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plant mitochondrial genome

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https://www.readbyqxmd.com/read/27908230/dna-import-into-mitochondria
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
Weiwei Qi, Yang Yang, Xuzhen Feng, Mingliang Zhang, Rentao Song
In flowering plants, many respiration related proteins are encoded by mitochondrial genome and the splicing of mitochondrion-encoded 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...
November 4, 2016: Genetics
https://www.readbyqxmd.com/read/27814661/plant-mitochondrial-dna
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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...
November 2, 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
#14
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
https://www.readbyqxmd.com/read/27782804/comparative-genomic-analysis-of-the-compound-brassica-napus-rf-locus
#15
Lydiane Gaborieau, Gregory G Brown
BACKGROUND: The plant trait of cytoplasmically-inherited male sterility (CMS) and its suppression by nuclear restorer-of-fertility (Rf) genes can be viewed as a genetic arms race between the mitochondrial and nuclear genomes. Most nuclear Rf genes have been shown to encode P-type pentatricopeptide repeat proteins (PPRs). Phylogenetic analysis of P-class PPRs from sequenced plants genomes has shown that Rf-proteins cluster in a distinct clade of P-class PPRs, RFL-PPRs, that display hallmarks of positive evolutionary selection...
October 26, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27776481/mitochondrial-genome-sequences-from-wild-and-cultivated-barley-hordeum-vulgare
#16
Hiroshi Hisano, Mai Tsujimura, Hideya Yoshida, Toru Terachi, Kazuhiro Sato
BACKGROUND: Sequencing analysis of mitochondrial genomes is important for understanding the evolution and genome structures of various plant species. Barley is a self-pollinated diploid plant with seven chromosomes comprising a large haploid genome of 5.1 Gbp. Wild barley (Hordeum vulgare ssp. spontaneum) and cultivated barley (H. vulgare ssp. vulgare) have cross compatibility and closely related genomes, although a significant number of nucleotide polymorphisms have been reported between their genomes...
October 24, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27775031/evolutionary-plasticity-of-restorer-of-fertility-like-proteins-in-rice
#17
Joanna Melonek, James D Stone, Ian Small
Hybrid seed production in rice relies on cytoplasmic male sterility (CMS) induced by specific mitochondrial proteins, whose deleterious effects are suppressed by nuclear Restorer of Fertility (RF) genes. The majority of RF proteins belong to a specific clade of the RNA-binding pentatricopeptide repeat protein family. We have characterised 'restorer-of-fertility-like' (RFL) sequences from 13 Oryza genomes and the Brachypodium distachyon genome. The majority of the RFL sequences are found in genomic clusters located at two or three chromosomal loci with only a minor proportion being present as isolated genes...
October 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27764252/the-chloroplast-genome-of-utricularia-reniformis-sheds-light-on-the-evolution-of-the-ndh-gene-complex-of-terrestrial-carnivorous-plants-from-the-lentibulariaceae-family
#18
Saura R Silva, Yani C A Diaz, Helen Alves Penha, Daniel G Pinheiro, Camila C Fernandes, Vitor F O Miranda, Todd P Michael, Alessandro M Varani
Lentibulariaceae is the richest family of carnivorous plants spanning three genera including Pinguicula, Genlisea, and Utricularia. Utricularia is globally distributed, and, unlike Pinguicula and Genlisea, has both aquatic and terrestrial forms. In this study we present the analysis of the chloroplast (cp) genome of the terrestrial Utricularia reniformis. U. reniformis has a standard cp genome of 139,725bp, encoding a gene repertoire similar to essentially all photosynthetic organisms. However, an exclusive combination of losses and pseudogenization of the plastid NAD(P)H-dehydrogenase (ndh) gene complex were observed...
2016: PloS One
https://www.readbyqxmd.com/read/27760804/the-reverse-transcriptase-rna-maturase-protein-matr-is-required-for-the-splicing-of-various-group-ii-introns-in-brassicaceae-mitochondria
#19
Laure D Sultan, Daria Mileshina, Felix Grewe, Katarzyna Rolle, Sivan Abudraham, Paweł Głodowicz, Adnan Khan Niazi, Ido Keren, Sofia Shevtsov, Liron Klipcan, Jan Barciszewski, Jeffrey P Mower, Andre Dietrich, Oren Ostersetzer
Group II introns are large catalytic RNAs that are ancestrally related to nuclear spliceosomal introns. Sequences corresponding to group II RNAs are found in many prokaryotes and are particularly prevalent within plants organellar genomes. Proteins encoded within the introns themselves (maturases) facilitate the splicing of their own host pre-RNAs. Mitochondrial introns in plants have diverged considerably in sequence and have lost their maturases. In angiosperms, only a single maturase has been retained in the mitochondrial DNA: the matR gene found within NADH dehydrogenase 1 (nad1) intron 4...
October 19, 2016: Plant Cell
https://www.readbyqxmd.com/read/27755544/using-c-elegans-forward-and-reverse-genetics-to-identify-new-compounds-with-anthelmintic-activity
#20
Mark D Mathew, Neal D Mathew, Angela Miller, Mike Simpson, Vinci Au, Stephanie Garland, Marie Gestin, Mark L Edgley, Stephane Flibotte, Aruna Balgi, Jennifer Chiang, Guri Giaever, Pamela Dean, Audrey Tung, Michel Roberge, Calvin Roskelley, Tom Forge, Corey Nislow, Donald Moerman
BACKGROUND: The lack of new anthelmintic agents is of growing concern because it affects human health and our food supply, as both livestock and plants are affected. Two principal factors contribute to this problem. First, nematode resistance to anthelmintic drugs is increasing worldwide and second, many effective nematicides pose environmental hazards. In this paper we address this problem by deploying a high throughput screening platform for anthelmintic drug discovery using the nematode Caenorhabditis elegans as a surrogate for infectious nematodes...
October 2016: PLoS Neglected Tropical Diseases
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