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mitochondrial genome evolution

Lisa N Barrow, Julie M Allen, Xi Huang, Staffan Bensch, Christopher C Witt
Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus, and Leucocytoozoon) represent an exciting multi-host, multi-parasite system in ecology and evolution. Global research in this field accelerated after 1) the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode, and 2) the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing the transition to genomic-scale sequencing techniques...
December 16, 2018: Molecular Ecology Resources
Jyung Mean Son, Changhan Lee
Aging is accompanied by a time-dependent progressive deterioration of multiple factors of the cellular system. The past several decades have witnessed major leaps in our understanding of the biological mechanism of aging using dietary, genetic, pharmacological, and physical interventions. Metabolic processes, including nutrient sensing pathways and mitochondrial function, have emerged as prominent regulators of aging. Mitochondria have been considered to play a key role largely due to their production of reactive oxygen species (ROS), resulting in DNA damage that accumulates over time and ultimately causes cellular failure...
December 14, 2018: BMB Reports
Achal Neupane, Chenchen Feng, Jiuhuan Feng, Arjun Kafle, Heike Bücking, Shin-Yi Lee Marzano
Arbuscular mycorrhizal fungi (AMF), including Rhizophagus spp., can play important roles in nutrient cycling of the rhizosphere. However, the effect of virus infection on AMF's role in nutrient cycling cannot be determined without first knowing the diversity of the mycoviruses in AMF. Therefore, in this study, we sequenced the R . irregularis isolate-09 due to its previously demonstrated high efficiency in increasing the N/P uptake of the plant. We identified one novel mitovirus contig of 3685 bp, further confirmed by reverse transcription-PCR...
December 12, 2018: Viruses
Eleni N Tsakiri, Sentiljana Gumeni, Kalliopi K Iliaki, Dimitra Benaki, Konstantinos Vougas, Gerasimos P Sykiotis, Vassilis G Gorgoulis, Emmanuel Mikros, Luca Scorrano, Ioannis P Trougakos
Metazoans viability depends on their ability to regulate metabolic processes and also to respond to harmful challenges by mounting anti-stress responses; these adaptations were fundamental forces during evolution. Central to anti-stress responses are a number of short-lived transcription factors that by functioning as stress sensors mobilize genomic responses aiming to eliminate stressors. We show here that increased expression of nuclear factor erythroid 2-related factor (Nrf2) in Drosophila activated cytoprotective modules and enhanced stress tolerance...
December 10, 2018: Aging Cell
Jiabin Liu, Jiaojiao Yu, Ming Zhou, Jiandong Yang
Japalura flaviceps is a subarboreal species, which is endemically distributed in China. Here, we determined the complete mitogenome of J. flaviceps. This mitogenome was a typical circular molecule of 17,140 bp in size, containing 13 protein-coding genes, 22 transfer-RNA-coding genes, two ribosomal-RNA-coding genes, and one control region. Our phylogenetic result using 15 genes divided all Agamidae lizards into six subfamilies and showed (((((Agaminae, Draconinae), Amphibolurinae), Hydrosaurinae), Uromastycinae), Leiolepinae), which was different from the previous studies...
December 7, 2018: International Journal of Biological Macromolecules
M Virginia Sanchez-Puerta, Alejandro Edera, Carolina L Gandini, Anna V Williams, Kate Howell, Paul G Nevill, Ian Small
Angiosperm mitochondrial horizontal gene transfer (HGT) has been widely reported during the past decades. With a few exceptions, foreign sequences are mitochondrial genes or intronic regions from other plants, indicating that HGT has played a major role in shaping mitochondrial genome evolution. Host-parasite relationships are a valuable system to study this phenomenon due to the high frequency of HGT. In particular, the interaction between mimosoid legumes and holoparasites of the genus Lophophytum represents an outstanding opportunity to discern HGT events...
December 7, 2018: Molecular Phylogenetics and Evolution
Daniel Kazdal, Alexander Harms, Volker Endris, Roland Penzel, Cristiano Oliveira, Mark Kriegsmann, Rémi Longuespée, Hauke Winter, Marc A Schneider, Thomas Muley, Nicole Pfarr, Wilko Weichert, Albrecht Stenzinger, Arne Warth
OBJECTIVES: The potential role of cancer associated somatic mutations of the mitochondrial genome (mtDNA) is controversial and still poorly understood. Our group and others recently challenged a direct tumorigenic impact and suggested a passenger-like character. In combination with the known increased mutation rate, somatic mtDNA mutations account for an interesting tool to delineate tumor evolution. Here, we comprehensively analyzed the spatial distribution of somatic mtDNA mutations throughout whole tumor sections of pulmonary adenocarcinoma (ADC)...
December 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
Cong J Hua, Wen X Li, Dong Zhang, Hong Zou, Ming Li, Ivan Jakovlić, Shan G Wu, Gui T Wang
BACKGROUND: Isopoda is a highly diverse order of crustaceans with more than 10,300 species, many of which are parasitic. Taxonomy and phylogeny within the order, especially those of the suborder Cymothoida Wägele, 1989, are still debated. Mitochondrial (mt) genomes are a useful tool for phylogenetic studies, but their availability for isopods is very limited. To explore these phylogenetic controversies on the mt genomic level and study the mt genome evolution in Isopoda, we sequenced mt genomes of two parasitic isopods, Tachaea chinensis Thielemann, 1910 and Ichthyoxenos japonensis Richardson, 1913, belonging to the suborder Cymothoida, and conducted comparative and phylogenetic mt genomic analyses across Isopoda...
December 10, 2018: Parasites & Vectors
Anton S Petrov, Elizabeth C Wood, Chad R Bernier, Ashlyn M Norris, Alan Brown, A Amunts
Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data...
December 4, 2018: Molecular Biology and Evolution
Kamil Myszczyński, Piotr Górski, Monika Ślipiko, Jakub Sawicki
BACKGROUND: Comparative analyses of chloroplast and mitochondrial genomes have shown that organelle genomes in bryophytes evolve slowly. However, in contrast to seed plants, the organellar genomes are yet poorly explored in bryophytes, especially among liverworts. Discovering another organellar genomes of liverwort species by sequencing provides new conclusions on evolution of bryophytes. RESULTS: In this work, the organellar genomes of Gymnomitrion concinnatum liverwort were sequenced, assembled and annotated for the first time...
December 3, 2018: BMC Plant Biology
Jose Maria Aguilar-Camacho, Liam Doonan, Grace P McCormack
The skeletons of sponges (Phylum Porifera) are comprised of collagen, often embedded with small siliceous structures (spicules) arranged in various forms to provide strength and flexibility. The main proteins responsible for the formation of the spicules in demosponges are the silicateins, which are related to the cathepsins L of other animals. While the silicatein active site, necessary for the formation of biosilica crystals, is characterized by the amino acids SHN, different variants of the silicatein genes have been found, some that retain SHN at the active site and some that don't...
November 28, 2018: Molecular Phylogenetics and Evolution
Wendan Mu, Jun Liu, Haibin Zhang
Complete mitochondrial genomes play important roles in studying genome evolution, phylogenetic relationships, and species identification. Sea cucumbers (Holothuroidea) are ecologically important and diverse members, living from the shallow waters to the hadal trench. In this study, we present the mitochondrial genome sequence of the sea cucumber Benthodytes marianensis collected from the Mariana Trench. To our knowledge, this is the first reported mitochondrial genome from the genus Benthodytes. This complete mitochondrial genome is 17567 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS)...
2018: PloS One
Ugo Cenci, Shannon J Sibbald, Bruce A Curtis, Ryoma Kamikawa, Laura Eme, Daniel Moog, Bernard Henrissat, Eric Maréchal, Malika Chabi, Christophe Djemiel, Andrew J Roger, Eunsoo Kim, John M Archibald
BACKGROUND: The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis). The timing and frequency of secondary endosymbiosis during eukaryotic evolution is currently unclear but may be resolved in part by studying cryptomonads, a group of single-celled eukaryotes comprised of both photosynthetic and non-photosynthetic species...
November 28, 2018: BMC Biology
Bowen Xie, Shuangyan Wang, Nian Jiang, Jian Jian Li
A mammalian cell houses two genomes located separately in the nucleus and mitochondria. During evolution, communications and adaptations between these two genomes occur extensively to achieve and sustain homeostasis for cellular functions and regeneration. Mitochondria provide the major cellular energy and contribute to gene regulation in the nucleus, whereas more than 98% of mitochondrial proteins are encoded by the nuclear genome. Such two-way signaling traffic presents an orchestrated dynamic between energy metabolism and consumption in cells...
November 24, 2018: Cancer Letters
Manuela Cascini, Kieren J Mitchell, Alan Cooper, Matthew J Phillips
Combined "total evidence" analysis of molecular and morphological data offers the opportunity to objectively merge fossils into the tree of life, and challenges the primacy of solely DNA based phylogenetic and dating inference, even among modern taxa. To investigate the relative utility of DNA, morphology, and total evidence for evolutionary inference, we sequenced the first near-complete mitochondrial genomes from extinct Australian megafauna: a 40-50 thousand year old giant short-faced kangaroo (Simosthenurus occidentalis) and giant wallaby (Protemnodon anak)...
November 27, 2018: Systematic Biology
Richard G Melvin, Nicole Lamichane, Essi Havula, Krista Kokki, Charles Soeder, Corbin D Jones, Ville Hietakangas
How dietary selection impacts genome evolution to define the optimal range of nutrient intake is a poorly understood question with medical relevance. We have addressed this question by analyzing Drosophila simulans and sechellia , recently diverged species with differential diet choice. D. sechellia larvae, specialized to a nutrient scarce diet, did not survive on sugar rich conditions, while the generalist species D. simulans was sugar tolerant. Sugar tolerance in D. simulans was a tradeoff for performance on low energy diet and was associated with global reprogramming of metabolic gene expression...
November 27, 2018: ELife
Kevin P Johnson, Christopher H Dietrich, Frank Friedrich, Rolf G Beutel, Benjamin Wipfler, Ralph S Peters, Julie M Allen, Malte Petersen, Alexander Donath, Kimberly K O Walden, Alexey M Kozlov, Lars Podsiadlowski, Christoph Mayer, Karen Meusemann, Alexandros Vasilikopoulos, Robert M Waterhouse, Stephen L Cameron, Christiane Weirauch, Daniel R Swanson, Diana M Percy, Nate B Hardy, Irene Terry, Shanlin Liu, Xin Zhou, Bernhard Misof, Hugh M Robertson, Kazunori Yoshizawa
Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects...
November 26, 2018: Proceedings of the National Academy of Sciences of the United States of America
Vaishali Katju, Ulfar Bergthorsson
Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mutations for four decades. In the pregenomic era, phenotypic measurement of fitness-related traits in MA lines were used to indirectly estimate key mutational parameters such as the genomic mutation rate, new mutational variance per generation, and the average fitness effect of mutations...
November 26, 2018: Genome Biology and Evolution
Yuanning Li, Kevin M Kocot, Michael G Tassia, Johanna T Cannon, Matthias Bernt, Kenneth M Halanych
The diverse array of codon reassignments has demonstrated that the genetic code is not universal in nature. Exploring mechanisms underlying codon reassignment is critical for understanding the evolution of the genetic code during translation. Hemichordata, comprising worm-like Enteropneusta and colonial filter-feeding Pterobranchia, is the sister taxon of echinoderms and is more distantly related to chordates. However, only a few hemichordate mitochondrial genomes have been sequenced hindering our understanding of mitochondrial genome evolution within Deuterostomia...
November 23, 2018: Genome Biology and Evolution
J P Vieira-da-Rocha, D G Passos-Silva, I C Mendes, E A Rocha, D A Gomes, C R Machado, R McCulloch
Genomes are affected by a wide range of damage, which has resulted in the evolution of a number of widely conserved DNA repair pathways. Most of these repair reactions have been described in the African trypanosome Trypanosoma brucei, which is a genetically tractable eukaryotic microbe and important human and animal parasite, but little work has considered how the DNA damage response operates throughout the T. brucei life cycle. Using quantitative PCR we have assessed damage induction and repair in both the nuclear and mitochondrial genomes of the parasite...
November 14, 2018: DNA Repair
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