scholarly journals Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution

Nature ◽  
2000 ◽  
Vol 403 (6770) ◽  
pp. 649-652 ◽  
Author(s):  
Claude Lemieux ◽  
Christian Otis ◽  
Monique Turmel
Keyword(s):  
Chloroplast Genome ◽  
Green Plant ◽  
Plant Evolution

scholarly journals Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 143 ◽  
Author(s):  
Melvin J Oliver ◽  
Andrew G Murdock ◽  
Brent D Mishler ◽  
Jennifer V Kuehl ◽  
Jeffrey L Boore ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Green Plant ◽  
Gene Content ◽  
Structural Arrangement ◽  
Chloroplast Genomes ◽  
Plant Chloroplast ◽  
Tortula Ruralis ◽  
Chloroplast Genome Sequence

scholarly journals Characteristics of the Completed Chloroplast Genome Sequence of Xanthium Spinosum: Comparative Analyses, Identification of Mutational Hotspots and Phylogenetic Implications

2020 ◽  
Author(s):  
Gurusamy Raman ◽  
KyuTae Park ◽  
Joo Hwan Kim ◽  
SeonJoo Park
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Plant Evolution ◽  
Rrna Genes ◽  
Trna Genes ◽  
Mutational Hotspots ◽  
Phylogenetic Implications ◽  
Intergenic Regions ◽  
Chloroplast Genome Sequence ◽  
Cp Genome

Abstract Background: The invasive alien species, Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, there are no extensive molecular studies for this plant. Results: Here, the complete chloroplast genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 bp and possessed quadripartite circular structure. The cp genome contained 115 unique genes, including 80 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Comparative analysis revealed that X. spinosum encoded a higher number of repeats (999 repeats) and 701 SSRs in their cp genome. Also, fourteen divergences (Pi > 0.03) were found in the intergenic regions. The accD gene underwent positive selection within Heliantheae, which contributes to further investigation of the adaptive plant evolution in the ecosystem. Additionally, the phylogenetic analysis revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and it is an early-diverging lineage of subtribe Ambrosiinae though it supports with very weak bootstrap value. Conclusion: The identified hotspot regions were thought to be useful molecular markers for resolving phylogenetic relationships and species validation of Xanthium.

scholarly journals Eukaryotic Components Remodeled Chloroplast Nucleoid Organization during the Green Plant Evolution

2015 ◽  
Vol 8 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Yusuke Kobayashi ◽  
Mari Takusagawa ◽  
Naomi Harada ◽  
Yoichiro Fukao ◽  
Shohei Yamaoka ◽  
...  
Keyword(s):  
Green Plant ◽  
Plant Evolution ◽  
Chloroplast Nucleoid

scholarly journals Comparative analysis of nuclear, chloroplast, and mitochondrial genomes of watermelon and melon provides evidence of gene transfer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Haonan Cui ◽  
Zhuo Ding ◽  
Qianglong Zhu ◽  
Yue Wu ◽  
Boyan Qiu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Mitochondrial Genome ◽  
Chloroplast Genome ◽  
Genetic Material ◽  
Nuclear Genome ◽  
Plant Evolution ◽  
Total Length ◽  
Organelle Genomes ◽  
Nuclear Genomes ◽  
Genetic Communication

AbstractDuring plant evolution, there is genetic communication between organelle and nuclear genomes. A comparative analysis was performed on the organelle and nuclear genomes of the watermelon and melon. In the watermelon, chloroplast-derived sequences accounted for 7.6% of the total length of the mitochondrial genome. In the melon, chloroplast-derived sequences accounted for approximately 2.73% of the total mitochondrial genome. In watermelon and melon, the chloroplast-derived small-fragment sequences are either a subset of large-fragment sequences or appeared multiple times in the mitochondrial genome, indicating that these fragments may have undergone multiple independent migration integrations or emerged in the mitochondrial genome after migration, replication, and reorganization. There was no evidence of migration from the mitochondria to chloroplast genome. A sequence with a total length of about 73 kb (47%) in the watermelon chloroplast genome was homologous to a sequence of about 313 kb in the nuclear genome. About 33% of sequences in the watermelon mitochondrial genome was homologous with a 260 kb sequence in the nuclear genome. A sequence with a total length of about 38 kb (25%) in the melon chloroplast genome was homologous with 461 sequences in the nuclear genome, with a total length of about 301 kb. A 3.4 Mb sequence in the nuclear genome was homologous with a melon mitochondrial sequence. These results indicate that, during the evolution of watermelon and melon, a large amount of genetic material was exchanged between the nuclear genome and the two organelle genomes in the cytoplasm.

Molecular approaches to the study of plant biosystematics

1990 ◽  
Vol 3 (1) ◽  
pp. 1 ◽  
Author(s):  
MT Clegg ◽  
ML Durbin
Keyword(s):  
Dna Sequencing ◽  
Chloroplast Genome ◽  
Molecular Cloning ◽  
Dna Sequence ◽  
Restriction Site ◽  
Genetic Relationships ◽  
Plant Evolution ◽  
The Family ◽  
Family Level ◽  
Pcr Method

Genetic relationships among organisms can be estimated from the pattern of DNA sequence change between hereditary molecules. The methods of molecular biology are increasingly being employed in systematic and evolutionary research to study genetic relationships and phylogeny. The investigator is faced with a variety of choices in initiating research in 'molecular biosystematics'. First, a gene or genome that provides a level of genetic resolution appropriate for the materials under study must be selected. Common choices in plants include the chloroplast genome (cpDNA) or components of the chloroplast genome, the nuclear ribosomal RNA genes (rDNA), or nuclear-encoded, single-copy genes. A second consideration is that several methods can be employed to provide direct or indirect measures of DNA sequence divergence. One widely used method determines genetic divergence based on restriction site changes. Restriction site analyses typically require some knowledge of the physical map of the DNA molecule under study. Empirical studies indicate that restriction site analyses of cpDNA provide good resolution for systematic investigations at or below the family level. A second method that is increasing in importance is DNA sequencing. Until quite recently, DNA sequencing required the molecular cloning of the gene or DNA fragment of interest and the implementation of a 'sequencing strategy' for the production of overlapping sequence runs. Two related technological developments have overcome both of these requirements, when the goal is the repetitive sequencing of a specific gene from a number of taxa. It is now possible to synthesise synthetic oligonucleotides that can be used to prime dideoxy sequencing at virtually any point in the gene of interest, based on previously determined sequence information. The second major innovation is the invention of the polymerase chain reaction technique (PCR). The PCR method permits the direct amplification of DNA fragments from heterogeneous DNA mixtures and thereby circumvents the molecular cloning requirement. Application of the PCR method to chloroplast genes, together with direct primer-mediated sequencing, provides a method for obtaining large data sets. CpDNA sequence data are especially valuable at or above the family level and provide a powerful means of resolving genetic relationships at the deepest levels of plant evolution.

scholarly journals The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes

PLoS ONE ◽  
2008 ◽  
Vol 3 (8) ◽  
pp. e2944 ◽  
Author(s):  
Luiz Gustavo Guedes Corrêa ◽  
Diego Mauricio Riaño-Pachón ◽  
Carlos Guerra Schrago ◽  
Renato Vicentini dos Santos ◽  
Bernd Mueller-Roeber ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Green Plant ◽  
Plant Evolution ◽  
Bzip Transcription Factors

scholarly journals A pan-plant protein complex map reveals deep conservation and novel assemblies

2019 ◽  
Author(s):  
Claire D. McWhite ◽  
Ophelia Papoulas ◽  
Kevin Drew ◽  
Rachael M. Cox ◽  
Viviana June ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Green Plant ◽  
Plant Evolution ◽  
Economic Systems ◽  
Plant Proteins ◽  
Protein Assemblies ◽  
Uncharacterized Protein ◽  
Protein Functions ◽  
Novel Interactions ◽  
Mutant Phenotypes

SUMMARYPlants are foundational to global ecological and economic systems, yet most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. Using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified novel interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical to agriculture. We also uncovered plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers the first cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.

scholarly journals Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

2019 ◽  
Author(s):  
Ryan A. Folk ◽  
Neeka Sewnath ◽  
Chun-Lei Xiang ◽  
Brandon T. Sinn ◽  
Robert P. Guralnick
Keyword(s):  
Plastid Genome ◽  
Gene Loss ◽  
Green Plant ◽  
Plant Evolution ◽  
Critically Endangered ◽  
Gene Content ◽  
Flowering Plant ◽  
Plastid Gene ◽  
Plastid Genomes ◽  
Mycoheterotrophic Plants

AbstractBackgroundPlastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of degradation and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome of Saniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context.ResultsWe find that the plastid genome of Saniculiphyllum has experienced pseudogenization of five genes of the NDH complex (ndhA, ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with an aquatic habit, as well as the more surprising pseudogenization of two genes more central to photosynthesis (ccsA and cemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional.ConclusionsSaniculiphyllum appears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.

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