scholarly journals Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae

2015 ◽  
Vol 7 (7) ◽  
pp. 2062-2082 ◽  
Author(s):  
Monique Turmel ◽  
Christian Otis ◽  
Claude Lemieux
Keyword(s):  
Chloroplast Genome ◽  
Dynamic Evolution ◽  
Green Algal

scholarly journals Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Thomas Sauvage ◽  
William E. Schmidt ◽  
Hwan Su Yoon ◽  
Valerie J. Paul ◽  
Suzanne Fredericq
Keyword(s):  
Chloroplast Genome ◽  
Structural Variation ◽  
Rapid Development ◽  
Nuclear Genome ◽  
Nanopore Sequencing ◽  
Homing Endonucleases ◽  
Hybrid Assembly ◽  
Bacterial Genomes ◽  
Current Output ◽  
Green Algal

Abstract Background The MinION Access Program (MAP, 2014–2016) allowed selected users to test the prospects of long nanopore reads for diverse organisms and applications through the rapid development of improving chemistries. In 2014, faced with a fragmented Illumina assembly for the chloroplast genome of the green algal holobiont Caulerpa ashmeadii, we applied to the MAP to test the prospects of nanopore reads to investigate such intricacies, as well as further explore the hologenome of this species with native and hybrid approaches. Results The chloroplast genome could only be resolved as a circular molecule in nanopore assemblies, which also revealed structural variants (i.e. chloroplast polymorphism or heteroplasmy). Signal and Illumina polishing of nanopore-assembled organelle genomes (chloroplast and mitochondrion) reflected the importance of coverage on final quality and current limitations. In hybrid assembly, our modest nanopore data sets showed encouraging results to improve assembly length, contiguity, repeat content, and binning of the larger nuclear and bacterial genomes. Profiling of the holobiont with nanopore or Illumina data unveiled a dominant Rhodospirillaceae (Alphaproteobacteria) species among six putative endosymbionts. While very fragmented, the cumulative hybrid assembly length of C. ashmeadii’s nuclear genome reached 24.4 Mbp, including 2.1 Mbp in repeat, ranging closely with GenomeScope’s estimate (> 26.3 Mbp, including 4.8 Mbp in repeat). Conclusion Our findings relying on a very modest number of nanopore R9 reads as compared to current output with newer chemistries demonstrate the promising prospects of the technology for the assembly and profiling of an algal hologenome and resolution of structural variation. The discovery of polymorphic ‘chlorotypes’ in C. ashmeadii, most likely mediated by homing endonucleases and/or retrohoming by reverse transcriptases, represents the first report of chloroplast heteroplasmy in the siphonous green algae. Improving contiguity of C. ashmeadii’s nuclear and bacterial genomes will require deeper nanopore sequencing to greatly increase the coverage of these larger genomic compartments.

Identification of Polycistronic Transcriptional Units and Non-canonical Introns in Green Algal Chloroplasts Based on Long-read RNA Sequencing Data

2020 ◽  
Author(s):  
Xiaoxiao Zou ◽  
Heroen Verbruggen ◽  
Tianjingwei Li ◽  
Jun Zhu ◽  
Zuo Chen ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Green Algae ◽  
Higher Plants ◽  
Green Algal ◽  
Chloroplast Genomes ◽  
Caulerpa Lentillifera ◽  
Transcriptional Units ◽  
Group Ii ◽  
Distinct Features ◽  
Algal Chloroplast

Abstract Background: Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome have been extensively studied in higher plants and several model species of algae, little is known about transcriptional features in green algal lineages. Results: Based on full-length cDNA (Iso-Seq) sequencing, we identified widely co-transcribed polycistronic transcriptional units (PTUs) in the green alga Caulerpa lentillifera. In addition to clusters of genes from the same pathway, we identified a series of PTUs of up to nine genes whose function in the plastid is not understood. The RNA data further allowed us to confirm widespread expression of fragmented genes and conserved open reading frames, which are both important features in green algal chloroplast genomes. In addition, a newly fragmented gene specific to C. lentillifera was discovered, which may represent a recent gene fragmentation event in chloroplast genome.Taking the accurate exon-intron boundary information, gene structural annotation was greatly improved across the siphonous green algae lineages. Our data also revealed a type of non-canonical Group II introns, with a deviant secondary structure and intronic ORFs lacking known splicing or mobility domains. These widespread introns have conserved positions in their genes and are excised precisely despite lacking clear consensus intron boundaries.Conclusion: Our study fills important knowledge gaps in chloroplast genome organization and transcription in green algae, and providing new insights into expression of polycistronic transcripts, freestanding ORFs and fragmented genes in algal chloroplast genomes. Moreover, we revealed an unusual type of Group II intron with distinct features and conserved positions in Bryopsidales. Our data represents interesting additions to knowledge of chloroplast intron structure and highlights clusters of uncharacterized genes that probably play important roles in plastid.

scholarly journals Dynamic Evolution of Telomeric Sequences in the Green Algal Order Chlamydomonadales

2012 ◽  
Vol 4 (3) ◽  
pp. 248-264 ◽  
Author(s):  
Jana Fulnečková ◽  
Tereza Hasíková ◽  
Jiří Fajkus ◽  
Alena Lukešová ◽  
Marek Eliáš ◽  
...  
Keyword(s):  
Dynamic Evolution ◽  
Telomeric Sequences ◽  
Green Algal

The Green Algal Ancestry of Land Plants as Revealed by the Chloroplast Genome

2007 ◽  
Vol 168 (5) ◽  
pp. 679-689 ◽  
Author(s):  
Monique Turmel ◽  
Jean‐François Pombert ◽  
Patrick Charlebois ◽  
Christian Otis ◽  
Claude Lemieux
Keyword(s):  
Chloroplast Genome ◽  
Land Plants ◽  
Green Algal

scholarly journals Structural variation and evolution of chloroplast tRNAs in green algae

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11524
Author(s):  
Fangbing Qi ◽  
Yajing Zhao ◽  
Ningbo Zhao ◽  
Kai Wang ◽  
Zhonghu Li ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Green Algae ◽  
Sequence Alignment ◽  
Structural Variation ◽  
Evolutionary Relationship ◽  
Multiple Sequence ◽  
Evolutionary Patterns ◽  
Systematic Analysis ◽  
Origin And Evolution ◽  
Green Algal

As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the Ψ-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. Based on the constructed phylogenetic tree, mutations were found to accompany the evolution of the Green algae chloroplast tRNA. Moreover, chloroplast tRNAs of Chlorophyceae are consistent with those of monocotyledons and gymnosperms in terms of evolutionary patterns, sharing a common multi-phylogenetic pattern and rooted in a rich common ancestor. Sequence alignment and systematic analysis of tRNA in chloroplast genome of Chlorophyceae, clarified the characteristics and rules of tRNA changes, which will promote the evolutionary relationship of tRNA and the origin and evolution of chloroplast.

scholarly journals Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae

2019 ◽  
Vol 11 (10) ◽  
pp. 2992-3007 ◽  
Author(s):  
David Žihala ◽  
Marek Eliáš
Keyword(s):  
Genetic Code ◽  
Protein Sequences ◽  
Dynamic Evolution ◽  
Translation System ◽  
Release Factor ◽  
Standard Genetic Code ◽  
Green Algal ◽  
Mitochondrial Genetic Code ◽  
Species Analysis ◽  
Direct Support

Abstract Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.

scholarly journals Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0250968
Author(s):  
Chuner Cai ◽  
Kai Gu ◽  
Hui Zhao ◽  
Sophie Steinhagen ◽  
Peimin He ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Chloroplast Genome ◽  
Genetic Markers ◽  
Yellow Sea ◽  
Algal Species ◽  
The Yellow Sea ◽  
Evolutionary Trends ◽  
Green Tides ◽  
Green Algal ◽  
Chloroplast Genomes

Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.

scholarly journals Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoxiao Zou ◽  
Heroen Verbruggen ◽  
Tianjingwei Li ◽  
Jun Zhu ◽  
Zou Chen ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Green Algae ◽  
Higher Plants ◽  
Green Algal ◽  
Chloroplast Genomes ◽  
Caulerpa Lentillifera ◽  
Transcriptional Units ◽  
Group Ii ◽  
Distinct Features ◽  
Algal Chloroplast

Abstract Background Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome having been extensively studied in higher plants and several model species of algae, little is known about the transcriptional features of green algal chloroplast-encoded genes. Results Based on full-length cDNA (Iso-Seq) sequencing, we identified widely co-transcribed polycistronic transcriptional units (PTUs) in the green alga Caulerpa lentillifera. In addition to clusters of genes from the same pathway, we identified a series of PTUs of up to nine genes whose function in the plastid is not understood. The RNA data further allowed us to confirm widespread expression of fragmented genes and conserved open reading frames, which are both important features in green algal chloroplast genomes. In addition, a newly fragmented gene specific to C. lentillifera was discovered, which may represent a recent gene fragmentation event in the chloroplast genome. With the newly annotated exon-intron boundary information, gene structural annotation was greatly improved across the siphonous green algae lineages. Our data also revealed a type of non-canonical Group II introns, with a deviant secondary structure and intronic ORFs lacking known splicing or mobility domains. These widespread introns have conserved positions in their genes and are excised precisely despite lacking clear consensus intron boundaries. Conclusion Our study fills important knowledge gaps in chloroplast genome organization and transcription in green algae, and provides new insights into expression of polycistronic transcripts, freestanding ORFs and fragmented genes in algal chloroplast genomes. Moreover, we revealed an unusual type of Group II intron with distinct features and conserved positions in Bryopsidales. Our data represents interesting additions to knowledge of chloroplast intron structure and highlights clusters of uncharacterized genes that probably play important roles in plastids.

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