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https://www.readbyqxmd.com/read/29222463/the-genome-sequence-of-bipolaris-cookei-reveals-mechanisms-of-pathogenesis-underlying-target-leaf-spot-of-sorghum
#1
Alex Z Zaccaron, Burton H Bluhm
Bipolaris cookei (=Bipolaris sorghicola) causes target leaf spot, one of the most prevalent foliar diseases of sorghum. Little is known about the molecular basis of pathogenesis in B. cookei, in large part due to a paucity of resources for molecular genetics, such as a reference genome. Here, a draft genome sequence of B. cookei was obtained and analyzed. A hybrid assembly strategy utilizing Illumina and Pacific Biosciences sequencing technologies produced a draft nuclear genome of 36.1 Mb, organized into 321 scaffolds with L50 of 31 and N50 of 378 kb, from which 11,189 genes were predicted...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29207474/emerging-roles-of-mitochondrial-ribosomal-proteins-in-plant-development
#2
REVIEW
Pedro Robles, Víctor Quesada
Mitochondria are the powerhouse of eukaryotic cells because they are responsible for energy production through the aerobic respiration required for growth and development. These organelles harbour their own genomes and translational apparatus: mitochondrial ribosomes or mitoribosomes. Deficient mitochondrial translation would impair the activity of this organelle, and is expected to severely perturb different biological processes of eukaryotic organisms. In plants, mitoribosomes consist of three rRNA molecules, encoded by the mitochondrial genome, and an undefined set of ribosomal proteins (mitoRPs), encoded by nuclear and organelle genomes...
December 2, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29203807/mitochondrial-genomic-variation-and-phylogenetic-relationships-of-three-groups-in-the-genus-scaphoideus-hemiptera-cicadellidae-deltocephalinae
#3
Yimin Du, Wu Dai, Christopher H Dietrich
The widespread leafhopper genus Scaphoideus Uhler is the most diverse genus in Scaphoideini and includes some species that are serious pests and vectors of plant pathogens. Here the first Scaphoideus mitogenome sequences are provided for three species, S. maai, S. nigrivalveus and S. varius, representing three main species groups in the Oriental region based on color pattern. The lengths of these three mitogenomes were 15,188, 15,235 and 15,207 bp, respectively. Gene order of three mitogenomes is highly conserved and identical to that of the putative ancestral insect...
December 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29202688/rethinking-the-evolution-of-eukaryotic-metabolism-novel-cellular-partitioning-of-enzymes-in-stramenopiles-links-serine-biosynthesis-to-glycolysis-in-mitochondria
#4
Melania Abrahamian, Meenakshi Kagda, Audrey M V Ah-Fong, Howard S Judelson
BACKGROUND: An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytosolic process. The universality of this canon has been challenged by recent genome data that suggest that some glycolytic enzymes made by stramenopiles bear mitochondrial targeting peptides. RESULTS: Mining of oomycete, diatom, and brown algal genomes indicates that stramenopiles encode two forms of enzymes for the second half of glycolysis, one with and the other without mitochondrial targeting peptides...
December 4, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29172252/prospects-on-the-evolutionary-mitogenomics-of-plants-a-case-study-on-the-olive-family-oleaceae
#5
Céline Van de Paer, Olivier Bouchez, Guillaume Besnard
The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high-throughput techniques, we reconstructed complete mitogenomes (ca...
November 24, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29162031/norgal-extraction-and-de-novo-assembly-of-mitochondrial-dna-from-whole-genome-sequencing-data
#6
Kosai Al-Nakeeb, Thomas Nordahl Petersen, Thomas Sicheritz-Pontén
BACKGROUND: Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling. RESULTS: Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers...
November 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29158974/whole-genome-sequencing-of-rhodotorula-mucilaginosa-isolated-from-the-chewing-stick-distemonanthus-benthamianus-insights-into-rhodotorula-phylogeny-mitogenome-dynamics-and-carotenoid-biosynthesis
#7
Han Ming Gan, Bolaji N Thomas, Nicole T Cavanaugh, Grace H Morales, Ashley N Mayers, Michael A Savka, André O Hudson
In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production...
2017: PeerJ
https://www.readbyqxmd.com/read/29144434/the-role-of-non-coding-rnas-in-cytoplasmic-male-sterility-in-flowering-plants
#8
REVIEW
Helena Štorchová
The interactions between mitochondria and nucleus substantially influence plant development, stress response and morphological features. The prominent example of a mitochondrial-nuclear interaction is cytoplasmic male sterility (CMS), when plants produce aborted anthers or inviable pollen. The genes responsible for CMS are located in mitochondrial genome, but their expression is controlled by nuclear genes, called fertility restorers. Recent explosion of high-throughput sequencing methods enabled to study transcriptomic alterations in the level of non-coding RNAs under CMS biogenesis...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29141004/lack-of-mitochondrial-muts-homolog-1-in-toxoplasma-gondii-disrupts-maintenance-and-fidelity-of-mitochondrial-dna-and-reveals-metabolic-plasticity
#9
Tamila Garbuz, Gustavo Arrizabalaga
The importance of maintaining the fidelity of the mitochondrial genome is underscored by the presence of various repair pathways within this organelle. Presumably, the repair of mitochondrial DNA would be of particular importance in organisms that possess only a single mitochondrion, like the human pathogens Plasmodium falciparum and Toxoplasma gondii. Understanding the machinery that maintains mitochondrial DNA in these parasites is of particular relevance, as mitochondrial function is a validated and effective target for anti-parasitic drugs...
2017: PloS One
https://www.readbyqxmd.com/read/29140976/independent-degradation-in-genes-of-the-plastid-ndh-gene-family-in-species-of-the-orchid-genus-cymbidium-orchidaceae-epidendroideae
#10
Hyoung Tae Kim, Mark W Chase
In this paper, we compare ndh genes in the plastid genome of many Cymbidium species and three closely related taxa in Orchidaceae looking for evidence of ndh gene degradation. Among the 11 ndh genes, there were frequently large deletions in directly repeated or AT-rich regions. Variation in these degraded ndh genes occurs between individual plants, apparently at population levels in these Cymbidium species. It is likely that ndh gene transfers from the plastome to mitochondrial genome (chondriome) occurred independently in Orchidaceae and that ndh genes in the chondriome were also relatively recently transferred between distantly related species in Orchidaceae...
2017: PloS One
https://www.readbyqxmd.com/read/29126284/genetic-drift-and-indel-mutation-in-the-evolution-of-yeast-mitochondrial-genome-size
#11
Shujie Xiao, Duong T Nguyen, Baojun Wu, Weilong Hao
Mitochondrial genomes (mitogenomes) are remarkably diverse in genome size and organization, but the origins of dynamic mitogenome architectures are still poorly understood. For instance, the mutational burden hypothesis postulates that the drastic difference between large plant mitogenomes and streamlined animal mitogenomes can be driven by their different mutation rates. However, inconsistent trends between mitogenome sizes and mutation rates have been documented in several lineages. These conflicting results highlight the need of systematic and sophisticated investigations on the evolution and diversity of mitogenome architecture...
November 8, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29126205/complex-analyses-of-inverted-repeats-in-mitochondrial-genomes-revealed-their-importance-and-variability
#12
Jana Cechová, Jirí Lýsek, Martin Bartas, Václav Brázda
Motivation: The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes. Results: IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals...
November 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29111964/a-phylogenetic-and-evolutionary-analysis-of-antimycin-biosynthesis
#13
Rebecca Joynt, Ryan F Seipke
Streptomyces species and other Actinobacteria are ubiquitous in diverse environments worldwide and are the source of, or inspiration for, the majority of antibiotics. The genomic era has enhanced biosynthetic understanding of these valuable chemical entities and has also provided a window into the diversity and distribution of natural product biosynthetic gene clusters. Antimycin is an inhibitor of mitochondrial cytochrome c reductase and more recently was shown to inhibit Bcl-2/Bcl-XL-related anti-apoptotic proteins commonly overproduced by cancerous cells...
November 7, 2017: Microbiology
https://www.readbyqxmd.com/read/29109252/poaceae-specific-ms1-encodes-a-phospholipid-binding-protein-for-male-fertility-in-bread-wheat
#14
Zheng Wang, Jian Li, Shaoxia Chen, Yanfang Heng, Zhuo Chen, Jing Yang, Kuanji Zhou, Jiawei Pei, Hang He, Xing Wang Deng, Ligeng Ma
Male sterility is an essential trait in hybrid seed production for monoclinous crops, including rice and wheat. However, compared with the high percentage of hybrid rice planted in the world, little commercial hybrid wheat is planted globally as a result of the lack of a suitable system for male sterility. Therefore, understanding the molecular nature of male fertility in wheat is critical for commercially viable hybrid wheat. Here, we report the cloning and characterization of Male Sterility 1 (Ms1) in bread wheat by using a combination of advanced genomic approaches...
November 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29100054/systems-phytohormone-responses-to-mitochondrial-proteotoxic-stress
#15
Xu Wang, Johan Auwerx
Mitochondrial function is controlled by two separate genomes. This feature makes mitochondria prone to proteotoxic stress when a stoichiometric imbalance occurs in the protein complexes that perform oxidative phosphorylation, which consist of both nuclear- and mitochondrial-encoded proteins. Such a proteotoxic stress is known to induce the mitochondrial unfolded protein response (UPR(mt)) in animals. It is unknown whether UPR(mt) occurs in plants. Here, we induced a mitonuclear protein imbalance in Arabidopsis through chemical or genetic interference...
November 2, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29061908/the-rna-editing-factor-slorrm4-is-required-for-normal-fruit-ripening-in-tomato
#16
Yongfang Yang, Guoning Zhu, Rui Li, Shijie Yan, Daqi Fu, Benzhong Zhu, Huiqin Tian, Yunbo Luo, Hongliang Zhu
RNA editing plays a key post-transcriptional role in gene expression. Existing studies on cytidine (C)-to-uridine (U) RNA editing in plants have focused on maize, rice, and Arabidopsis. However, the importance and regulation of RNA editing in several critical agronomic processes are not well understood, a notable example of which is fruit ripening. Here, we analyzed the expression profile of 33 RNA editing factors and identified 11 putative tomato fruit ripening-related factors. A rapid virus-induced gene silencing (VIGS) assay indicated that organelle RNA recognition motif-containing protein SlORRM4 affected tomato fruit ripening...
October 23, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29044717/a-genome-scale-analysis-of-mrnas-targeting-to-plant-mitochondria-upstream-augs-in-5-utrs-reduce-mitochondrial-association
#17
Timothée Vincent, Audrey Vingadassalon, Elodie Ubrig, Kevin Azeredo, Ola Srour, Valérie Cognat, Stéfanie Graindorge, Thalia Salinas, Laurence Maréchal-Drouard, Anne-Marie Duchêne
Intracellular sorting of mRNAs is an essential process to regulate gene expression and protein localization. Most of mitochondrial proteins are nuclear-encoded and imported into mitochondria, through post-translational or co-translational processes. In the latter case, mRNAs are found enriched in the vicinity of mitochondria. A genome-scale analysis of mRNAs associated with mitochondria has been performed to determine plant cytosolic mRNAs targeted to the mitochondrial surface. Many messengers encoding mitochondrial proteins were found associated with mitochondria...
October 17, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28988325/advances-in-understanding-the-molecular-mechanisms-of-cytoplasmic-male-sterility-and-restoration-in-rice
#18
Huiwu Tang, Yongyao Xie, Yao-Guang Liu, Letian Chen
Cytoplasmic male sterility (CMS) in plants is a male reproductive defect determined by mitochondrial genes and inherited maternally. CMS can be suppressed by nuclear restorer of fertility (Rf) genes. Therefore, CMS/Rf systems provide a classic model for the study of mitochondrial-nuclear interactions in plants. Moreover, CMS/Rf systems are economical, effective tools for the production of hybrid seeds. For example, CMS/Rf systems have been applied in over forty countries to breed hybrid rice (Oryza sativa L...
October 7, 2017: Plant Reproduction
https://www.readbyqxmd.com/read/28987861/genome-wide-transcriptome-profiling-of-genes-associated-with-arsenate-toxicity-in-an-arsenic-tolerant-rice-mutant
#19
Sun-Goo Hwang, Sandeep Chapagain, Jae Woo Lee, A-Reum Han, Cheol Seong Jang
The presence of arsenic (As) in polluted environments, such as ground water, affects the accumulation of As in rice grains and causes a serious threat to human health. However, the precise molecular regulations related to As toxicity and tolerance in rice remain largely unknown. In the present study, we developed an arsenic-tolerant type 1 (ATT1) rice mutant by γ-irradiation mutagenesis and performed genome-wide transcriptome analysis for the characterization of As-responsive genes. Toxicity inhibited transcriptional regulation of putative genes involved in photosynthesis, mitochondrial electron transport, and lipid biosynthesis metabolism in wild-type (WT) and ATT1 rice mutant...
September 27, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28986910/ribosome-profiling-in-maize
#20
Prakitchai Chotewutmontri, Nicholas Stiffler, Kenneth P Watkins, Alice Barkan
Ribosome profiling (also known as Ribo-seq) provides a genome-wide, high-resolution, and quantitative accounting of mRNA segments that are occupied by ribosomes in vivo. The method has been used to address numerous questions in bacteria, yeast, and metazoa, but its application to questions in plant biology is just beginning. This chapter provides a detailed protocol for profiling ribosomes in plant leaf tissue. The method was developed and optimized with maize, but it has been used successfully with Arabidopsis and tobacco as well...
2018: Methods in Molecular Biology
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