Deborah Charlesworth

Mitochondrial DNA

Gynodioecy

Silene

Silene conica

Silene noctiflora

Sex determination in Silene

Pithovirus

List of resurrected species

Chickpea

Dosage compensation

Lepidoptera

Chickpea

Sex

Seed

Artemisia (genus)

Sexually transmitted infection

اتیلن - ویکی‌پدیا، دانشنامهٔ آزاد

যৌনতা - উইকিপিডিয়া

Seed

Artemisia (genus)

Sexually transmitted infection

Mitochondrial genomes1

• Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. (biomedcentral.com)

Plant mitochondrial1

• The advent of high-throughput sequencing technologies has greatly promoted the research for plant mitochondrial (mt) genomes. (biomedcentral.com)

Genes1

• The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. (biomedcentral.com)

Repeated sequences1

• Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2 , which is the longest organellar intron reported to date in plants. (biomedcentral.com)

Mitogenomes2

• Most (~ 80%, 176 out of 214) of the plant mitogenomes deposited in the GenBank database ( https://www.ncbi.nlm.nih.gov/genome/organelle/ ) were generated in the past several years (since 2011). (biomedcentral.com)
• To date (as of July 2018), 53 bryophyte and 108 vascular plant complete mitogenomes have been reported ( https://www.ncbi.nlm.nih.gov/genome/organelle/ ). (biomedcentral.com)

Single1

• In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome. (biomedcentral.com)

Chromosomes10

• Unlike in the nucleus, where mitosis and meiosis ensure faithful transmission of chromosomes, the mechanisms of inheritance in fragmented mitochondrial genomes remain mysterious. (pnas.org)
• Complete genomes from two populations revealed a high degree of similarity in the sequence, structure, and relative abundance of mitochondrial chromosomes. (pnas.org)
• Thus, these mitochondrial genomes retain a full gene complement but carry a highly variable set of chromosomes that are filled with presumably dispensable sequence. (pnas.org)
• The fragmentation of genomes into chromosomes is a very general property of eukaryotic nuclear genomes. (pnas.org)
• In the case of Silene, the pair of automsomal chromosomes are transformed into heteromorphic sex-determining chromosomes expressed as XY. (wikipedia.org)
• The Evolution of Sex Chromosomes and Dosage Compensation in Plants , Genome Biology and Evolution , vol. 9 pp.627-645. (univ-lyon1.fr)
• SEX-DETector: a probabilistic approach to study sex chromosomes in non-model organisms , Genome Biology and Evolution , vol. 8 pp.2530-2543. (univ-lyon1.fr)
• One of the strategies facilitating accomplishment of this goal is use of genomic resources created from smaller segments of the genome - chromosomes or chromosome arms. (cas.cz)
• As first noted by Morgan, recombination rates between the X and the Y chromosomes are unusually low compared to the rest of the genome. (felixbeaudryresearch.com)
• Y chromosomes were found to have very high rates of evolution at non-synonymous sites compared to synonymous sites: e.g. in apes, Drosophila , stickleback, birds, clam shrimp and plants including Silene , Rumex and papaya. (felixbeaudryresearch.com)

Gene15

• Angiosperm mitochondrial genomes are characterized by a number of unusual properties, including their large and variable sizes (ranging from ∼200 kb to over 10 Mb), low gene densities, extensive posttranscriptional modifications, and propensity to capture foreign DNA sequences ( 24 , 25 ). (pnas.org)
• The highly rearranged mitochondrial genomes with a variation in gene flanking regions make Silene vulgaris an excellent model for the study of mitochondrial gene expression in plants. (cas.cz)
• Conclusions Frequent homologous recombination events that are widespread in plant mitochondrial genomes may change chromosomal configurations and also the control of gene transcription including CMS gene expression. (cas.cz)
• 2012. Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris , an angiosperm with pervasive cytoplasmic male sterility. (virginia.edu)
• In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome. (biomedcentral.com)
• A detailed comparison of C. apetalus and C. quitensis cp genomes revealed identical gene content and order. (peerj.com)
• With the use of a whole-genome bacterial artificial chromosome (BAC) library, we amplified and sequenced a ~200 kb region containing the male-determining gene Nix . (biomedcentral.com)
• As exemplified above, the evolution of separate sexes can originate from an initial gene, or whole-genome, duplication event, resulting in a situation more permissive of gain-of-function mutations, possibly required for this transition. (plantcell.org)
• This project uses RAD sequencing and genome skim data to investigate patterns of gene flow in sympatric populations (largely Northern Californian) and elucidate how interspecific hybridization influences plastome content and function. (pyrola.org)
• However, it appears that the contribution of parentel genomes need not to be equal and that altered gene expression is common. (cas.cz)
• Limited functional genomics resources and whole genome association studies could be substantially improved through the application of molecular approach for the characterization of gene content and identification of molecular markers. (springeropen.com)
• The mitochondrial genomes of flowering plants vary greatly in size, gene content, gene order, mutation rate and level of RNA editing. (biomedcentral.com)
• The Magnolia genome has evolved at an even lower rate, revealing a roughly 5,000-fold range of synonymous-site divergence among angiosperms whose mitochondrial gene space has been comprehensively sequenced. (biomedcentral.com)
• On the genome level, there are three, compatible mechanisms: changes in gene content, structural differences in gene products, and quantitative differences in gene expression. (lu.se)
• The analysis showed that L. bicolor has a relatively large genome, and that the large genome size is partly due to an expansion of gene family sizes. (lu.se)

Sequence18

• For example, there are no inversions between the genomes, and there are only nine SNPs in 25 kb of protein-coding sequence. (pnas.org)
• An extraordinary variation in mitochondrial DNA sequence exists in angiosperm Silene vulgaris. (cas.cz)
• Complete Plastid Genome Sequence of the Basal Asterid Ardisia polysticta Miq. (semanticscholar.org)
• Three chronological B. rapa genomes (recent, young, and old) were reconstructed with sequence divergences, revealing a trace of recursive WGD events. (biomedcentral.com)
• The whole genome sequence (WGS) of Brassica A has been released with the B. rapa ssp. (biomedcentral.com)
• The application of HMMs to plant genomes enabled us to identify 49 families that encompass all Angiosperms ('higher plants') SDRs, each family being sufficiently conserved to enable simpler analyses based only on overall sequence similarity. (biomedcentral.com)
• Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. (biomedcentral.com)
• The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. (biomedcentral.com)
• Identification of the plastid genome sequence allowed organelle genome comparison. (biomedcentral.com)
• Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. (biomedcentral.com)
• Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. (biomedcentral.com)
• In addition, the increasing availability of plant organelle and nuclear genome sequence data provides an understanding of the mechanisms driving plant genome evolution. (biomedcentral.com)
• Despite its importance, technical obstacles of DNA isolation and sequence assembly limit the sequencing of mitochondrial genomes. (biomedcentral.com)
• Large repeats and the dynamic mitochondrial genome organization complicate sequence assembly. (biomedcentral.com)
• 2014). Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP. (duke.edu)
• Use the available genome sequence to identify M. violaceum transcripts within the flower transcriptomes. (nrp.ac.uk)
• In this LabRoots webinar, Jonas Korlach the CSO of PacBio provides an introduction to PacBio HiFi sequence reads, which are both long (up to 25 kb currently) and accurate (>99%) at the individual single-molecule sequence read level andhave allowed for advances in de novo genome assemblies. (pacb.com)
• Angiosperm mitochondrial genomes are remarkably variable in both structure and sequence content. (biomedcentral.com)

Angiosperm3

• We study plant genomes in various contexts, including the evolution of the angiosperm flower (Darwin's abominable mystery) and plant domestication. (univ-lyon1.fr)
• In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. (biomedcentral.com)
• RNA editing is another source of variability among angiosperm mitochondrial genomes. (biomedcentral.com)

Recombination5

• Anderson JB, Wickens C, Khan M, Cowen LE, Federspiel N, Jones T, Kohn LM (2001) Infrequent genetic exchange and recombination in the mitochondrial genome of Candida albicans . (springer.com)
• The mitochondrial genome of the legume ''Vigna radiata'' and the analysis of recombination across short mitochondrial repeats. (openwetware.org)
• MareyMap Online: A User-Friendly Web Application and Database Service for Estimating Recombination Rates Using Physical and Genetic Maps , Genome biology and evolution , vol. 9 pp.2506-2509. (univ-lyon1.fr)
• Removal of retrotransposon DNA from the plant genome is thought to require recombination [ 15 ]. (biomedcentral.com)
• Mus , Drosophila , Caenorhabditis , Silene ), with a focus on the evolutionary consequences of recombination arrest. (unil.ch)

Vulgaris5

• Transcription of atp1 is influenced by both genomic configuration and nuclear background in the highly rearranged mitochondrial genomes of Silene vulgaris. (cas.cz)
• Results We assembled the complete mitochondrial genome from the haplotype KRA of S. vulgaris. (cas.cz)
• We found the loss of three editing sites in the KRA mitochondrial genome and identified four sites with highly distinct editing rates between KRA and another S. vulgaris haplotypes (KOV). (cas.cz)
• Sebasky, M.E., Keller, S.R. and Taylor, D.R. 2016 Investigating past range dynamics for a weed of cultivation, Silene vulgaris . (virginia.edu)
• Olson MS, McCauley DE and Taylor DR (2005) Genetics and adaptation in structured populations: Sex ratio evolution in Silene vulgaris. (ecologycenter.us)

Evolutionary9

• The diversity in mitochondrial genome architecture across eukaryotes ( 1 , 2 ) tells a history of highly divergent evolutionary trajectories since the origin of mitochondria from an alphaproteobacterial endosymbiont ( 3 ⇓ - 5 ). (pnas.org)
• By contrast, little is known about the basic mechanisms of inheritance and evolutionary maintenance of multichromosomal mitochondrial genomes. (pnas.org)
• Evolutionary rate variation in organelle genomes: the role of mutational processes. (virginia.edu)
• Using rapidly evolving genetic markers to make inferences about the recent evolutionary history of the domesticated apple, we found that the European crabapple has made an unexpectedly large contribution to the genome of the domesticated apple. (plos.org)
• This paper first introduces our present knowledge of the origin of mitochondria and chloroplasts, and the organization and inheritance patterns of their genomes, and then carries on to review the evolutionary processes influencing mitochondrial and chloroplast genomes. (springer.com)
• The differences in evolutionary phenomena between the nuclear and cytoplasmic genomes are highlighted. (springer.com)
• Bergstrom CT, Pritchard J (1998) Germline bottlenecks and the evolutionary maintenance of mitochondrial genomes. (springer.com)
• The recently released Brassica rapa draft genome provides an ideal opportunity to update our knowledge of the conserved genomic structures in Brassica , and to study evolutionary innovations of the mesohexaploid plant, B. rapa . (biomedcentral.com)
• Evolutionary forces affecting synonymous variations in plant genomes. (nih.gov)

Eukaryotic5

• TRANSPOSABLE elements (TEs) are ubiquitous in pro- and eukaryotic genomes. (genetics.org)
• Flowering plants are a prime example of a eukaryotic lineage with extreme and highly diverse mitochondrial genome structures. (pnas.org)
• Subtelomeric domains immediately adjacent to telomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes. (g3journal.org)
• These results provide further evidence that subtelomeric domains are among the most dynamic regions in eukaryotic genomes. (g3journal.org)
• Transposable elements (TEs) are selfish, autonomously replicating DNA sequences that constitute a major component of eukaryotic genomes and contribute to genome evolution through their movement and amplification. (readbyqxmd.com)

Flowering plants2

• Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. (biomedcentral.com)
• Rapid evolution of enormous, multichromosomal genomes in flowering plants. (openwetware.org)

Microbotryum3

• Synteny between genomes of Microbotryum intermedium (in orange) and M. salviae (in purple). (wenjuanma.com)
• Fig. 1 Sampling and population structure of the 38 studied anther-smut fungal Microbotryum strains on Silene caroliniana and S. virginica inferred based on autosomal genome-wide single-nucleotide polymorphisms (SNPs). (wenjuanma.com)
• Molecular mimicry and the hijacking of sex determination mechanisms in dioecious Silene dioica by the anther smut fungus Microbotryum violaceum. (nrp.ac.uk)

Chloroplast genomes1

• Analysis of whole chloroplast genomes from the genera of the Clauseneae, the curry tribe (Rutaceae, Citrus family). (si.edu)

Biology and Evolution2

• Progress and Prospects in Gender Visibility at SMBE Annual Meetings , Genome biology and evolution , vol. 10 pp.901-908. (univ-lyon1.fr)
• Genome Biology and Evolution 9: 627-645. (peercommunityin.org)

Noctiflora1

• To determine the extent to which such genomes are stably maintained, we analyzed intraspecific variation in the mitochondrial genome of S. noctiflora . (pnas.org)

Plant mitochondrial genomes1

• This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. (biomedcentral.com)

Hybridization1

• José Carlos del Valle, Inés Casimiro-Soriguer, Ma Luisa Buide, Eduardo Narbona & Justen B. Whittall 2019: Whole Plastome Sequencing Within Silene Section Psammophilae Reveals Mainland Hybridization and Divergence With the Balearic Island Populations. (sav.sk)

Rumex1

• In some plants such as kiwifruit, melon, willow, papaya, date palm and strawberry, genetic divergence is limited, while in others such as Silene , Cannabis , and some loci in Rumex the level of divergence is remarkable. (felixbeaudryresearch.com)

Dioica1

• Identification and properties of UDP-glucose: cyanidin-3-O-glucosyltransferase isolated from petals of the red campion (Silene dioica). (genome.jp)

Lychnis1

• Distinction between the traditional genera Lychnis and Silene in morphology is that Lychnis usually has five styles and an entire capsule, whereas Silene has three styles and a split capsule ( Desfeux and Lejeune, 1996 ). (ashs.org)

Complete mitochondrial genome1

• Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms. (biomedcentral.com)

Autosomal1

• 3 ] published in Genome Biology revealed an unexpected trend in genetic diversity in wild and domestic papaya populations: X-linked loci harbor the lowest levels of diversity within the genome, ten-fold lower than autosomal diversity and twelve-fold lower than Y-linked diversity. (beds.ac.uk)

Transposable elements2

• Transposable elements are ubiquitous components of all genomes. (biomedcentral.com)
• The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L. (sav.sk)

Ncbi.nlm.nih.gov2

• Most (~ 80%, 176 out of 214) of the plant mitogenomes deposited in the GenBank database ( https://www.ncbi.nlm.nih.gov/genome/organelle/ ) were generated in the past several years (since 2011). (biomedcentral.com)
• To date (as of July 2018), 53 bryophyte and 108 vascular plant complete mitogenomes have been reported ( https://www.ncbi.nlm.nih.gov/genome/organelle/ ). (biomedcentral.com)

Whole chloroplast1

• Methods for obtaining and analyzing whole chloroplast genome sequences. (openwetware.org)

Plastid and mitochondrial1

• Non-enriched whole genome DNA libraries, both shotgun and paired-end, include plastid and mitochondrial DNA that is sequenced along with the nuclear DNA during the sequencing run. (biomedcentral.com)

Single nucleotide po1

• Screening of single nucleotide polymorphisms (SNPs) in parents and 10 F1 progeny identified 39 de novo mutations and yielded a rate of 7.31 × 10-9 (95% confidence interval: 5.20 × 10-9 - 8.00 × 10-9) mutations per site per haploid genome per generation. (pacb.com)

Cytoplasmic2

• The inheritance of cytoplasmic genomes is not universally maternal. (springer.com)
• On the other hand, the variability occasionally observed in the inheritance mechanisms of cytoplasmic genomes reduces heritability and increases environmental components in phenotypic features and, consequently, decreases the potential for adaptive evolution. (springer.com)

Haploid Genome1

• Cytogenetic and Molecular Evidence and Sequencing of a Haploid Genome \ Soukupova M. · Nevrtalova E. · Čížková J. · Vogel I. · Cegan R. · Hobza R. · Vyskot B. (nhbs.com)

Repeats1

• The complete cp genome of C. apetalus has the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. (peerj.com)