Complete mitochondrial genome of the harmful algal bloom species Thalassiosira nordenskioeldii (Mediophyceae, Bacillariophyta) from the east China sea

Abstract

Thalassiosira nordenskioeldii is a common harmful algal bloom (HAB) species with worldwide distribution. Although barcode sequences of this ecologically important species have been published, no genome data have been published for T. nordenskioeldii. In this study, we constructed the complete mitochondrial genome (mtDNA) of a T. nordenskioeldii strain isolated from the East China Sea. The T. nordenskioeldii mtDNA is circular and has a length of 47,038 bp and a GC content of 30.84%. The mtDNA encodes 69 genes, including 40 protein-coding (PCGs), 27 tRNA and two rRNA genes. Phylogenetic analysis using concatenated amino acid sequences of 31 shared PCGs from 37 diatom mtDNAs revealed that the mtDNA of T. nordenskioeldii was fully resolved in a clade with that of Thalassiosira profunda. The mtDNA of T. nordenskioeldii showed high collinearity with those of T. profunda and Skeletonema marinoi with only minor rearrangements. The completion of Thalassiosira mtDNAs will facilitate evolutionary studies on species of the order Thalassiosirales and the class Mediophyceae.

Keywords:

• Diatoms
• HAB species
• mitochondrial genome
• Thalassiosira nordenskioeldii

The type species of the genus Thalassiosira (Cleve 1873), Thalassiosira nordenskioeldii Cleve 1873, is a harmful algal bloom (HAB) species with worldwide distribution (Hoppenrath et al. 2007; Li et al. 2013). Although T. nordenskioeldii is a common HAB species that frequently causes HABs, molecular information of this species is still limited. Sequences of only a few common molecular markers of T. nordenskioeldii including cox1, rbcL and 18S rDNA have been published (Eharam, Inagaki, et al. 2000a; Ehara, Watanabe, et al. 2000; Alverson et al. 2007). Notably, a group II intron has been characterized in the cox1 gene of T. nordenskioeldii (Ehara, Watanabe, et al. 2000b). Here, we constructed the first complete mtDNA of T. nordenskioeldii using the strain CNS00052 isolated from water samples collected in the East China Sea (33°59.934′N, 121°13.59′E) in April 2019. Its specimen is deposited in the collection of marine algae in KLMEES of IOCAS (Nansheng Chen, [email protected]) under the voucher number CNS00052.

The total DNA was extracted using DNAsecure Plant Kit (Tiangen Biotech, Beijing, China). The DNA Library was prepared using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA). After qualification, the library was sequenced using an Illumina NovaSeq 6000 platform (Novogene, Beijing). Sequencing results were assembled using Platanus Allee v2.2.2 (Kajitani et al. 2019), and the target scaffolds were selected using BLASTN v2.10.0. BWA v0.7.17 (Li and Durbin 2010) was used to align and verify the circular sequence of the mtDNA. The complete T. nordenskioeldii mtDNA (GenBank accession number: MW387419) was 47,038 bp in length with a GC content of 30.84%. The circular mtDNA encodes 69 genes, including 27 tRNA genes, two rRNA genes and 40 protein-coding genes (PCGs), which include five open reading frames (orfs) with unknown functions. Introns have been found to occur frequently in cox1 of T. nordenskioeldii strains, such as the CCMP992 strain (AB038235) isolated from the east coast of USA and the CCMP997 strain from Norway (Ehara, Watanabe, et al. 2000). However, no intron was found in the complete cox1 of the CNS00052 strain, whose cox1 was 1,521 bp in length encoding 506 amino acids, suggesting high genomic variations among T. nordenskioeldii strains. Comparative analysis of the full-length cox1 genes of T. nordenskioeldii strains indicated that the cox1 genes (AB038235 and AB037974) reported previously (Ehara, Watanabe, et al. 2000) were incomplete. Of the 40 PCGs, 37 initiated with the ATG start codon, while the other three PCGs started with TTG, GTG and ATT, respectively. The stop codons of the 40 PCGs included TAA (31 of 40) and TAG (9 of 40).

To construct the maximum likelihood (ML) phylogenetic tree, all of the 31 PCGs, including atp6, 8, 9; cob; cox1, 2, 3; nad1-7, 4 L, 9, 11; rpl2, 5, 6, 14, 16; rps3, 4, 8, 10, 11, 13, 14, 19; and tatC from 37 diatom mtDNAs including the mtDNA of T. nordenskioeldii, and the mtDNAs of two outgroup taxa, Oomycota species Phytophthora ramorum (EU427470) and Saprolegnia ferax (NC_005984), were first aligned using MAFFT v7.471 (Katoh and Standley 2013) and trimmed using trimAL v1.4 (Capella-Gutierrez et al. 2009) individually with default parameters (Figure 1). Amino acid sequences of all 31 PCGs of 39 species (including T. nordenskioeldii) were concatenated using Phyutility (Smith and Dunn 2008), and the best-fit models for all PCGs were predicted using ModelFinder (Kalyaanamoorthy et al. 2017) with four categories for each partition and a bootstrap value of 1000. The phylogenetic tree was constructed using IQtree v1.6.12 (Trifinopoulos et al. 2016). In the phylogenetic tree, Thalassiosira nordenskioeldii grouped with species from Thalassiosira and Skeletonema species with 100% support, which belong to the class Mediophyceae, order Thalassiosirales (Stoermer 2003). Thalassiosira nordenskioeldii clustered well with T. profunda (MW013551). The tree topologies was similar to those reported previously by Kaczmarska et al. (2006) and Alverson et al. (2007), which were constructed using the full-length 18S rDNA, the partial 28S rDNA and two chloroplast DNA (psbC and rbcL) sequences. All phylogenetic trees showed that T. nordenskioeldii and T. profunda of the family Thalassiosiraceae had closer evolutionary relationship with Skeletonema marinoi of the family Skeletonemataceae than that with T. pseudonana, although Thalassiosiraceae and Skeletonemataceae were different families in the order Thalassiosirales (Stoermer 2003), supporting the proposal that the taxonomical position of T. pseudonana needs to be revised (Alverson et al. 2011). Furthermore, the mtDNA of T. nordenskioeldii showed high collinearity with those of T. profunda and S. marinoi (NC_028615) with only minor rearrangements. Two translocation events situated atp6 and rps10 to the region between rns and rnl, and another translocation event brought atp9 to the position between nad2 and nad6. The completion of more mtDNAs of Thalassiosira species is critical for comparing and classifying species of the order Thalassiosirales and the class Mediophyceae.

Figure 1. Maximum likelihood (ML) phylogenetic tree of T. nordenskioeldii based on concatenated amino acid sequences of 31 genes from 36 diatom mtDNAs, with Phytophthora ramorum (EU427470) and Saprolegnia ferax (NC_005984) serving as outgroup taxa. The numbers beside branch nodes are the percentages based on 1000 bootstrap replicates.

Acknowledgements

We are thankful to all staffs of marine ecological environment genomics research group in Institute of Oceanology, Chinese Academy of Sciences.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MW387419, under the accession no. MW387419. The associated BioProject, SRA and Bio-Sample numbers are PRJNA684688 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA684688), SRR13279234 (https://www.ncbi.nlm.nih.gov/sra/SRR13279234) and SAMN17125947 (https://www.ncbi.nlm.nih.gov/biosample/SAMN17125947/), respectively.

Additional information

Funding

This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences, [Grant No. XDB42000000], Chinese Academy of Sciences; Pioneer Hundred Talents Program (to Nansheng Chen); Taishan Scholar Project Special Fund (to Nansheng Chen); Qingdao Innovation and Creation Plan (Talent Development Program-5th Annual Pioneer and Innovator Leadership Award to Nansheng Chen, 19-3-2-16-zhc); the Key Research Program of Frontier Sciences, Chinese Academy of Sciences [No. QYZDB-SSW-DQC023] (to Feng Liu), and the Major Scientific and Technological Innovation Project of Shandong Province [No. 2019JZZY020706] (to Feng Liu). Data acquisition and sample collections were supported by National Natural Science Foundation of China (NSFC) Open Research Cruise (Cruise No. NORC2019-01), funded by Shiptime Sharing Project of NSFC.