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plant mitochondrial genome

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https://www.readbyqxmd.com/read/28097404/complete-mitochondrial-genome-of-the-endophytic-fungus-pestalotiopsis-fici-features-and-evolution
#1
Shu Zhang, Xiu-Na Wang, Xiao-Ling Zhang, Xing-Zhong Liu, Yong-Jie Zhang
Endophytic fungi (EF) live within plants and have profound impacts on plant communities. They are astonishingly diverse but poorly studied at the genome level. Herein, we assembled the mitochondrial genome (mitogenome) of the EF Pestalotiopsis fici, annotated and compared it with those of other relatives to better understand the evolution of the EF lineage. Except for standard fungal mitochondrial genes, the 69,529-bp circular mitogenome of P. fici harbors 18 introns acquired possibly through lateral transfer from other fungi and nine free-standing open reading frames with some scarcely seen in fungal mitogenomes...
January 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28025274/mitochondrial-phylogenomics-resolves-the-global-spread-of-higher-termites-ecosystem-engineers-of-the-tropics
#2
Thomas Bourguignon, Nathan Lo, Jan Šobotník, Simon Y W Ho, Naeem Iqbal, Eric Coissac, Maria Lee, Martin M Jendryka, David Sillam-Dussès, Barbora Křížková, Yves Roisin, Theodore A Evans
The higher termites (Termitidae) are keystone species and ecosystem engineers. They have exceptional biomass and play important roles in decomposition of dead plant matter, in soil manipulation, and as the primary food for many animals, especially in the tropics. Higher termites are most diverse in rainforests, with estimated origins in the late Eocene (∼54 Ma), postdating the breakup of Pangaea and Gondwana when most continents became separated. Since termites are poor fliers, their origin and spread across the globe requires alternative explanation...
December 25, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27999582/the-propensity-of-pentatricopeptide-repeat-genes-to-evolve-into-restorers-of-cytoplasmic-male-sterility
#3
REVIEW
Lydiane Gaborieau, Gregory G Brown, Hakim Mireau
Cytoplasmic male sterility (CMS) is a widespread phenotype in plants, which present a defect in the production of functional pollen. The male sterilizing factors usually consist of unusual genes or open reading frames encoded by the mitochondrial genome. CMS can be suppressed by specific nuclear genes called restorers of fertility (Rfs). In the majority of cases, Rf genes produce proteins that act directly on the CMS conferring mitochondrial transcripts by binding them specifically and promoting processing events...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27997742/reconstructing-the-plant-mitochondrial-genome-for-marker-discovery-a-case-study-using-pinus
#4
Kevin Donnelly, Joan Cottrell, Richard A Ennos, Giovanni Guiseppe Vendramin, Stuart A'Hara, Sarah King, Annika Perry, Witold Wachowiak, Stephen Cavers
Whole-genome-shotgun (WGS) sequencing of total genomic DNA was used to recover ~1 Mbp of novel mitochondrial (mtDNA) sequence from Pinus sylvestris (L.) and three members of the closely-related Pinus mugo species complex. DNA was extracted from megagametophyte tissue from six mother trees from locations across Europe and 100 bp paired-end sequencing was performed on the Illumina HiSeq platform. Candidate mtDNA sequences were identified by their size and coverage characteristics, and by comparison with published plant mitochondrial genomes...
December 20, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27942959/the-ppr-protein-slow-growth-4-is-involved-in-editing-of-nad4-and-affects-the-splicing-of-nad2-intron-1
#5
Stefan Weißenberger, Jürgen Soll, Chris Carrie
SLO4 is a mitochondrial PPR protein that is involved in editing nad4, possibly required for the efficient splicing of nad2 intron1. Pentatricopeptide repeat (PPR) proteins constitute a large protein family in flowering plants and are thought to be mostly involved in organellar RNA metabolism. The subgroup of PLS-type PPR proteins were found to be the main specificity factors of cytidine to uridine RNA editing. Identifying the targets of PLS-type PPR proteins can help in elucidating the molecular function of proteins encoded in the organellar genomes...
December 9, 2016: Plant Molecular Biology
https://www.readbyqxmd.com/read/27936192/insecticidal-activity-of-melaleuca-alternifolia-essential-oil-and-rna-seq-analysis-of-sitophilus-zeamais-transcriptome-in-response-to-oil-fumigation
#6
Min Liao, Jin-Jing Xiao, Li-Jun Zhou, Yang Liu, Xiang-Wei Wu, Ri-Mao Hua, Gui-Rong Wang, Hai-Qun Cao
BACKGROUND: The cereal weevil, Sitophilus zeamais is one of the most destructive pests of stored cereals worldwide. Frequent use of fumigants for managing stored-product insects has led to the development of resistance in insects. Essential oils from aromatic plants including the tea oil plant, Melaleuca alternifolia may provide environmentally friendly alternatives to currently used pest control agents. However, little is known about molecular events involved in stored-product insects in response to plant essential oil fumigation...
2016: PloS One
https://www.readbyqxmd.com/read/27908230/dna-import-into-mitochondria
#7
REVIEW
Yu M Konstantinov, A Dietrich, F Weber-Lotfi, N Ibrahim, E S Klimenko, V I Tarasenko, T A Bolotova, M V Koulintchenko
In recent decades, it has become evident that the condition for normal functioning of mitochondria in higher eukaryotes is the presence of membrane transport systems of macromolecules (proteins and nucleic acids). Natural competence of the mitochondria in plants, animals, and yeasts to actively uptake DNA may be directly related to horizontal gene transfer into these organelles occurring at much higher rate compared to the nuclear and chloroplast genomes. However, in contrast with import of proteins and tRNAs, little is known about the biological role and molecular mechanism underlying import of DNA into eukaryotic mitochondria...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27905116/unparalleled-replacement-of-native-mitochondrial-genes-by-foreign-homologs-in-a-holoparasitic-plant
#8
M Virginia Sanchez-Puerta, Laura E García, Josefina Wohlfeiler, Luis F Ceriotti
Horizontal gene transfer (HGT) among flowering plant mitochondria occurs frequently and, in most cases, leads to nonfunctional transgenes in the recipient genome. Parasitic plants are particularly prone to this phenomenon, but their mitochondrial genomes (mtDNA) have been largely unexplored. We undertook a large-scale mitochondrial genomic study of the holoparasitic plant Lophophytum mirabile (Balanophoraceae). Comprehensive phylogenetic analyses were performed to address the frequency, origin, and impact of HGT...
November 30, 2016: New Phytologist
https://www.readbyqxmd.com/read/27903241/abundant-rna-editing-sites-of-chloroplast-protein-coding-genes-in-ginkgo-biloba-and-an-evolutionary-pattern-analysis
#9
Peng He, Sheng Huang, Guanghui Xiao, Yuzhou Zhang, Jianing Yu
BACKGROUND: RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27847816/analysis-of-the-complete-mitochondrial-genome-sequence-of-the-diploid-cotton-gossypium-raimondii-by-comparative-genomics-approaches
#10
Changwei Bi, Andrew H Paterson, Xuelin Wang, Yiqing Xu, Dongyang Wu, Yanshu Qu, Anna Jiang, Qiaolin Ye, Ning Ye
Cotton is one of the most important economic crops and the primary source of natural fiber and is an important protein source for animal feed. The complete nuclear and chloroplast (cp) genome sequences of G. raimondii are already available but not mitochondria. Here, we assembled the complete mitochondrial (mt) DNA sequence of G. raimondii into a circular genome of length of 676,078 bp and performed comparative analyses with other higher plants. The genome contains 39 protein-coding genes, 6 rRNA genes, and 25 tRNA genes...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27843751/assembly-and-analysis-of-the-complete-salix-purpurea-l-salicaceae-mitochondrial-genome-sequence
#11
Suyun Wei, Xuelin Wang, Changwei Bi, Yiqing Xu, Dongyang Wu, Ning Ye
Plant mitochondrial (mt) genomes possess several complex features, including a variable size, a dynamic genome structure, and complicated patterns of gene loss and gain throughout evolutionary history. Studies of plant mt genomes can, therefore, provide unique insights into organelle evolution. We assembled the complete Salix purpurea L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. The pseudo-molecule obtained has a typical circular structure 598,970 bp long, with an overall GC content of 55...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27829020/comparative-genome-wide-analysis-of-the-malate-dehydrogenase-gene-families-in-cotton
#12
Muhammad Imran, Kai Tang, Jin-Yuan Liu
Malate dehydrogenases (MDHs) play crucial roles in the physiological processes of plant growth and development. In this study, 13 and 25 MDH genes were identified from Gossypium raimondii and Gossypium hirsutum, respectively. Using these and 13 previously reported Gossypium arboretum MDH genes, a comparative molecular analysis between identified MDH genes from G. raimondii, G. hirsutum, and G. arboretum was performed. Based on multiple sequence alignments, cotton MDHs were divided into five subgroups: mitochondrial MDH, peroxisomal MDH, plastidial MDH, chloroplastic MDH and cytoplasmic MDH...
2016: PloS One
https://www.readbyqxmd.com/read/27815362/mitochondrial-function-and-maize-kernel-development-requires-dek2-a-pentatricopeptide-repeat-protein-involved-in-nad1-mrna-splicing
#13
Weiwei Qi, Yang Yang, Xuzhen Feng, Mingliang Zhang, Rentao Song
In flowering plants, many respiration-related proteins are encoded by the mitochondrial genome and the splicing of mitochondrion-encoded messenger RNA (mRNA) involves a complex collaboration with nuclear-encoded proteins. Pentatricopeptide repeat (PPR) proteins have been implicated in these RNA-protein interactions. Maize defective kernel 2 (dek2) is a classic mutant with small kernels and delayed development. Through positional cloning and allelic confirmation, we found Dek2 encodes a novel P-type PPR protein that targets mitochondria...
January 2017: Genetics
https://www.readbyqxmd.com/read/27814661/plant-mitochondrial-dna
#14
Stewart A Morley, Brent L Nielsen
Plants possess mitochondrial genomes that are large and complex compared to animals. Nearly all animal mitochondrial genomes are about 16.5. kbp in length, whereas plant mitochondrial genomes range between 200-2,000 kbp. This is curious if we assume modern mitochondria originated from a common alpha-proteobacterial ancestor. Despite their size, plant mitochondrial genomes do not contain significantly more genes than their animal counterparts. Most of the additional DNA found in plant mitochondrial genomes consists of large introns, repeats and non-coding regions...
January 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/27808238/mitochondrial-genomes-and-comparative-genomics-of-aphanomyces-astaci-and-aphanomyces-invadans
#15
Jenny Makkonen, Arto Vesterbacka, Frank Martin, Japo Jussila, Javier Diéguez-Uribeondo, Raine Kortet, Harri Kokko
The genus Aphanomyces (Saprolegniales, Oomycetes) includes species with a variety of ecologies from saprotrophs to plant and animal parasites. Two important species in this genus are A. astaci, the cause of crayfish plague and its close relative, A. invadans, which causes the epizootic ulcerative syndrome on fish. In this study, we have assembled and annotated the mitochondrial (mt) genomes of A. astaci and A. invadans from the whole genome shotgun sequence reads (PRJNA187372; PRJNA258292, respectively). The assembly was generated from A...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27808159/limited-mitogenomic-degradation-in-response-to-a-parasitic-lifestyle-in-orobanchaceae
#16
Weishu Fan, Andan Zhu, Melisa Kozaczek, Neethu Shah, Natalia Pabón-Mora, Favio González, Jeffrey P Mower
In parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27808039/neurodegeneration-in-accelerated-aging
#17
Moren Scheibye-Knudsen
The growing proportion of elderly people represents an increasing economic burden, not least because of age-associated diseases that pose a significant cost to the health service. Finding possible interventions to age-associated disorders therefore have wide ranging implications. A number of genetically defined accelerated aging diseases have been characterized that can aid in our understanding of aging. Interestingly, all these diseases are associated with defects in the maintenance of our genome. A subset of these disorders, Cockayne syndrome, Xeroderma pigmentosum group A and ataxia-telangiectasia, show neurological involvement reminiscent of what is seen in primary human mitochondrial diseases...
November 2016: Danish Medical Journal
https://www.readbyqxmd.com/read/27806045/multiple-origins-of-the-pathogenic-yeast-candida-orthopsilosis-by-separate-hybridizations-between-two-parental-species
#18
Markus S Schröder, Kontxi Martinez de San Vicente, Tâmara H R Prandini, Stephen Hammel, Desmond G Higgins, Eduardo Bagagli, Kenneth H Wolfe, Geraldine Butler
Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27801426/participation-of-non-coding-rnas-in-plant-organelle-biogenesis
#19
Michal Rurek
The biogenesis of plant mitochondria and plastids is a multistep process that depends on the expression of both, organellar and nuclear genes. A growing body of evidence suggests that the indispensable coordination of different steps in this process may be gained by participation of the non-coding RNAs. A plethora of non-coding RNAs of diverse length, both intraorganellar ones, as well as encoded by the nuclear genome (including microRNAs and short interfering RNAs), were also suggested to play a role in the stress response by regulating the expression levels of targeted genes important for organelle biogenesis...
2016: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/27793078/genome-wide-investigation-and-expression-analyses-of-the-pentatricopeptide-repeat-protein-gene-family-in-foxtail-millet
#20
Jia-Ming Liu, Zhao-Shi Xu, Pan-Pan Lu, Wei-Wei Li, Ming Chen, Chang-Hong Guo, You-Zhi Ma
BACKGROUND: Pentatricopeptide repeat (PPR) proteins are encoded by a large gene family of approximately 450 members in Arabidopsis and 477 in rice, which characterized by tandem repetitions of a degenerate 35 amino acid characteristic sequence motifs. A large majority of the PPR genes in the higher plants are localized in organelles. Their functions remain as yet largely unknown. The majority of characterized PPR proteins have been found to function in modulating the expression plastid and mitochondrial genes in plants...
October 28, 2016: BMC Genomics
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