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 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.

The gain of two chloroplast tRNA introns marks the green algal ancestors of land plants

Nature ◽  
1990 ◽  
Vol 345 (6272) ◽  
pp. 268-270 ◽  
Author(s):  
J. R. Manhart ◽  
J. D. Palmer
Keyword(s):  
Land Plants ◽  
Green Algal

scholarly journals The Complete Chloroplast Genome Sequence of Pelargonium × hortorum: Organization and Evolution of the Largest and Most Highly Rearranged Chloroplast Genome of Land Plants

2006 ◽  
Vol 23 (11) ◽  
pp. 2175-2190 ◽  
Author(s):  
Timothy W. Chumley ◽  
Jeffrey D. Palmer ◽  
Jeffrey P. Mower ◽  
H. Matthew Fourcade ◽  
Patrick J. Calie ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Land Plants ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence

scholarly journals Algal ancestor of land plants was preadapted for symbiosis

2015 ◽  
Vol 112 (43) ◽  
pp. 13390-13395 ◽  
Author(s):  
Pierre-Marc Delaux ◽  
Guru V. Radhakrishnan ◽  
Dhileepkumar Jayaraman ◽  
Jitender Cheema ◽  
Mathilde Malbreil ◽  
...  
Keyword(s):  
Root Colonization ◽  
Land Plant ◽  
Land Plants ◽  
Recent Common Ancestor ◽  
Mycorrhizal Symbiosis ◽  
Specific Expression ◽  
Symbiotic Associations ◽  
Most Recent Common Ancestor ◽  
Green Algal ◽  
Colonization Of Land

Colonization of land by plants was a major transition on Earth, but the developmental and genetic innovations required for this transition remain unknown. Physiological studies and the fossil record strongly suggest that the ability of the first land plants to form symbiotic associations with beneficial fungi was one of these critical innovations. In angiosperms, genes required for the perception and transduction of diffusible fungal signals for root colonization and for nutrient exchange have been characterized. However, the origin of these genes and their potential correlation with land colonization remain elusive. A comprehensive phylogenetic analysis of 259 transcriptomes and 10 green algal and basal land plant genomes, coupled with the characterization of the evolutionary path leading to the appearance of a key regulator, a calcium- and calmodulin-dependent protein kinase, showed that the symbiotic signaling pathway predated the first land plants. In contrast, downstream genes required for root colonization and their specific expression pattern probably appeared subsequent to the colonization of land. We conclude that the most recent common ancestor of extant land plants and green algae was preadapted for symbiotic associations. Subsequent improvement of this precursor stage in early land plants through rounds of gene duplication led to the acquisition of additional pathways and the ability to form a fully functional arbuscular mycorrhizal symbiosis.

scholarly journals Extensive chloroplast genome rearrangement amongst three closely related Halamphora spp. (Bacillariophyceae), and evidence for rapid evolution as compared to land plants

PLoS ONE ◽  
2019 ◽  
Vol 14 (7) ◽  
pp. e0217824 ◽  
Author(s):  
Sarah E. Hamsher ◽  
Kyle G. Keepers ◽  
Cloe S. Pogoda ◽  
Joshua G. Stepanek ◽  
Nolan C. Kane ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Rearrangement ◽  
Rapid Evolution ◽  
Land Plants

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 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.

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