Understanding the Evolution of Mitochondrial Genomes in Phaeophyceae Inferred from Mitogenomes of Ishige okamurae (Ishigeales) and Dictyopteris divaricata (Dictyotales)

Liu, Feng; Zhang, Yongyu; Bi, Yuping; Chen, Weizhou; Moejes, Fiona Wanjiku

doi:10.1007/s00239-018-9881-5

Cited by 11 publications

(11 citation statements)

References 55 publications

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“…A reversal event related to only a tRNA gene, trnE(uuc), happened in cpDNAs of Uau2 and Uau3, not in Uau1 and other Ulva cpDNAs, indicating that it was a recent rearrangement at intraspecific level. Compared with PCGs and/or rRNA genes, tRNA genes show more mobility in organellar genomes of eukaryotic algae (e.g., brown algae, diatoms, red algae) (e.g., Ruck et al, 2014;Liu et al, 2017aLiu et al, , 2019. Previously, intraspecific rearrangement was observed to occur in mitochondrial genomes of U. compressa.…”

Section: Integrated Analysis Of Rearrangement Events and Phylogenomic Relationshipsmentioning

confidence: 99%

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

Liu

Melton

2021

Front. Mar. Sci.

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To understand the evolution of Ulva chloroplast genomes at intraspecific and interspecific levels, in this study, three complete chloroplast genomes of Ulva compressa Linnaeus were sequenced and compared with the available Ulva cpDNA data. Our comparative analyses unveiled many noticeable findings. First, genome size variations of Ulva cpDNAs at intraspecific and interspecific levels were mainly caused by differences in gain or loss of group I/II introns, integration of foreign DNA fragments, and content of non-coding intergenic spacer regions. Second, chloroplast genomes of U. compressa shared the same 100 conserved genes as other Ulva cpDNA, whereas Ulva flexuosa appears to be the only Ulva species with the minD gene retained in its cpDNA. Third, five types of group I introns, most of which carry a LAGLIDADG or GIY-YIG homing endonuclease, and three of group II introns, usually encoding a reverse transcriptase/maturase, were detected at 26 insertion sites of 14 host genes in the 23 Ulva chloroplast genomes, and many intron insertion-sites have been found for the first time in Chlorophyta. Fourth, one degenerate group II intron previously ignored has been detected in the infA genes of all Ulva species, but not in the closest neighbor, Pseudoneochloris marina, and the other chlorophycean taxa, indicating that it should be the result of an independent invasion event that occurred in a common ancestor of Ulva species. Finally, the seven U. compressa cpDNAs represented a novel gene order which was different from that of other Ulva cpDNAs. The structure of Ulva chloroplast genomes is not conserved, but remarkably plastic, due to multiple rearrangement events.

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Section: Integrated Analysis Of Rearrangement Events and Phylogenomic Relationshipsmentioning

confidence: 99%

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

Liu

Melton

2021

Front. Mar. Sci.

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“…The lengths of three rRNA genes are 1939 bp (rnl rRNA), 874 bp (rns rRNA), and 126 bp (rrn5 rRNA). All genes show the typical gene arrangement conforming to the Sargassaceae family consensus (Liu et al 2019). Phylogeographic tree showed that S. patens clustered together with S. aquifolium (Figure 1).…”

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confidence: 76%

Phylogenetic analysis of the complete mitochondrial genome of Sargassum patens C. Agardh (Phaeophyceae)

2020

Mitochondrial DNA Part B

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“…There were a variety of rearrangements in three classes, which pointed to that the mtDNA structure was diverse between species in the phylum of Bacillariophyta. Other comparative analyses of mtDNAs had also shown a number of gene rearrangements in the class Eustigmatophyceae and class Phaeophyceae of algae, respectively ( Sevcikova et al, 2016 ; Liu et al, 2019b ). Compared to mtDNAs of different orders in the phylum of Bacillariophyta, the mtDNAs within same orders were more conserved.…”

Section: Discussionmentioning

confidence: 99%

Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes

et al. 2022

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Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically significant groups of phytoplankton, comprising 100,000–200,000 species in three classes Bacillariophyceae, Mediophyceae, and Coscinodiscophyceae. However, due to the limited resolution of common molecular markers including 18S rDNA, 28S rDNA, ITS, rbcL, and cox1, diatom biodiversity has not been adequately ascertained. Organelle genomes including mitochondrial genomes (mtDNAs) have been proposed to be “super barcodes” for distinguishing diatom species because of their rich genomic content, and the rapid progress of DNA sequencing technologies that has made it possible to construct mtDNAs with increasing throughout and decreasing cost. Here, we constructed complete mtDNAs of 15 diatom species including five Coscinodiscophyceae species (Guinardia delicatula, Guinardia striata, Stephanopyxis turris, Paralia sulcata, and Actinocyclus sp.), four Mediophyceae species (Hemiaulus sinensis, Odontella aurita var. minima, Lithodesmioides sp., and Helicotheca tamesis), and six Bacillariophyceae species (Nitzschia ovalis, Nitzschia sp., Nitzschia traheaformis, Cylindrotheca closterium, Haslea tsukamotoi, and Pleurosigma sp.) to test the practicality of using mtDNAs as super barcodes. We found that mtDNAs have much higher resolution compared to common molecular markers as expected. Comparative analysis of mtDNAs also suggested that mtDNAs are valuable in evolutionary studies by revealing extensive genome rearrangement events with gene duplications, gene losses, and gains and losses of introns. Synteny analyses of mtDNAs uncovered high conservation among species within an order, but extensive rearrangements including translocations and/or inversions between species of different orders within a class. Duplication of cox1 was discovered for the first time in diatoms in Nitzschia traheaformis and Haslea tsukamotoi. Molecular dating analysis revealed that the three diatom classes split 100 Mya and many diatom species appeared since 50 Mya. In conclusion, more diatom mtDNAs representing different orders will play great dividends to explore biodiversity and speciation of diatoms in different ecological regions.

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Understanding the Evolution of Mitochondrial Genomes in Phaeophyceae Inferred from Mitogenomes of Ishige okamurae (Ishigeales) and Dictyopteris divaricata (Dictyotales)

Cited by 11 publications

References 55 publications

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

Phylogenetic analysis of the complete mitochondrial genome of Sargassum patens C. Agardh (Phaeophyceae)

Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes

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