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.

Chloroplast Genomes for Five Skeletonema Species: Comparative and Phylogenetic Analysis

“…The two HAB species S. marinoi and S. pseudocostatum diverged approximated 16 Mya (95% HPD 5.66-29.85 Mya), which was consistent with results estimated previously using 18S rDNA (about 14 Mya) (Sorhannus, 2007). The divergence time estimated in this study among Skeletonema species was generally similar or slight large than that estimated based on the mtDNA PCGs, indicating the clock rate was similar across the two organelles (Liu et al, 2021). This study provided the divergence time among the Skeletonema species based on the cpDNAs for the first time.…”

“…The phylogenetic analysis supported that S. pseudocostatum and S. tropicum could clustered into sister clade in agreement with the topology in recent studies using 18S rDNA, 28S rDNA, and cox1 gens (Kooistra et al, 2008;Yamada et al, 2017). However, the topologies of the phylogenetic trees were not identical, the tree using the cpDNA PCGs obtained in this study was very similar with the tree based on 28S rDNA (Kooistra et al, 2008;Yamada et al, 2017), and was almost identical with the cox1 tree (except the positions of S. costatum and S. grevillei) (Liu et al, 2021), but was different from the tree based on 18S rDNA (Yamada et al, 2017), confirming that these different genes can have incongruent histories.…”

“…In this study, we constructed complete cpDNAs of six Skeletonema strains (CNS00100, CNS00166, CNS00243, CNS00303, CNS00342, and CNS00438) isolated from Chinese coastal seawaters. These six Skeletonema strains were annotated as S. marinoi , S. tropicum , S. costatum , S. costatum , S. pseudocostatum , and S. grevillei , respectively, based on their morphological features and similarity to corresponding reference molecular markers ( Liu et al, 2021 ). Although CNS00243 and CNS00303 were identified as different Skeletonema species originally, both the strains were proved to be S. costatum by our recent study ( Liu et al, 2021 ).…”

“…These six Skeletonema strains were annotated as S. marinoi , S. tropicum , S. costatum , S. costatum , S. pseudocostatum , and S. grevillei , respectively, based on their morphological features and similarity to corresponding reference molecular markers ( Liu et al, 2021 ). Although CNS00243 and CNS00303 were identified as different Skeletonema species originally, both the strains were proved to be S. costatum by our recent study ( Liu et al, 2021 ). By now, the cpDNA of only a single Skeletonema species, which is S. pseudocostatum , has been constructed ( Hamedi et al, 2019 ).…”

Molecular taxonomical identification and phylogenetic relationships of some marine dominant algal species during red tide and harmful algal blooms along Egyptian coasts in the Alexandria region

“…Khaw et al ( 2020 ) reported 18S rDNA priming as a simple method for cultured eukaryotic microalgae identification. Also, mitochondrial and chloroplast genomes were efficient in phylogenetic analyses and comparative genomic analyses of coastal diatoms (Liu et al 2021a , b ). Kobayashi et al ( 2014 ) referred to the multiple sequence alignment of heat shock protein and the phylogenetic tree of some algae as well as their protein and cDNA expression patterns determining the survival threshold temperature in Cyanidioschyzon merolae and Chlamydomonas reinhardtii .…”