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 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 Phylogeny and Comparative Analysis of Chinese Chamaesium Species Revealed by the Complete Plastid Genome

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 965 ◽  
Author(s):  
Xian-Lin Guo ◽  
Hong-Yi Zheng ◽  
Megan Price ◽  
Song-Dong Zhou ◽  
Xing-Jin He
Keyword(s):  
Plastid Genome ◽  
Molecular Phylogenetics ◽  
Genome Structure ◽  
Gc Content ◽  
Plastid Genomes ◽  
Second Generation Sequencing ◽  
Ssr Loci ◽  
Small Genus ◽  
Generation Sequencing ◽  
Simple Sequence

Chamaesium H. Wolff (Apiaceae, Apioideae) is a small genus mainly distributed in the Hengduan Mountains and the Himalayas. Ten species of Chamaesium have been described and nine species are distributed in China. Recent advances in molecular phylogenetics have revolutionized our understanding of Chinese Chamaesium taxonomy and evolution. However, an accurate phylogenetic relationship in Chamaesium based on the second-generation sequencing technology remains poorly understood. Here, we newly assembled nine plastid genomes from the nine Chinese Chamaesium species and combined these genomes with eight other species from five genera to perform a phylogenic analysis by maximum likelihood (ML) using the complete plastid genome and analyzed genome structure, GC content, species pairwise Ka/Ks ratios and the simple sequence repeat (SSR) component. We found that the nine species’ plastid genomes ranged from 152,703 bp (C. thalictrifolium) to 155,712 bp (C. mallaeanum), and contained 133 genes, 34 SSR types and 585 SSR loci. We also found 20,953–21,115 codons from 53 coding sequence (CDS) regions, 38.4–38.7% GC content of the total genome and low Ka/Ks (0.27–0.43) ratios of 53 aligned CDS. These results will facilitate our further understanding of the evolution of the genus Chamaesium.

Empirical investigation of mutation rate for herbicide resistance

Weed Science ◽  
2019 ◽  
Vol 67 (4) ◽  
pp. 361-368 ◽  
Author(s):  
Federico A. Casale ◽  
Darci A. Giacomini ◽  
Patrick J. Tranel
Keyword(s):  
Mutation Rate ◽  
Herbicide Resistance ◽  
De Novo ◽  
Selection Process ◽  
Theoretical Calculations ◽  
Acetolactate Synthase ◽  
De Novo Mutation ◽  
De Novo Mutations ◽  
Sources Of Resistance ◽  
Resistant Mutants

AbstractIn a predictable natural selection process, herbicides select for adaptive alleles that allow weed populations to survive. These resistance alleles may be available immediately from the standing genetic variation within the population or may arise from immigration via pollen or seeds from other populations. Moreover, because all populations are constantly generating new mutant genotypes by de novo mutations, resistant mutants may arise spontaneously in any herbicide-sensitive weed population. Recognizing that the relative contribution of each of these three sources of resistance alleles influences what strategies should be applied to counteract herbicide-resistance evolution, we aimed to add experimental information to the resistance evolutionary framework. Specifically, the objectives of this experiment were to determine the de novo mutation rate conferring herbicide resistance in a natural plant population and to test the hypothesis that the mutation rate increases when plants are stressed by sublethal herbicide exposure. We used grain amaranth (Amaranthus hypochondriacus L.) and resistance to acetolactate synthase (ALS)-inhibiting herbicides as a model system to discover spontaneous herbicide-resistant mutants. After screening 70.8 million plants, however, we detected no spontaneous resistant genotypes, indicating the probability of finding a spontaneous ALS-resistant mutant in a given sensitive population is lower than 1.4 × 10−8. This empirically determined upper limit is lower than expected from theoretical calculations based on previous studies. We found no evidence that herbicide stress increased the mutation rate, but were not able to robustly test this hypothesis. The results found in this study indicate that de novo mutations conferring herbicide resistance might occur at lower frequencies than previously expected.

scholarly journals Extensivede novomutation rate variation between individuals and across the genome ofChlamydomonas reinhardtii

2015 ◽  
Author(s):  
Rob W Ness ◽  
Andrew D Morgan ◽  
Radhakrishnan B Vasanthakrishnan ◽  
Nick Colegrave ◽  
Peter D Keightley
Keyword(s):  
Mutation Rate ◽  
Evolutionary Biology ◽  
De Novo ◽  
Spontaneous Mutation ◽  
Gc Content ◽  
Rate Variation ◽  
De Novo Mutations ◽  
Local Sequence ◽  
Wild Strains ◽  
Genomic Regions

Describing the process of spontaneous mutation is fundamental for understanding the genetic basis of disease, the threat posed by declining population size in conservation biology, and in much evolutionary biology. However, directly studying spontaneous mutation is difficult because of the rarity of de novo mutations. Mutation accumulation (MA) experiments overcome this by allowing mutations to build up over many generations in the near absence of natural selection. In this study, we sequenced the genomes of 85 MA lines derived from six genetically diverse wild strains of the green algaChlamydomonas reinhardtii. We identified 6,843 spontaneous mutations, more than any other study of spontaneous mutation. We observed seven-fold variation in the mutation rate among strains and that mutator genotypes arose, increasing the mutation rate dramatically in some replicates. We also found evidence for fine-scale heterogeneity in the mutation rate, driven largely by the sequence flanking mutated sites, and by clusters of multiple mutations at closely linked sites. There was little evidence, however, for mutation rate heterogeneity between chromosomes or over large genomic regions of 200Kbp. Using logistic regression, we generated a predictive model of the mutability of sites based on their genomic properties, including local GC content, gene expression level and local sequence context. Our model accurately predicted the average mutation rate and natural levels of genetic diversity of sites across the genome. Notably, trinucleotides vary 17-fold in rate between the most mutable and least mutable sites. Our results uncover a rich heterogeneity in the process of spontaneous mutation both among individuals and across the genome.

scholarly journals Direct estimation of the spontaneous mutation rate by short-term mutation accumulation lines in Chironomus riparius

2016 ◽  
Author(s):  
Ann-Marie Oppold ◽  
Markus Pfenninger
Keyword(s):  
Mutation Rate ◽  
De Novo ◽  
Spontaneous Mutation ◽  
Single Point ◽  
Point Mutations ◽  
Mutation Accumulation ◽  
Occurrence Rate ◽  
Spontaneous Mutation Rate ◽  
Biting Midge ◽  
Mutational Spectrum

AbstractMutations are the ultimate basis of evolution, yet their occurrence rate is known only for few species. We directly estimated the spontaneous mutation rate and the mutational spectrum in the non-biting midge C. riparius with a new approach. Individuals from ten mutation accumulation lines over five generations were deep genome sequenced to count de novo mutations (DNMs) that were not present in a pool of F1 individuals, representing parental genotypes. We identified 51 new single site mutations of which 25 were insertions or deletions and 26 single point mutations. This shift in the mutational spectrum compared to other organisms was explained by the high A/T content of the species. We estimated a haploid mutation rate of 2.1 x 10−9 (95% confidence interval: 1.4 x 10−9 – 3.1 x 10−9) which is in the range of recent estimates for other insects and supports the drift barrier hypothesis. We show that accurate mutation rate estimation from a high number of observed mutations is feasible with moderate effort even for non-model species.

scholarly journals Comparative Survey of Morphological Variations and Plastid Genome Sequencing Reveals Phylogenetic Divergence between Four Endemic Ilex Species

Forests ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 964
Author(s):  
Tao Su ◽  
Mengru Zhang ◽  
Zhenyu Shan ◽  
Xiaodong Li ◽  
Biyao Zhou ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Strong Association ◽  
Nuclear Genome ◽  
Image Cytometry ◽  
Single Copy ◽  
Reproductive Organs ◽  
Rrna Genes ◽  
Phenotypic Traits ◽  
Trna Genes ◽  
Plastid Genomes

Holly (Ilex L.), from the monogeneric Aquifoliaceae, is a woody dioecious genus cultivated as pharmaceutical and culinary plants, ornamentals, and industrial materials. With distinctive leaf morphology and growth habitats, but uniform reproductive organs (flowers and fruits), the evolutionary relationships of Ilex remain an enigma. To date, few contrast analyses have been conducted on morphology and molecular patterns in Ilex. Here, the different phenotypic traits of four endemic Ilex species (I. latifolia, I. suaveolens, I. viridis, and I. micrococca) on Mount Huangshan, China, were surveyed through an anatomic assay and DNA image cytometry, showing the unspecified link between the examined morphology and the estimated nuclear genome size. Concurrently, the newly-assembled plastid genomes in four Ilex have lengths ranging from 157,601 bp to 157,857 bp, containing a large single-copy (LSC, 87,020–87,255 bp), a small single-copy (SSC, 18,394–18,434 bp), and a pair of inverted repeats (IRs, 26,065–26,102 bp) regions. The plastid genome annotation suggested the presence of numerable protein-encoding genes (89–95), transfer RNA (tRNA) genes (37–40), and ribosomal RNA (rRNA) genes (8). A comprehensive comparison of plastomes within eight Ilex implicated the conserved features in coding regions, but variability in the junctions of IRs/SSC and the divergent hotspot regions potentially used as the DNA marker. The Ilex topology of phylogenies revealed the incongruence with the traditional taxonomy, whereas it informed a strong association between clades and geographic distribution. Our work herein provided novel insight into the variations in the morphology and phylogeography in Aquifoliaceae. These data contribute to the understanding of genetic diversity and conservation in the medicinal Ilex of Mount Huangshan.

scholarly journals Direct Measure of the De Novo Mutation Rate in Autism and Schizophrenia Cohorts

2010 ◽  
Vol 87 (3) ◽  
pp. 316-324 ◽  
Author(s):  
Philip Awadalla ◽  
Julie Gauthier ◽  
Rachel A. Myers ◽  
Ferran Casals ◽  
Fadi F. Hamdan ◽  
...  
Keyword(s):  
Mutation Rate ◽  
De Novo ◽  
De Novo Mutation ◽  
Direct Measure

scholarly journals Comparative analysis of the complete plastid genomes of Mangifera species and gene transfer between plastid and mitochondrial genomes

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10774
Author(s):  
Yingfeng Niu ◽  
Chengwen Gao ◽  
Jin Liu
Keyword(s):  
Plastid Genome ◽  
Genome Structure ◽  
Dna Barcode ◽  
Intergenic Spacer ◽  
Mitochondrial Genomes ◽  
Dna Barcodes ◽  
Total Size ◽  
Genome Data ◽  
Plastid Genomes ◽  
High Support

Mango is an important commercial fruit crop belonging to the genus Mangifera. In this study, we reported and compared four newly sequenced plastid genomes of the genus Mangifera, which showed high similarities in overall size (157,780–157,853 bp), genome structure, gene order, and gene content. Three mutation hotspots (trnG-psbZ, psbD-trnT, and ycf4-cemA) were identified as candidate DNA barcodes for Mangifera. These three DNA barcode candidate sequences have high species identification ability. We also identified 12 large fragments that were transferred from the plastid genome to the mitochondrial genome, and found that the similarity was more than 99%. The total size of the transferred fragment was 35,652 bp, accounting for 22.6% of the plastid genome. Fifteen intact chloroplast genes, four tRNAs and numerous partial genes and intergenic spacer regions were identified. There are many of these genes transferred from mitochondria to the chloroplast in other species genomes. Phylogenetic analysis based on whole plastid genome data provided a high support value, and the interspecies relationships within Mangifera were resolved well.

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