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

Qing Xu,Nansheng Chen,Yichao Wang,Shuya Liu,Mengjia Zhang

doi:10.1186/s12864-021-07999-z

Abstract

BackgroundSkeletonema 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.ResultsIn 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.ConclusionsThe 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.

Highlights

Skeletonema species are prominent primary producers, some of which can cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions
We constructed Mitochondrial genome (mtDNA) of six Skeletonema strains, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum, which were isolated from coastal waters in China
We explored divergence times for Skeletonema species and other species in the class Mediophyceae based on their shared protein-coding genes (PCGs) of mtDNAs

Summary

Introduction

Skeletonema species are prominent primary producers, some of which can cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi. Most Skeletonema species are cosmopolitan distributions, and are important primary producers especially in estuarine and marine waters [3]. S. tropicum were found at tropical locations including Mediterranean Sea [3], the East China Sea [3], the South China Sea [6], the Jiaozhou Bay of the Yellow Sea [13], and the Lagoa dos Patos in Brazil during summer and autumn [3]. S. potamos grows in freshwaters and brackish waters with salinities 2–34 [16], such as the River Danube, Hungary [17] and Patos Lagoon, Brazil [18]

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