Mitochondrial genome of the harmful algal bloom species Odontella regia (Mediophyceae, Bacillariophyta)

Wang, Yichao; Yang, Chong‐Ren; Wang, Jing; Liu, Feng; Chen, Nansheng

doi:10.1007/s10811-020-02364-1

Cited by 10 publications

(17 citation statements)

References 75 publications

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“…mtDNAs have been used as “super barcode” for comparative genomics analysis [ 42 ]. Furthermore, mtDNAs usually show relatively higher evolutionary rates than nuclear genomes, which make them an appropriate platform for developing molecular markers with high resolution [ 43 , 44 ]. By now, mtDNA of only a single Skeletonema species, S. marinoi , has been constructed [ 45 ].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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“…The circular mtDNA of C. wailesii was 36,071 bp in size (GenBank accession number: MW122841). The mtDNA encoded a set of 64 genes found in most diatom mtDNAs (Wang et al 2021;Zhang et al 2021), including 34 proteincoding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 24 transfer RNA (tRNA) genes, and 4 open reading frames (orfs). The heavy strand (þ) encoded 56 genes while the light strand (-) had 8 genes.…”

Section: Diatoms; Mitochondrial Genome; Coscinodiscus Wailesii; Coscinodiscophyceaementioning

confidence: 99%

The complete mitochondrial genome and phylogenetic analysis of Coscinodiscus wailesii (Coscinodiscophyceae, Bacillariophyta)

Huang

Wang

Huang

et al. 2021

Mitochondrial DNA Part B

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Coscinodiscus is a species-rich genus with about 400 species described, many of which are harmful algal bloom species with significant negative ecological impact. Despite of their importance in primary production and as harmful algal bloom species, genome data for species in this genus is limited. No mitochondrial genome (mtDNA) of any species in this genus has been reported. Here, the complete mtDNA sequence of the Coscinodiscus wailesii Gran & Angst 1931 was constructed and analyzed. The circular mtDNA was 36,071 bp in length, encoding 64 genes, including 34 protein coding genes (PCGs), 24 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 4 conserved open reading frames (orfs). The overall AT content of C. wailesii mtDNA was 75.00%, which was slightly lower than that of Melosira undulate (78.40%). Maximum likelihood (ML) phylogenetic analysis using 29 shared proteincoding genes revealed that C. wailesii clustered well with M. undulata, which was the only species of class Coscinodiscophyceae whose mtDNA has been fully constructed. The complete mtDNAs of more Coscinodiscus species will be valuable for studying the evolutionary relationships among species in the genus Coscinodiscus and in the Class of Coscinodiscophyceae.

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“…The strain CNS00554 analyzed in this study was isolated in water samples collected during an expedition to the Jiaozhou Bay, China (36°08.031’N, 120°11.309’E) in August 2020 onboard the research vehicle ‘Innovation,’ using same sampling protocol as previously reported in Wang et al ( 2021 ). The strain CNS00554 was annotated as C. granii based on its morphological features (Hasle and Lange 1992 ; Goessling et al 2016 ) ( Figure 1(B,C) ) and molecular characterization based on common molecular markers including full-length 18S rDNA (Damsté et al 2004 ) and rbcL (Theriot et al 2010 ) (Figure S1).…”

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“…The circular mtDNA of C. granii was 34,970 bp in size (GenBank accession number: MW435847). The mtDNA encoded a set of 60 genes, including 32 PCGs, two rRNA genes, 24 tRNA genes, and two orf s. Genes rps2 , rps10 , and rpl5 that are found in mtDNAs of many other diatom species (Wang et al 2021 ) were absent from the mtDNA of C. granii . The two orf s identified in C. granii shared no similarity with these three genes.…”

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Complete mitochondrial genome of Coscinodiscus granii (Coscinodiscophyceae, Bacillariophyta)

Huang

Zhao

et al. 2021

Mitochondrial DNA Part B

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Coscinodiscus is a genus common in marine phytoplankton, with some species thought to have a significant negative ecological impact. However, the availability of their genome sequences is rather limited. Here, we assembled and annotated the first complete mitochondrial genome (mtDNA) of the species Coscinodiscus granii L.F.Gough 1905, as part of our efforts to gain a better understanding of the genetic characteristics of Coscinodiscus taxa at a genomic level. The circular mtDNA was 34,970 bp in length and encoded 60 genes, including 32 protein-coding genes (PCGs), 24 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and two conserved open reading frames (orfs). The overall GC content of C. granii mtDNA was 24.30%, which was slightly lower than that of C. wailesii (25.00%), the first species in the genus Coscinodiscus whose mtDNA has been reported, and higher than that of Melosira undulata (21.60%), the first species in the class Coscinodiscophyceae whose mtDNA has been reported. As expected for congeneric species, phylogenetic analysis using concatenated amino acid sequences of 27 shared PCGs suggested that C. granii has a closer evolutionary relationship with C. wailesii. Coscinodiscus was found to be monophyletic in the phylogeny. The complete mtDNAs of more Coscinodiscus species will facilitate the exploration of the evolutionary relationships of species in the Class Coscinodiscophyceae.

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Mitochondrial genome of the harmful algal bloom species Odontella regia (Mediophyceae, Bacillariophyta)

Cited by 10 publications

References 75 publications

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

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

The complete mitochondrial genome and phylogenetic analysis of Coscinodiscus wailesii (Coscinodiscophyceae, Bacillariophyta)

Complete mitochondrial genome of Coscinodiscus granii (Coscinodiscophyceae, Bacillariophyta)

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