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https://www.readbyqxmd.com/read/28213476/editing-of-mitochondrial-transcripts-nad3-and-cox2-by-dek10-is-essential-for-mitochondrial-function-and-maize-plant-development
#1
Weiwei Qi, Zhongrui Tian, Lei Lu, Xiuzu Chen, Xinze Chen, Wei Zhang, Rentao Song
Respiration, the core of mitochondrial metabolism, depends on the function of five respiratory complexes. Many respiratory chain related proteins are encoded by the mitochondrial genome and their RNAs undergo post-transcriptional modifications by nuclear genome expressed factors, including pentatricopeptide repeat (PPR) proteins. Maize defective kernel 10 (dek10) is a classic mutant with small kernels and delayed development. Through positional cloning we found that Dek10 encodes an E-subgroup PPR protein localized in mitochondria...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28202452/entire-plastid-phylogeny-of-the-carrot-genus-daucus-apiaceae-concordance-with-nuclear-data-and-mitochondrial-and-nuclear-dna-insertions-to-the-plastid
#2
David M Spooner, Holly Ruess, Massimo Iorizzo, Douglas Senalik, Philipp Simon
PREMISE OF THE STUDY: We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences. METHODS: We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP). KEY RESULTS: Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D...
February 15, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28201983/comparative-analysis-of-the-mitochondrial-genomes-of-colletotrichum-gloeosporioides-sensu-lato-insights-into-the-evolution-of-a-fungal-species-complex-interacting-with-diverse-plants
#3
Xiaofei Liang, Xianglin Tian, Wenkui Liu, Tingyu Wei, Wei Wang, Qiuyue Dong, Bo Wang, Yanan Meng, Rong Zhang, Mark L Gleason, Guangyu Sun
BACKGROUND: The fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show considerable variation in host and tissue adaptation strategies. Accurate species delimitation in C. gloeosporioides s.l. is very challenging due to nascent lineage boundaries and phenotypic plasticity, which strongly impedes studies of the complex's host-interaction biology...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28186130/identification-of-symmetrical-rna-editing-events-in-the-mitochondria-of-salvia-miltiorrhiza-by-strand-specific-rna-sequencing
#4
Bin Wu, Haimei Chen, Junjie Shao, Hui Zhang, Kai Wu, Chang Liu
Salvia miltiorrhiza is one of the most widely-used medicinal plants. Here, we systematically analyzed the RNA editing events in its mitochondria. We developed a pipeline using REDItools to predict RNA editing events from stand-specific RNA-Seq data. The predictions were validated using reverse transcription, RT-PCR amplification and Sanger sequencing experiments. Putative sequences motifs were characterized. Comparative analyses were carried out between S. miltiorrhiza, Arabidopsis thaliana and Oryza sativa...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28150734/mitochondrial-genome-diversity-in-dagger-and-needle-nematodes-nematoda-longidoridae
#5
J E Palomares-Rius, C Cantalapiedra-Navarrete, A Archidona-Yuste, V C Blok, P Castillo
Dagger and needle nematodes included in the family Longidoridae (viz. Longidorus, Paralongidorus, and Xiphinema) are highly polyphagous plant-parasitic nematodes in wild and cultivated plants and some of them are plant-virus vectors (nepovirus). The mitochondrial (mt) genomes of the dagger and needle nematodes, Xiphinema rivesi, Xiphinema pachtaicum, Longidorus vineacola and Paralongidorus litoralis were sequenced in this study. The four circular mt genomes have an estimated size of 12.6, 12.5, 13.5 and 12...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28097404/complete-mitochondrial-genome-of-the-endophytic-fungus-pestalotiopsis-fici-features-and-evolution
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
COMPARATIVE STUDY
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
#16
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
#17
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
#18
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
#19
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
#20
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
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