scholarly journals Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7500 ◽  
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Plant Species ◽  
Mutation Rate ◽  
Plastid Genome ◽  
Gene Content ◽  
High Mutation Rate ◽  
Base Pairs ◽  
Plastid Genomes ◽  
The Family

Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

scholarly journals Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

2018 ◽  
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Plant Species ◽  
Mutation Rate ◽  
Plastid Genome ◽  
Gene Content ◽  
High Mutation Rate ◽  
Base Pairs ◽  
Plastid Genomes ◽  
The Family

AbstractAlthough most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their genomes, especially plastid genomes, markedly differ from the genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing on other plants. The genome is highly reduced (18 622 base pairs versus approximately 150 kilobase pairs in autotrophic plants) and possesses an outstanding AT content, 86.8%, the highest of all sequenced plant plastid genomes. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologues from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

scholarly journals Direct estimate of the spontaneous mutation rate uncovers the effects of drift and recombination in theChlamydomonas reinhardtiiplastid genome

2015 ◽  
Author(s):  
Rob W Ness ◽  
Susanne A Kraemer ◽  
Nick Colegrave ◽  
Peter D Keightley
Keyword(s):  
Mutation Rate ◽  
Genetic Drift ◽  
Plastid Genome ◽  
De Novo ◽  
Spontaneous Mutation ◽  
Genome Structure ◽  
Nuclear Genome ◽  
De Novo Mutation ◽  
Direct Estimate ◽  
Plastid Genomes

Plastids perform crucial cellular functions, including photosynthesis, across a wide variety of eukaryotes. Since endosymbiosis, plastids have maintained independent genomes that now display a wide diversity of gene content, genome structure, gene regulation mechanisms, and transmission modes. The evolution of plastid genomes depends on an input ofde novomutation, but our knowledge of mutation in the plastid is limited to indirect inference from patterns of DNA divergence between species. Here, we use a mutation accumulation experiment, where selection acting on mutations is rendered ineffective, combined with whole-plastid genome sequencing to directly characterize de novo mutation inChlamydomonas reinhardtii. We show that the mutation rates of the plastid and nuclear genomes are similar, but that the base spectra of mutations differ significantly. We integrate our measure of the mutation rate with a population genomic dataset of 20 individuals, and show that the plastid genome is subject to substantially stronger genetic drift than the nuclear genome. We also show that high levels of linkage disequilibrium in the plastid genome are not due to restricted recombination, but are instead a consequence of increased genetic drift. One likely explanation for increased drift in the plastid genome is that there are stronger effects of genetic hitchhiking. The presence of recombination in the plastid is consistent with laboratory studies inC. reinhardtiiand demonstrates that although the plastid genome is thought to be uniparentally inherited, it recombines in nature at a rate similar to the nuclear genome.

scholarly journals The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1179
Author(s):  
Ueric José Borges de Souza ◽  
Luciana Cristina Vitorino ◽  
Layara Alexandre Bessa ◽  
Fabiano Guimarães Silva
Keyword(s):  
Plastid Genome ◽  
Structural Characteristics ◽  
Gc Content ◽  
Single Copy ◽  
Chloroplast Genes ◽  
Artocarpus Heterophyllus ◽  
Plastid Genomes ◽  
The Family ◽  
High Degree ◽  
Degree Of Similarity

Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae.

scholarly journals Comparative genomics plastomes of the Amaryllidaceae family species

2020 ◽  
Vol 16 (6) ◽  
Author(s):  
Horace José Jimenez ◽  
Allan Deyws Francisco da Silva ◽  
Luiza Suely Semen Martins ◽  
Reginaldo De Carvalho ◽  
Rômulo Maciel De Moraes Filho
Keyword(s):  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Gc Content ◽  
Base Pairs ◽  
Important Species ◽  
Gene Space ◽  
Chloroplast Genomes ◽  
The Family ◽  
Matk Gene ◽  
High Conservation

The genus Allium covers more than 800 species, signaling among the largest among monocotyledons. The genus contains many economically important species, including garlic, leeks, onions, chives and Chinese chives. Due to the high conservation of chloroplast genomes compared to nuclear genomes and mitochondrial genome, sequence of chloroplasts in Amaryllidaceae have been consistently used for species identification and various in silico programs and strategies have been used to identify, characterize and compare plastid genome regions. Plastome from 15 species of the Amaryllidaceae family revealed similarity in both sequences and in the organization of their gene regions. The base pairs (bp) number ranged from 145,819 (A. paradoxum) to 159,125 (A. ursinum). In respect the GC content, the species presented a variation between 36.7% (A. schoenoprasum and A. sativum) and 37.5% (A. coddii) and the gene space ranged from 84.760 (A. paradoxum) to 94.766 (A. sativum). The genes that encode proteins showed values between 78 (A. paradoxum) to 89 (A. cepa). Phylogenetic trees acquired through alignment of complete plastomas and the plastidial matK gene revealed similarity to the proposed classification for the family. For the genus Allium, there was the formation of three clades with perfect correspondence of the clusters to the three evolutionary lines of the genus.

scholarly journals Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

2020 ◽  
Author(s):  
Furrukh Mehmood ◽  
Abdullah . ◽  
Zartasha Ubaid ◽  
Yiming Bao ◽  
Peter Poczai ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
De Novo ◽  
Single Copy ◽  
Base Pairs ◽  
Insertion And Deletion ◽  
Plastid Genomes ◽  
Mutational Hotspots ◽  
The Family ◽  
Molecular Marker Development ◽  
Small Genus

Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled, complete, plastomed genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,198 base pairs (bp) to 154,361 bp and contained a pair of inverted repeats (IRa and IRb) of 25,027--25,071 bp that were separated by a large single-copy (LSC) region of 85,675--85,760 bp and a small single-copy (SSC) region of 18,457--18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastid genomes, which revealed close resemblance among the species. Both the substitution and insertion and deletion analyses confirmed that the IR region was significantly conserved compared with the LSC and SSC regions. Further comparative analysis among the Withania species highlighted 30 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification.

scholarly journals ­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8392 ◽  
Author(s):  
Janice Valencia-D ◽  
José Murillo-A ◽  
Clara Inés Orozco ◽  
Carlos Parra-O ◽  
Kurt M. Neubig
Keyword(s):  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Bootstrap Support ◽  
Nucleotide Substitutions ◽  
Plastid Genomes ◽  
The Family ◽  
High Bootstrap ◽  
Single Genus

Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.

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.

scholarly journals Generation of Rodent Malaria Parasites with a High Mutation Rate by Destructing Proofreading Activity of DNA Polymerase δ

DNA Research ◽  
2014 ◽  
Vol 21 (4) ◽  
pp. 439-446 ◽  
Author(s):  
Hajime Honma ◽  
Makoto Hirai ◽  
Shota Nakamura ◽  
Hassan Hakimi ◽  
Shin-ichiro Kawazu ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Mutation Rate ◽  
High Mutation Rate ◽  
Malaria Parasites ◽  
Rodent Malaria ◽  
Dna Polymerase Δ

Plant induced spatial distribution of nematodes in a semi-natural grassland

Nematology ◽  
2007 ◽  
Vol 9 (1) ◽  
pp. 131-142 ◽  
Author(s):  
Maria Viketoft
Keyword(s):  
Multivariate Analysis ◽  
Spatial Distribution ◽  
Spatial Structure ◽  
Plant Species ◽  
Trifolium Repens ◽  
Individual Plant ◽  
Nematode Communities ◽  
The Family ◽  
Natural Grassland ◽  
Nematode Fauna

AbstractThis study describes the nematode community in a semi-natural grassland and investigates if certain individual plant species can cause a spatial structure in the nematode fauna. Nematode communities were analysed in soil under Trifolium repens, Festuca ovina and from randomly taken samples. Seventy-nine nematode genera were identified. Some of the species found have not previously been reported from Sweden. Multivariate analysis separated the nematode communities associated with the two selected plant species from each other, and several individual nematode genera differed in abundance between the plant species. Trifolium repens supported greater populations of the plant feeder Tylenchorhynchus and the bacterial feeders Eucephalobus, Chiloplacus, Eumonhystera and Panagrolaimus, but fewer numbers of the bacterial feeder Achromadora. Soil under F. ovina contained more nematodes from the family Alaimidae. A comparison is given with other studies from grassland systems in Sweden.

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