Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation

Abstract

Background: Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Mitochondrial genome (mtDNA) has been extensively used as "super barcode" in the phylogenetic analyses and comparative genomic analyses. However, of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi.

Results: In this study, we constructed full-length mtDNAs for six strains of five Skeletonema species, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum (with two strains), which were isolated from coastal waters in China. The mtDNAs of all of these Skeletonema species were compact with short intergenic regions, no introns, and no repeat regions. Comparative analyses of these Skeletonema mtDNAs revealed high conservation, with a few discrete regions of high variations, some of which could be used as molecular markers for distinguishing Skeletonema species and for tracking the biogeographic distribution of these species with high resolution and specificity. We estimated divergence times among these Skeletonema species using 34 mtDNAs genes with fossil data as calibration point in PAML, which revealed that the Skeletonema species formed the independent clade diverging from Thalassiosira species approximately 48.30 Mya.

Conclusions: The availability of mtDNAs of five Skeletonema species provided valuable reference sequences for further evolutionary studies including speciation time estimation and comparative genomic analysis among diatom species. Divergent regions could be used as molecular markers for tracking different Skeletonema species in the fields of coastal regions.

Keywords: Comparative genomics; Divergence time; Harmful algal blooms; Mitochondrial genome; Molecular marker; Skeletonema species.

Fig. 1

A Micrographs of six Skeletonema strains. B Phylogenetic tree of Skeletonema inferred from cox1 genes. The six Skeletonema strains in blue were obtained in this study, and their cox1 sequences have been uploaded to NCBI (MW438979-MW438984); the other sequences were downloaded from NCBI GenBank. Phylogenetic trees were generated using the Maximum Likelihood (ML) method with 1000 bootstrap replicates. Evolutionary model was Tamura-Nei model with gamma distribution (G = 0.187)

Fig. 2

Circular maps of the complete mtDNAs of six Skeletonema species. The PCGs, rRNAs and tRNAs are labeled outside the circles. The assignment of genes is indicated by colors according to the different functional groups. The ring of bar graphs inside the circle shows the GC content in dark gray

Fig. 3

The phylogenetic tree based on concatenated amino acid sequences of 31 mitochondrial protein-coding genes (atp6, 8, 9; cob; cox1–3; nad1–7, 4 L, 9, 11; rpl2, 5, 6, 14, 16; rps 3, 4, 8, 10, 11, 13, 14, 19; and tatC) using Maximum likelihood (ML) methods. The branch values were SH-aLRT support (%) / aBayes support / ultrafast bootstrap support (%). The strains indicated in blue were obtained in this study. Phytophthora ramorum and Saprolegnia ferax were used as outgroups

Fig. 4

A Synteny relationships among six Skeletonema mtDNAs based on Mauve analysis. B mtDNA gene arrangements of six Skeletonema species. Blocks with the same color represent the same type of genes

Fig. 5

A Agarose gels image of PCR products for region VI among the six Skeletonema mtDNAs. The full-length gels are presented in Additional file 15. The brands sequences were S. marinoi, S. tropicum, S. costatum (CNS00243), S. costatum (CNS00303), S. pseudocostatum and S. grevillea, respectively. The brands of Marker M1 and M2 were on the right. B DNA alignment information of region VI for the six Skeletonema species

Fig. 6

Time-calibrated phylogeny of 15 mtDNAs based on 34 PCGs in the class Mediophyceae and outgroup (Melosira undulata). We added two Bacillariophyceae species (Synedra acus and Fragilariopsis kerguelensis) to establish appropriate fossil calibration points. The red dots represent calibration points and the 95% highest posterior density interval for node ages are shown with translucent blue bars