Mitochondrial Genome of Prasinophyte Alga <i>Pyramimonas parkeae</i>

Hrdá, Štěpánka; Hroudová, Miluše; Vlček, Čestmı́r; Hampl, Vladimı́r

doi:10.1111/jeu.12371

Cited by 4 publications

(5 citation statements)

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“…, Hrdá et al. ). The cox 1 introns in both P. parkeae SCCAP K‐0007 and C. tetramitiformis were group II introns that were homologous to reverse transcriptase (cd01651), while the introns present in Monomastix sp.…”

Section: Resultsmentioning

confidence: 97%

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Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis

Satjarak

Burns

Kim

et al. 2017

Journal of Phycology

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Mitochondria are archetypal eukaryotic organelles that were acquired by endosymbiosis of an ancient species of alpha-proteobacteria by the last eukaryotic common ancestor. The genetic information contained within the mitochondrial genome has been an important source of information for resolving relationships among eukaryotic taxa. In this study, we utilized mitochondrial and chloroplast genomes to explore relationships among prasinophytes. Prasinophytes are represented by diverse early-diverging green algae whose physical structures and genomes have the potential to elucidate the traits of the last common ancestor of the Viridiplantae (or Chloroplastida). We constructed de novo mitochondrial genomes for two prasinophyte algal species, Pyramimonas parkeae and Cymbomonas tetramitiformis, representing the prasinophyte clade. Comparisons of genome structure and gene order between these species and to those of other prasinophytes revealed that the mitochondrial genomes of P. parkeae and C. tetramitiformis are more similar to each other than to other prasinophytes, consistent with other molecular inferences of the close relationship between these two species. Phylogenetic analyses using the inferred amino acid sequences of mitochondrial and chloroplast protein-coding genes resolved a clade consisting of P. parkeae and C. tetramitiformis; and this group (representing the prasinophyte clade I) branched with the clade II, consistent with previous studies based on the use of nuclear gene markers.

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Section: Resultsmentioning

confidence: 97%

“…, Hrdá et al. ). To improve representation of mitochondrial genomes, we performed de novo reconstructions of the mitochondrial genomes of Pyramimonas parkeae NIES254 and Cymbomonas tetramitiformis PLY262, representing prasinophyte clade I based on previous chloroplast 16S rRNA gene phylogenetic analyses (Leliaert et al.…”

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confidence: 97%

Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis

Satjarak

Burns

Kim

et al. 2017

Journal of Phycology

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“…They show important variation in size (24.3 kb in Pycnococcus provasolii to 54.5 kb in Prasinoderma coloniale ) and gene content (36 in Pycnococcus to 63 in Ostreococcus and Micromonas ), but no general trend toward a reduced gene complement when they are compared to the mitogenomes of Nephroselmis (45.2 kb, 66 genes) (Turmel et al. 1999a), Pyramimonas parkeae (NIES254: 53.4 kb, 58 genes; SCCAP K-0007: 43.3 kb, 59 genes) (Hrda et al. 2017; Satjarak et al.…”

Section: Introductionmentioning

confidence: 99%

Tracing the Evolution of the Plastome and Mitogenome in the Chloropicophyceae Uncovered Convergent tRNA Gene Losses and a Variant Plastid Genetic Code

Turmel

Santos

Otis

et al. 2019

Genome Biology and Evolution

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The tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera ( Chloropicon and Chloroparvula ) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better delineate the phylogenetic affinities of these taxa and to infer the suite of changes that their organelle genomes sustained during evolution. The relationships resolved in organelle-based phylogenomic trees were essentially congruent with previously reported rRNA trees, and similar evolutionary trends but distinct dynamics were identified for the plastome and mitogenome. Although the plastome sustained considerable changes in gene content and order at the time the two genera split, subsequently it remained stable and maintained a very small size. The mitogenome, however, was remodeled more gradually and showed more fluctuation in size, mainly as a result of expansions/contractions of intergenic regions. Remarkably, the plastome and mitogenome lost a common set of three tRNA genes, with the trnI (cau) and trnL (uaa) losses being accompanied with important variations in codon usage. Unexpectedly, despite the disappearance of trnI (cau) from the plastome in the Chloroparvula lineage, AUA codons (the codons recognized by this gene product) were detected in certain plastid genes. By comparing the sequences of plastid protein-coding genes from chloropicophycean and phylogenetically diverse chlorophyte algae with those of the corresponding predicted proteins, we discovered that the AUA codon was reassigned from isoleucine to methionine in Chloroparvula . This noncanonical genetic code has not previously been uncovered in plastids.

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“…The mitogenome is usually more divergent than the plastome among green algae. To date, complete or almost complete mitogenome sequences are available for only five prasinophyte picoalgae, which represent the Mamiellales, Prasinococcales and Pycnococcaceae (Moreau, et al 2012;Pombert, et al 2013;Robbens, et al 2007;Turmel, et al 2010;Worden, et al 2009 (Hrda, et al 2017; and Cymbomonas tetramitiformis (73.5 kb, 56 genes) . As observed for Pyramimonas, the mitogenomes of mamiellalean taxa and Prasinoderma carry a large IR with variable gene content.…”

Section: Introductionmentioning

confidence: 99%

Tracing the evolution of the plastome and mitogenome in the Chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code

Turmel

Santos²,

Otis

et al. 2019

Preprint

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The tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera (Chloropicon and Chloroparvula) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better delineate the phylogenetic affinities of these taxa and to infer the suite of changes that their organelle genomes sustained during evolution. The relationships resolved in organelle-based phylogenomic trees were essentially congruent with previously reported rRNA trees, and similar evolutionary trends but distinct dynamics were identified for the plastome and mitogenome. Although the plastome sustained considerable changes in gene content and order at the time the two genera split, subsequently it remained stable and maintained a very small size. The mitogenome, however, was remodeled more gradually and showed more fluctuation in size, mainly as a result of expansions/contractions of intergenic regions. Remarkably, the plastome and mitogenome lost a common set of three tRNA genes, with the trnI(cau) and trnL(uaa) losses being accompanied with important variations in codon usage. Unexpectedly, despite the disappearance of trnI(cau) from the plastome in the Chloroparvula lineage, AUA codons (the codons recognized by this gene product) were detected in certain plastid genes. By comparing the sequences of plastid protein-coding genes from chloropicophycean and phylogenetically diverse chlorophyte algae with those of the corresponding predicted proteins, we discovered that the AUA codon was reassigned from isoleucine to methionine in Chloroparvula. This noncanonical genetic code has not previously been uncovered in plastids.

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Mitochondrial Genome of Prasinophyte Alga Pyramimonas parkeae

Cited by 4 publications

References 54 publications

Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis

Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis

Tracing the Evolution of the Plastome and Mitogenome in the Chloropicophyceae Uncovered Convergent tRNA Gene Losses and a Variant Plastid Genetic Code

Tracing the evolution of the plastome and mitogenome in the Chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code

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