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https://www.readbyqxmd.com/read/29617954/agora-organellar-genome-annotation-from-the-amino-acid-and-nucleotide-references
#1
Jaehee Jung, Jong Im Kim, Young-Sik Jeong, Gangman Yi
Summary: Next-generation sequencing (NGS) technologies have led to the accumulation of highthroughput sequence data from various organisms in biology. To apply gene annotation of organellar genomes for various organisms, more optimized tools for functional gene annotation are required. Almost all gene annotation tools are mainly focused on the chloroplast genome of land plants or the mitochondrial genome of animals.We have developed a web application AGORA for the fast, user-friendly, and improved annotations of organellar genomes...
March 29, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29601191/selective-gene-delivery-for-integrating-exogenous-dna-into-plastid-and-mitochondrial-genomes-using-peptide-dna-complexes
#2
Takeshi Yoshizumi, Kazusato Oikawa, Jo-Ann Chuah, Yutaka Kodama, Keiji Numata
Selective gene delivery into organellar genomes (mitochondrial and plastid genomes) has been limited because of a lack of appropriate platform technology, even though these organelles are essential for metabolite and energy production. Techniques for selective organellar modification are needed to functionally improve organelles and produce transplastomic/transmitochondrial plants. However, no method for mitochondrial genome modification has yet been established for multicellular organisms, including plants...
March 30, 2018: Biomacromolecules
https://www.readbyqxmd.com/read/29581177/recx-interacts-with-mitochondrial-reca-to-maintain-mitochondrial-genome-stability
#3
Masaki Odahara, Yasuhiko Sekine
The chloroplast and mitochondrial genomes are essential for photosynthesis and respiration, respectively. RECA and RECG, which are plant-specific homologs of the bacterial homologous recombination repair proteins RecA and RecG, maintain organelle genome stability by suppressing aberrant recombination between short dispersed repeats (SDRs) in the moss Physcomitrella patens. In this study, we analysed the plant-specific factor RECX, a homolog of bacterial RecX that regulates RecA. RECX fused to GFP co-localised with mitochondrial RECA1 and chloroplast RECA2 on mitochondrial and chloroplast nucleoids, respectively...
March 26, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29547671/whole-genome-sequencing-of-brassica-oleracea-var-capitata-reveals-new-diversity-of-the-mitogenome
#4
Kiwoung Yang, Ujjal Kumar Nath, Manosh Kumar Biswas, Md Abdul Kayum, Go-Eun Yi, Jonghoon Lee, Tae-Jin Yang, Ill-Sup Nou
Plant mitochondrial genomes (mtDNAs) vary in sequence structure. We assembled the Brassica oleracea var. capitata mtDNA using a mean coverage depth of 25X whole genome sequencing (WGS) and confirmed the presence of eight contigs/fragments by BLASTZ using the previously reported KJ820683 and AP012988 mtDNA as reference. Assembly of the mtDNA sequence reads resulted in a circular structure of 219,975 bp. Our assembled mtDNA, NCBI acc. no. KU831325, contained 34 protein-coding genes, 3 rRNA genes, and 19 tRNA genes with similarity to the KJ820683 and AP012988 reference mtDNA...
2018: PloS One
https://www.readbyqxmd.com/read/29541088/optimized-method-of-extracting-rice-chloroplast-dna-for-high-quality-plastome-resequencing-and-de-novo-assembly
#5
Takeshi Takamatsu, Marouane Baslam, Takuya Inomata, Kazusato Oikawa, Kimiko Itoh, Takayuki Ohnishi, Tetsu Kinoshita, Toshiaki Mitsui
Chloroplasts, which perform photosynthesis, are one of the most important organelles in green plants and algae. Chloroplasts maintain an independent genome that includes important genes encoding their photosynthetic machinery and various housekeeping functions. Owing to its non-recombinant nature, low mutation rates, and uniparental inheritance, the chloroplast genome (plastome) can give insights into plant evolution and ecology and in the development of biotechnological and breeding applications. However, efficient methods to obtain high-quality chloroplast DNA (cpDNA) are currently not available, impeding powerful sequencing and further functional genomics research...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29522990/identification-of-a-unique-insertion-in-plant-organellar-dna-polymerases-responsible-for-5-drp-lyase-and-strand-displacement-activities-implications-for-base-excision-repair
#6
Carlos H Trasviña-Arenas, Noe Baruch-Torres, Francisco J Cordoba-Andrade, Víctor M Ayala-García, Paola L García-Medel, Corina Díaz-Quezada, Antolín Peralta-Castro, José Juan Ordaz-Ortiz, Luis G Brieba
Plant mitochondrial and chloroplast genomes encode essential proteins for oxidative phosphorylation and photosynthesis. For proper cellular function, plant organelles must ensure genome integrity. Although plant organelles repair damaged DNA using the multi-enzyme Base Excision Repair (BER) pathway, the details of this pathway in plant organelles are largely unknown. The initial enzymatic steps in BER produce a 5'-deoxyribose phosphate (5'-dRP) moiety that must be removed to allow DNA ligation and in plant organelles, the enzymes responsible for the removal of a 5'-dRP group are unknown...
February 27, 2018: DNA Repair
https://www.readbyqxmd.com/read/29495437/the-complexity-of-mitochondrial-complex-iv-an-update-of-cytochrome-c-oxidase-biogenesis-in-plants
#7
REVIEW
Natanael Mansilla, Sofia Racca, Diana E Gras, Daniel H Gonzalez, Elina Welchen
Mitochondrial respiration is an energy producing process that involves the coordinated action of several protein complexes embedded in the inner membrane to finally produce ATP. Complex IV or Cytochrome c Oxidase (COX) is the last electron acceptor of the respiratory chain, involved in the reduction of O₂ to H₂O. COX is a multimeric complex formed by multiple structural subunits encoded in two different genomes, prosthetic groups (heme a and heme a ₃), and metallic centers (CuA and CuB ). Tens of accessory proteins are required for mitochondrial RNA processing, synthesis and delivery of prosthetic groups and metallic centers, and for the final assembly of subunits to build a functional complex...
February 27, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29495281/plant-mitochondrial-inner-membrane-protein-insertion
#8
REVIEW
Renuka Kolli, Jürgen Soll, Chris Carrie
During the biogenesis of the mitochondrial inner membrane, most nuclear-encoded inner membrane proteins are laterally released into the membrane by the TIM23 and the TIM22 machinery during their import into mitochondria. A subset of nuclear-encoded mitochondrial inner membrane proteins and all the mitochondrial-encoded inner membrane proteins use the Oxa machinery-which is evolutionarily conserved from the endosymbiotic bacterial ancestor of mitochondria-for membrane insertion. Compared to the mitochondria from other eukaryotes, plant mitochondria have several unique features, such as a larger genome and a branched electron transport pathway, and are also involved in additional cellular functions such as photorespiration and stress perception...
February 24, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29463014/exploring-the-history-of-chloroplast-capture-in-arabis-using-whole-chloroplast-genome-sequencing
#9
Akira Kawabe, Hiroaki Nukii, Hazuka Y Furihata
Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian Arabis species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the complete chloroplast genomes of A. hirsuta , A. nipponica, and A. flagellosa were sequenced in order to analyze their divergence and their relationships. The chloroplast genomes of A. nipponica and A. flagellosa were similar, which indicates chloroplast replacement...
February 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29453633/comparative-analysis-of-the-mitochondrial-genome-of-the-fungus-colletotrichum-lindemuthianum-the-causal-agent-of-anthracnose-in-common-beans
#10
Casley Borges de Queiroz, Mateus Ferreira Santana, Pedro M Pereira Vidigal, Marisa Vieira de Queiroz
Fungi of the genus Colletotrichum are economically important and are used as models in plant-pathogen interaction studies. In this study, the complete mitochondrial genomes of two Colletotrichum lindemuthianum isolates were sequenced and compared with the mitochondrial genomes of seven species of Colletotrichum. The mitochondrial genome of C. lindemuthianum is a typical circular molecule 37,446 bp (isolate 89 A 2 2-3) and 37,440 bp (isolate 83.501) in length. The difference of six nucleotides between the two genomes is the result of a deletion in the ribosomal protein S3 (rps3) gene in the 83...
February 16, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29439501/the-roles-of-mitochondrion-in-intergenomic-gene-transfer-in-plants-a-source-and-a-pool
#11
Nan Zhao, Yumei Wang, Jinping Hua
Intergenomic gene transfer (IGT) is continuous in the evolutionary history of plants. In this field, most studies concentrate on a few related species. Here, we look at IGT from a broader evolutionary perspective, using 24 plants. We discover many IGT events by assessing the data from nuclear, mitochondrial and chloroplast genomes. Thus, we summarize the two roles of the mitochondrion: a source and a pool. That is, the mitochondrion gives massive sequences and integrates nuclear transposons and chloroplast tRNA genes...
February 11, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29423233/organellar-genome-assembly-methods-and-comparative-analysis-of-horticultural-plants
#12
Xuelin Wang, Feng Cheng, Dekai Rohlsen, Changwei Bi, Chunyan Wang, Yiqing Xu, Suyun Wei, Qiaolin Ye, Tongming Yin, Ning Ye
Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants...
2018: Horticulture Research
https://www.readbyqxmd.com/read/29420807/transoceanic-dispersal-and-plate-tectonics-shaped-global-cockroach-distributions-evidence-from-mitochondrial-phylogenomics
#13
Thomas Bourguignon, Tang Qian, Simon Y W Ho, Frantisek Juna, Zongqing Wang, Daej A Arab, Stephen L Cameron, James Walker, David Rentz, Theodore A Evans, Nathan Lo
Following the acceptance of plate tectonics theory in the latter half of the 20th century, vicariance became the dominant explanation for the distributions of many plant and animal groups. In recent years, however, molecular-clock analyses have challenged a number of well-accepted hypotheses of vicariance. As a widespread group of insects with a fossil record dating back 300 million years, cockroaches provide an ideal model for testing hypotheses of vicariance through plate tectonics vs transoceanic dispersal...
February 6, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29417579/two-pivotal-rna-editing-sites-in-the-mitochondrial-atp1mrna-are-required-for-atp-synthase-to-produce-sufficient-atp-for-cotton-fiber-cell-elongation
#14
Peng He, Guanghui Xiao, Hao Liu, Lihua Zhang, Li Zhao, Meiju Tang, Sheng Huang, Yingjie An, Jianing Yu
RNA editing is a post-transcriptional maturation process affecting organelle transcripts in land plants. However, the molecular functions and physiological roles of RNA editing are still poorly understood. Using high-throughput sequencing, we identified 692 RNA editing sites in the Gossypium hirsutum mitochondrial genome. A total of 422 editing sites were found in the coding regions and all the edits are cytidine (C) to uridine (U) conversions. Comparative analysis showed that two editing sites in Ghatp1, C1292 and C1415, had a prominent difference in editing efficiency between fiber and ovule...
February 8, 2018: New Phytologist
https://www.readbyqxmd.com/read/29393558/the-virome-of-the-arbuscular-mycorrhizal-fungus-gigaspora-margarita-reveals-the-first-report-of-dna-fragments-corresponding-to-replicating-non-retroviral-rna-viruses-in-fungi
#15
Massimo Turina, Stefano Ghignone, Nausicaa Astolfi, Alessandro Silvestri, Paola Bonfante, Luisa Lanfranco
Arbuscular Mycorrhizal Fungi (AMF) are key components of the plant microbiota. AMF genetic complexity is increased by the presence of endobacteria, which live inside many species. A further component of such complexity is the virome associated to AMF, whose knowledge is still very limited. Here, by exploiting transcriptomic data we describe the virome of Gigaspora margarita. A BLAST search for viral RNA-dependent RNA polymerases sequences allowed the identification of four mitoviruses, one Ourmia-like narnavirus, one Giardia-like virus, and two sequences related to Fusarium graminearum mycoviruses...
February 2, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29382740/a-plastidial-pantoate-transporter-with-a-potential-role-in-pantothenate-synthesis
#16
Lili Huang, Michal Pyc, Saleh Alseekh, Donald R McCarty, Valérie de Crécy-Lagard, Jesse F Gregory, Christopher S Henry, Alisdair R Fernie, Robert T Mullen, Andrew D Hanson
The pantothenate (vitamin B5) synthesis pathway in plants is not fully defined because the sub-cell-ular site of its ketopantoate → pantoate reduction step is unclear. However, the pathway is known to be split between cytosol, mit-o-chondria, and potentially plastids, and inferred to involve mitochondrial or plast-idial transport of ketopantoate or pantoate. No proteins that mediate these transport steps have been identified. Compar-at-ive genomic and transcriptomic analyses identified Arabidopsis thal-iana BASS1 (At1g78560) and its maize ( Zea mays ) ortholog as candidates for such a transport role...
January 30, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29364919/genome-wide-analyses-of-the-bemisia-tabaci-species-complex-reveal-contrasting-patterns-of-admixture-and-complex-demographic-histories
#17
S Elfekih, P Etter, W T Tay, M Fumagalli, K Gordon, E Johnson, P De Barro
Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1) have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now, researchers have relied on a single mitochondrial gene and/or a handful of nuclear markers to study this species complex...
2018: PloS One
https://www.readbyqxmd.com/read/29364229/isolation-and-respiratory-measurements-of-mitochondria-from-arabidopsis-thaliana
#18
Wenhui Lyu, Jennifer Selinski, Lu Li, David A Day, Monika W Murcha, James Whelan, Yan Wang
Mitochondria are essential organelles involved in numerous metabolic pathways in plants, most notably the production of adenosine triphosphate (ATP) from the oxidation of reduced compounds such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADH2). The complete annotation of the Arabidopsis thaliana genome has established it as the most widely used plant model system, and thus the need to purify mitochondria from a variety of organs (leaf, root, or flower) is necessary to fully utilize the tools that are now available for Arabidopsis to study mitochondrial biology...
January 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29358189/cms-g-from-beta-vulgaris-ssp-maritima-is-maintained-in-natural-populations-despite-containing-an-atypical-cytochrome-c-oxidase
#19
Etienne H Meyer, Caroline Lehmann, Stéphane Boivin, Lea Brings, Isabelle De Cauwer, Ralph Bock, Kristina Kühn, Pascal Touzet
While mitochondrial mutants of the respiratory machinery are rare and often lethal, Cytoplasmic Male Sterility (CMS), a mitochondrially inherited trait that results in pollen abortion is frequently encountered in wild populations. It generates a breeding system called gynodioecy. In Beta vulgaris ssp. maritima , a gynodioecious species, we found CMS-G to be widespread across the distribution range of the species. Despite the sequencing of the mitochondrial genome of CMS-G, the mitochondrial sterilizing factor causing CMS-G is still unknown...
January 22, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29332167/non-coding-rnas-and-plant-male-sterility-current-knowledge-and-future-prospects
#20
REVIEW
Ankita Mishra, Abhishek Bohra
Latest outcomes assign functional role to non-coding (nc) RNA molecules in regulatory networks that confer male sterility to plants. Male sterility in plants offers great opportunity for improving crop performance through application of hybrid technology. In this respect, cytoplasmic male sterility (CMS) and sterility induced by photoperiod (PGMS)/temperature (TGMS) have greatly facilitated development of high-yielding hybrids in crops. Participation of non-coding (nc) RNA molecules in plant reproductive development is increasingly becoming evident...
February 2018: Plant Cell Reports
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