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plant chloroplast mitochondrial genome

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https://www.readbyqxmd.com/read/29928286/white-panicle3-a-novel-nucleus-encoded-mitochondrial-protein-is-essential-for-proper-development-and-maintenance-of-chloroplasts-and-mitochondria-in-rice
#1
Hongchang Li, Guobiao Ji, Yun Wang, Qian Qian, Jichen Xu, Sodmergen, Guozhen Liu, Xianfeng Zhao, Mingsheng Chen, Wenxue Zhai, Dayong Li, Lihuang Zhu
Mitochondria and chloroplasts are interacting organelles that play important roles in plant development. In addition to a small number proteins encoded by their own genomes, the majority of mitochondrial and chloroplast proteins are encoded in the cell nucleus and imported into the organelle. As a consequence, coordination between mitochondria, chloroplasts, and the nucleus is of crucial importance to plant cells. Variegated mutants are chloroplast-defective mutants and are considered to be ideal models for studying the intercommunication between these organelles...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29758275/employing-hypothesis-testing-and-data-from-multiple-genomic-compartments-to-resolve-recalcitrant-backbone-nodes-in-goodenia-s-l-goodeniaceae
#2
Rachel S Jabaily, Kelly A Shepherd, Pryce S Michener, Caroline J Bush, Rodrigo Rivero, Andrew G Gardner, Emily B Sessa
Goodeniaceae is a primarily Australian flowering plant family with a complex taxonomy and evolutionary history. Previous phylogenetic analyses have successfully resolved the backbone topology of the largest clade in the family, Goodenia s.l., but have failed to clarify relationships within the species-rich and enigmatic Goodenia clade C, a prerequisite for taxonomic revision of the group. We used genome skimming to retrieve sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa representing Goodenia s...
May 11, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29670636/positive-selection-driving-cytoplasmic-genome-evolution-of-the-medicinally-important-ginseng-plant-genus-panax
#3
Peng Jiang, Feng-Xue Shi, Ming-Rui Li, Bao Liu, Jun Wen, Hong-Xing Xiao, Lin-Feng Li
Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29617954/agora-organellar-genome-annotation-from-the-amino-acid-and-nucleotide-references
#4
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/29581177/recx-interacts-with-mitochondrial-reca-to-maintain-mitochondrial-genome-stability
#5
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 analyzed the plant-specific factor RECX, a homolog of bacterial RecX that regulates RecA. RECX fused to GFP colocalized with mitochondrial RECA1 and chloroplast RECA2 on mitochondrial and chloroplast nucleoids, respectively...
May 2018: Plant Physiology
https://www.readbyqxmd.com/read/29541088/optimized-method-of-extracting-rice-chloroplast-dna-for-high-quality-plastome-resequencing-and-de-novo-assembly
#6
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
#7
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...
May 2018: DNA Repair
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/29439501/the-roles-of-mitochondrion-in-intergenomic-gene-transfer-in-plants-a-source-and-a-pool
#10
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
#11
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/29297348/comparative-analysis-of-inverted-repeats-of-polypod-fern-polypodiales-plastomes-reveals-two-hypervariable-regions
#12
Maria D Logacheva, Anastasiya A Krinitsina, Maxim S Belenikin, Kamil Khafizov, Evgenii A Konorov, Sergey V Kuptsov, Anna S Speranskaya
BACKGROUND: Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes. RESULTS: We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns...
December 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29172252/prospects-on-the-evolutionary-mitogenomics-of-plants-a-case-study-on-the-olive-family-oleaceae
#13
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
#14
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/28986910/ribosome-profiling-in-maize
#15
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
https://www.readbyqxmd.com/read/28947489/the-plastid-and-mitochondrial-peptidase-network-in-arabidopsis-thaliana-a-foundation-for-testing-genetic-interactions-and-functions-in-organellar-proteostasis
#16
REVIEW
Kristina Majsec, Nazmul H Bhuiyan, Qi Sun, Sunita Kumari, Vivek Kumar, Doreen Ware, Klaas J van Wijk
Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement...
November 2017: Plant Cell
https://www.readbyqxmd.com/read/28922794/genome-wide-variation-patterns-uncover-the-origin-and-selection-in-cultivated-ginseng-panax-ginseng-meyer
#17
Ming-Rui Li, Feng-Xue Shi, Ya-Ling Li, Peng Jiang, Lili Jiao, Bao Liu, Lin-Feng Li
Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28852146/the-extraordinary-variation-of-the-organellar-genomes-of-the-aneura-pinguis-revealed-advanced-cryptic-speciation-of-the-early-land-plants
#18
Kamil Myszczyński, Alina Bączkiewicz, Katarzyna Buczkowska, Monika Ślipiko, Monika Szczecińska, Jakub Sawicki
Aneura pinguis is known as a species complex with several morphologically indiscernible species, which are often reproductively isolated from each other and show distinguishable genetic differences. Genetic dissimilarity of cryptic species may be detected by genomes comparison. This study presents the first complete sequences of chloroplast and mitochondrial genomes of six cryptic species of A. pinguis complex: A. pinguis A, B, C, E, F, J. These genomes have been compared to each other in order to reconstruct phylogenetic relationships and to gain better understanding of the evolutionary process of cryptic speciation in this complex...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#19
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28573928/diversity-of-mitochondrial-plastid-dnas-mtpts-in-seed-plants
#20
Xin-Cun Wang, Haimei Chen, Dan Yang, Chang Liu
Mitochondrial plastid DNAs (MTPTs) refer to plastid-derived DNA fragments in mitochondrial genomes. While the MTPTs have been described for numerous species, its overall patterns have not been examined in details. Here, we carried out a systematic analysis of MTPTs among 73 plant species, including 28 algae, 1 liverwort, 2 moss, 1 lycophyte, 1 gymnosperm, 1 magnoliid, 12 monocots, 26 eudicots and 1 relic angiosperm Amborella trichopoda. A total of 300 MTPT gene clusters were found in 39 seed plants, which represented 144 MTPT gene cluster types...
May 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
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