIO1101 showed that it was most closely related to Thraustochytrium aureum among the examined species.

Keywords:

• DHA
• mitogenome
• phylogeny
• sequencing
• Schizochytrium sp. TIO1101

Schizochytrium sp. is a commercial alga used to produce docosahexaenoic acid (DHA), a long-chain polyunsaturated fatty acid, that is beneficial for human health (Metz et al. 2001; Burja et al. 2006; Fan et al. 2007). Schizochytrium sp. TIO1101, collected from Yundang Lake (Xiamen City, China), was isolated and characterized using pine pollen as bait and was deposited to China General Microbiological Culture Collection Center (CGMCC) with CGMCC no. 4603. The content of DHA in Schizochytrium sp. TIO1101 was reported to be 45% of the total fatty acids with an oil content up to 55% of the cell dry weight (Cheng et al. 2011). However, the metabolic mechanism for DHA synthesis in Schizochytrium sp. TIO1101 is unknown and until now only two gene sequences, those of 18S ribosomal RNA and malonyl-CoA acyl carrier protein transacylase (fabD), have been reported (Cheng et al. 2013). Schizochytrium sp. is considered to be a member of Stramenopiles, which are eukaryotes (Cavalier-Smith et al. 1994), whereas its reproductive style is characteristic of prokaryotes (Honda et al. 1998). Therefore, the evolutionary position of Schizochytrium sp. is still obscure. We sequenced the complete mitochondrial genome (mitogenome) of Schizochytrium sp. TIO1101, to obtain further insight into the phylogenetic position of Schizochytrium sp.

The complete mitogenome of Schizochytrium sp. TIO1101 was sequenced on an Illumina HiSeq 2500 platform (Illumina Inc., San Deigo, CA) and assembled de novo using SOAPdenovo2 (http://soap.genomics.org.cn). The assembled mitogenome sequence has been deposited in GenBank under accession number KU183024. To annotate the mitogenome, we used the online Dual Organellar GenoMe Annotator (Wyman et al. 2004) and ORF Finder programs (Cheng et al. 2013) with default conditions and the Thraustochytrium aureum mitogenome (GenBank accession no. AF288091.2) as a reference. We obtained a circular map 31 494 bp long with 33.92% GC content, consisting of 33 protein-coding genes (PCGs), 21 transfer RNA genes (tRNA) and two ribosomal RNA genes (rRNA) (Figure S1). The 33 PCGs comprised 15 ribosomal protein-coding genes (rpl and rps), 10 NADH dehydrogenase genes (nad), three ATP synthase genes (atp), three cytochrome c oxidase genes (cox), one cytochrome b gene (cob) and one sec-independent protein translocase component (tatC), sharing the same start codon (ATG) but different stop codons (TAA, TGA or TTA). The shortest PCG was rps19 (165 bp) and the longest was nad5 (1968 bp). All the tRNA genes were on the H-strand. The two rRNA genes encoded one large and one small subunit rRNA. The gene content and genome organization of the Schizochytrium sp. TIO1101 mitogenome are similar to that of the T. aureum mitogenome, indicating their genetic affinity.

The complete mitogenomes of 19 Stramenopiles species (including Schizochytrium sp. TIO1101) were used to construct a maximum-likelihood phylogenetic tree with nine Oomycetes species as the outgroup, using RaxML 8.1.5 software (Stamatakis 2006) (Figure 1). To build the phylogenetic tree, we used the translated amino acid sequences of 19 protein-coding genes that were conserved in the 19 examined species. The tree shows that Schizochytrium sp. TIO1101 was most closely related to T. aureum than to the other species.

Figure 1. Phylogenetic analyses of Schizochytrium sp. TIO1101. A maximum-likelihood tree was constructed using amino acid of 19 mitochondrial protein-coding genes (nad1, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, atp6, atp9, rps12, rps13, rpl2, rpl14, rpl16, cox1, cox2, cox3 and cob) with 1000 replications of bootstrap re-sampling. GenBank accession numbers are provided after each species name. Organisms in bold text correspond to the species analyzed in this study.

Funding information

This work was supported by the National Natural Science Foundation of China (No. 41476148), the Regional Demonstration of Marine Economy Innovative Development Project (No. 12PYY001SF08), and the Xiamen Southern Oceanographic Center Grant (No. 14CZP028HJ02).

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.