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

Liu, Feng; Melton, James T.

doi:10.3389/fmars.2021.668542

Cited by 12 publications

(37 citation statements)

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“…IRs in green algae showed large fluctuation in size from 6.8 to 45.5 kb and sustained losses in major groups of green algal. For example, Ulva ( Liu and Melton, 2021 ), Bryopsidales ( Cremen et al, 2018 ), and Chlorellales ( Turmel et al, 2009 ) lack the IR regions. Some members of Ulvophyceae and Ulvales do have IRs which encode the rRNA, but gene contents and gene orders showed greater diversity.…”

Section: Resultsmentioning

confidence: 99%

Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants

et al. 2022

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The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of Viridiplantae comprising 3,654 taxa from 298 families and 111 orders and compared the genomic organizations in their plastid genomic DNA among major clades, which include gene gain/loss, gene copy number, GC content, and gene blocks. We discovered that some important genes that exhibit similar functions likely formed gene blocks, such as the psb family presumably showing co-occurrence and forming gene blocks in Viridiplantae. The inverted repeats (IRs) in plastid genomes have doubled in size across land plants, and their GC content is substantially higher than non-IR genes. By employing three different data sets [all nucleotide positions (nt123), only the first and second codon positions (nt12), and amino acids (AA)], our phylogenomic analyses revealed Chlorokybales + Mesostigmatales as the earliest-branching lineage of streptophytes. Hornworts, mosses, and liverworts forming a monophylum were identified as the sister lineage of tracheophytes. Based on nt12 and AA data sets, monocots, Chloranthales and magnoliids are successive sister lineages to the eudicots + Ceratophyllales clade. The comprehensive taxon sampling and analysis of different data sets from plastid genomes recovered well-supported relationships of green plants, thereby contributing to resolving some long-standing uncertainties in the plant phylogeny.

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Section: Resultsmentioning

confidence: 99%

Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants

et al. 2022

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“…The Ulva mitochondrial introns observed are mainly distributed at 29 insertion sites in seven genes (atp1, cox1, cox2, nad3, nad5, rnl, and rns) and usually harbor an intronic orf which encoded an LAGLIDADG homing endonuclease (LHE) or a GIY-YIG homing endonuclease (GHE) or a reverse Liu et al 10.3389/fpls.2022.937398 transcriptase/maturase (RTM). Six types of group I/II introns have been found in Ulva mitogenomes, and in particular, the mitochondrial LHEs in group II introns have close relationships with that in group IB introns (Liu and Melton, 2021).…”

Section: Introductionmentioning

confidence: 96%

“…Organelle genome as a molecular marker can make us more accurately understand the concept of Ulva species and more comprehensively understand their genetic diversity and evolutionary relationships, which could not be done by a single or several DNA markers. Recently, organelle genomes of Ulva species showed a variety of obvious dynamic changes involving genome size, integration of exogenous DNA fragments, gene content, acquisition or loss of intron, genome rearrangement, and abundance of repeat sequence, at the interspecific and intraspecific level (Liu and Melton, 2021;Liu F. et al, 2022). Based on the phylogenetic analysis of organelle genome data, Ulva species are obviously divided into two independent genetic lineages (I and II) (Liu and Melton, 2021;Liu F. et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, organelle genomes of Ulva species showed a variety of obvious dynamic changes involving genome size, integration of exogenous DNA fragments, gene content, acquisition or loss of intron, genome rearrangement, and abundance of repeat sequence, at the interspecific and intraspecific level (Liu and Melton, 2021;Liu F. et al, 2022). Based on the phylogenetic analysis of organelle genome data, Ulva species are obviously divided into two independent genetic lineages (I and II) (Liu and Melton, 2021;Liu F. et al, 2022). In addition, nuclear genomes of two Ulva species, Ulva mutabilis and Ulva prolifera, have been sequenced and deposited in the GenBank database up to now (De Clerck et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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Tandem integration of circular plasmid contributes significantly to the expanded mitochondrial genomes of the green-tide forming alga Ulva meridionalis (Ulvophyceae, Chlorophyta)

Liu

Wang

Song³

2022

Front. Plant Sci.

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Comparative mitogenomics of Ulva species have revealed remarkable variations in genome size due to the integration of exogenous DNA fragments, the proliferation of group I/II introns, and the change of repeat sequences. The genus Ulva is a species-rich taxonomic group, containing a variety of green-tide forming algae. In this study, five complete mitogenomes of the green-tide forming macroalga, Ulva meridionalis R. Horimoto and S. Shimada, were assembled and compared with the available ulvophyceae mtDNAs. The main circular mitogenomes of U. meridionalis ranged from 82.94 to 111.49 kb in size, and its 111.49-kb mitogenome was the largest Ulva mitogenome sequenced so far. The expansion of U. meridionalis mitogenomes is mainly due to the tandem integration of a 5.36-kb mitochondrial circular plasmid (pUme), as well as the proliferation of introns. An intact DNA-directed RNA polymerase gene (rpo) was present in pUme of U. meridionalis and was then detected in two putative plasmids (pUmu1 and pUmu2) found in Ulva mutabilis. The observed integration of the circular plasmid into U. meridionalis mitogenomes seems to occur via homologous recombination, and is a more recent evolutionary event. Many highly homologous sequences of these three putative plasmids can be detected in the other Ulva mtDNAs sequenced thus far, indicating the integration of different mitochondrial plasmid DNA into the mitogenomes is a common phenomenon in the evolution of Ulva mitogenomes. The random incidence of destruction of plasmid-derived rpos and open reading frames (orfs) suggests that their existence is not the original characteristic of Ulva mitogenomes and there is no selective pressure to maintain their integrity. The frequent integration and rapid divergence of plasmid-derived sequences is one of the most important evolutionary forces to shape the diversity of Ulva mitogenomes.

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“…Studies on the green tide forming alga Ulva compressa showed multiple intraspecific variations among the ulvophycean mitogenomes [93]. These genomes had variable intron and intronic ORF content.…”

Section: Distribution and Impact Of Introns On Organellar Genome Architecturementioning

confidence: 99%

Organellar Introns in Fungi, Algae, and Plants

Mukhopadhyay

Hausner

2021

Cells

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Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.

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

Cited by 12 publications

References 71 publications

Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants

Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants

Tandem integration of circular plasmid contributes significantly to the expanded mitochondrial genomes of the green-tide forming alga Ulva meridionalis (Ulvophyceae, Chlorophyta)

Organellar Introns in Fungi, Algae, and Plants

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