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https://www.readbyqxmd.com/read/28331594/the-first-complete-mitogenome-of-the-south-china-deep-sea-giant-isopod-bathynomus-sp-crustacea-isopoda-cirolanidae-allows-insights-into-the-early-mitogenomic-evolution-of-isopods
#1
Yanjun Shen, Qi Kou, Zaixuan Zhong, Xinzheng Li, Lisheng He, Shunping He, Xiaoni Gan
In this study, the complete mitochondrial (mt) genome sequence of the South China deep-sea giant isopod Bathynomus sp. was determined, and this study is the first to explore in detail the mt genome of a deep-sea member of the order Isopoda. This species belongs to the genus Bathynomus, the members of which are saprophagous residents of the deep-sea benthic environment; based on their large size, Bathynomus is included in the "supergiant group" of isopods. The mt genome of Bathynomus sp. is 14,965 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes, only 18 transfer RNA genes, and a noncoding control region 362 bp in length, which is the smallest control region discovered in Isopoda to date...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28330975/mitogenomes-and-relatedness-do-not-predict-frequency-of-tool-use-by-sea-otters
#2
Katherine Ralls, Nancy Rotzel McInerney, Roderick B Gagne, Holly B Ernest, M Tim Tinker, Jessica Fujii, Jesus Maldonado
Many ecological aspects of tool-use in sea otters are similar to those in Indo-Pacific bottlenose dolphins. Within an area, most tool-using dolphins share a single mitochondrial haplotype and are more related to each other than to the population as a whole. We asked whether sea otters in California showed similar genetic patterns by sequencing mitogenomes of 43 otters and genotyping 154 otters at 38 microsatellite loci. There were six variable sites in the mitogenome that yielded three haplotypes, one found in only a single individual...
March 2017: Biology Letters
https://www.readbyqxmd.com/read/28330913/reconciling-evidence-from-ancient-and-contemporary-genomes-a-major-source-for-the-european-neolithic-within-mediterranean-europe
#3
Joana B Pereira, Marta D Costa, Daniel Vieira, Maria Pala, Lisa Bamford, Nourdin Harich, Lotfi Cherni, Farida Alshamali, Jiři Hatina, Sergey Rychkov, Gheorghe Stefanescu, Turi King, Antonio Torroni, Pedro Soares, Luísa Pereira, Martin B Richards
Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic...
March 29, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28327635/the-evolutionary-and-phylogeographic-history-of-woolly-mammoths-a-comprehensive-mitogenomic-analysis
#4
Dan Chang, Michael Knapp, Jacob Enk, Sebastian Lippold, Martin Kircher, Adrian Lister, Ross D E MacPhee, Christopher Widga, Paul Czechowski, Robert Sommer, Emily Hodges, Nikolaus Stümpel, Ian Barnes, Love Dalén, Anatoly Derevianko, Mietje Germonpré, Alexandra Hillebrand-Voiculescu, Silviu Constantin, Tatyana Kuznetsova, Dick Mol, Thomas Rathgeber, Wilfried Rosendahl, Alexey N Tikhonov, Eske Willerslev, Greg Hannon, Carles Lalueza-Fox, Ulrich Joger, Hendrik Poinar, Michael Hofreiter, Beth Shapiro
Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28294452/phylogenetic-relationships-and-divergence-dates-of-softshell-turtles-testudines-trionychidae-inferred-from-complete-mitochondrial-genomes
#5
Haifeng Li, Juanjuan Liu, Lei Xiong, Huanhuan Zhang, Huaxing Zhou, Huazong Yin, Wanxing Jing, Jun Li, Qiong Shi, Yuqin Wang, Jianjun Liu, Liuwang Nie
The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, there are disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma...
March 15, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28289222/fossil-and-genomic-evidence-constrains-the-timing-of-bison-arrival-in-north-america
#6
Duane Froese, Mathias Stiller, Peter D Heintzman, Alberto V Reyes, Grant D Zazula, André E R Soares, Matthias Meyer, Elizabeth Hall, Britta J L Jensen, Lee J Arnold, Ross D E MacPhee, Beth Shapiro
The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada's Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28287095/aboriginal-australian-mitochondrial-genome-variation-an-increased-understanding-of-population-antiquity-and-diversity
#7
Nano Nagle, Mannis van Oven, Stephen Wilcox, Sheila van Holst Pellekaan, Chris Tyler-Smith, Yali Xue, Kaye N Ballantyne, Leah Wilcox, Luka Papac, Karen Cooke, Roland A H van Oorschot, Peter McAllister, Lesley Williams, Manfred Kayser, R John Mitchell
Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28274686/curious-bivalves-systematic-utility-and-unusual-properties-of-anomalodesmatan-mitochondrial-genomes
#8
S T Williams, P G Foster, C Hughes, E M Harper, J D Taylor, D T J Littlewood, P Dyal, K P Hopkins, A G Briscoe
Mitogenomic trees for Bivalvia have proved problematic in the past, but several highly divergent lineages were missing from these analyses and increased representation of these groups may yet improve resolution. Here, we add seven new sequences from the Anomalodesmata and one unidentified semelid species (Bryopa lata, Euciroa cf. queenslandica, Laternula elliptica, Laternula truncata, Lyonsia norwegica, Myadora brevis, Tropidomya abbreviata, "Abra" sp.). We show that relationships in a mitogenomic tree for the Class are improved by the addition of seven anomalodesmatans from this highly divergent clade, but are still not completely consistent with relationships recovered in studies of nuclear genes...
March 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28273067/aboriginal-mitogenomes-reveal-50-000-years-of-regionalism-in-australia
#9
Ray Tobler, Adam Rohrlach, Julien Soubrier, Pere Bover, Bastien Llamas, Jonathan Tuke, Nigel Bean, Ali Abdullah-Highfold, Shane Agius, Amy O'Donoghue, Isabel O'Loughlin, Peter Sutton, Fran Zilio, Keryn Walshe, Alan N Williams, Chris S M Turney, Matthew Williams, Stephen M Richards, Robert J Mitchell, Emma Kowal, John R Stephen, Lesley Williams, Wolfgang Haak, Alan Cooper
Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair samples, whose origins enable us to reconstruct Australian phylogeographic history before European settlement...
March 8, 2017: Nature
https://www.readbyqxmd.com/read/28265498/digging-deeper-new-gene-order-rearrangements-and-distinct-patterns-of-codons-usage-in-mitochondrial-genomes-among-shrimps-from-the-axiidea-gebiidea-and-caridea-crustacea-decapoda
#10
Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Gary C B Poore, Christopher M Austin
BACKGROUND: Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information...
2017: PeerJ
https://www.readbyqxmd.com/read/28226235/plant-mitochondrial-genomes-dynamics-and-mechanisms-of-mutation
#11
José M Gualberto, Kathleen J Newton
The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified...
February 9, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28222679/comparative-mitogenomics-indicates-respiratory-competence-in%C3%A2-parasitic-viscum-despite%C3%A2-loss-of-complex-i%C3%A2-and-extreme-sequence%C3%A2-divergence-and-reveals-horizontal-gene-transfer-and-remarkable%C3%A2-variation-in-genome-size
#12
Elizabeth Skippington, Todd J Barkman, Danny W Rice, Jeffrey D Palmer
BACKGROUND: Aerobically respiring eukaryotes usually contain four respiratory-chain complexes (complexes I-IV) and an ATP synthase (complex V). In several lineages of aerobic microbial eukaryotes, complex I has been lost, with an alternative, nuclear-encoded NADH dehydrogenase shown in certain cases to bypass complex I and oxidize NADH without proton translocation. The first loss of complex I in any multicellular eukaryote was recently reported in two studies; one sequenced the complete mitogenome of the hemiparasitic aerial mistletoe, Viscum scurruloideum, and the other sequenced the V...
February 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28204600/evolutionary-and-functional-mitogenomics-associated-with-the-genetic-restoration-of-the-florida-panther
#13
Alexander Ochoa, David P Onorato, Robert R Fitak, Melody E Roelke-Parker, Melanie Culver
No abstract text is available yet for this article.
February 16, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28202952/imputation-approach-for-deducing-a-complete-mitogenome-sequence-from-low-depth-coverage-next-generation-sequencing-data-application-to-ancient-remains-from-the-moon-pyramid-mexico
#14
Fuzuki Mizuno, Masahiko Kumagai, Kunihiko Kurosaki, Michiko Hayashi, Saburo Sugiyama, Shintaroh Ueda, Li Wang
It is considered that more than 15 depths of coverage are necessary for next-generation sequencing (NGS) data to obtain reliable complete nucleotide sequences of the mitogenome. However, it is difficult to satisfy this requirement for all nucleotide positions because of problems obtaining a uniform depth of coverage for poorly preserved materials. Thus, we propose an imputation approach that allows a complete mitogenome sequence to be deduced from low-depth-coverage NGS data. We used different types of mitogenome data files as panels for imputation: a worldwide panel comprising all the major haplogroups, a worldwide panel comprising sequences belonging to the estimated haplogroup alone, a panel comprising sequences from the population most closely related to an individual under investigation, and a panel comprising sequences belonging to the estimated haplogroup from the population most closely related to an individual under investigation...
February 16, 2017: Journal of Human Genetics
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
#15
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/28198504/complete-mitochondrial-genome-of-the-amur-hedgehog-erinaceus-amurensis-erinaceidae-and-higher-phylogeny-of-the-family-erinaceidae
#16
N H Kim, S J Lim, H M Chae, Y C Park
We sequenced and characterized the complete mitogenome (KX964606) of the Amur hedgehog Erinaceus amurensis to provide more data for comparative mitogenomics of the genus Erinaceus (Erinaceidae). The mitogenome of E. amurensis is a circular molecule 16,941 bp long, consisting of a control region and a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes, and two rRNA genes (12S rRNA and 16S rRNA). The mitogenome of E. amurensis is AT-biased, with a nucleotide composition of 33.9% A, 21...
February 8, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28188878/towards-a-higher-level-ensifera-phylogeny-inferred-from-mitogenome-sequences
#17
Zhijun Zhou, Ling Zhao, Nian Liu, Huifang Guo, Bei Guan, Juanxia Di, Fuming Shi
Although mitogenomes are useful tools for inferring evolutionary history, only a few representative ones can be used for most Ensifera lineages. Thirty-two ensiferan mitogenomes were determined using ABI Sanger sequencing and standard primer walking of 2-3 overlapping Long-PCR fragments, or Illumina® HiSeq2000 for "shotgun" sequenced long-PCR-amplified mitochondrial or total genomic DNA. Six patterns of gene arrangements, including the novel trnR-trnS(AGN)-trnA-trnN-trnG-nad3 in Lipotactes tripyrga (Lipotactinae), were identified from 59 ensiferan mitogenomes...
March 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28188868/gene-sequence-variations-and-expression-patterns-of-mitochondrial-genes-are-associated-with-the-adaptive-evolution-of-two-gynaephora-species-lepidoptera-lymantriinae-living-in-different-high-elevation-environments
#18
Qi-Lin Zhang, Li Zhang, Tian-Xuan Zhao, Juan Wang, Qian-Hua Zhu, Jun-Yuan Chen, Ming-Long Yuan
The adaptive evolution of animals to high-elevation environments has been extensively studied in vertebrates, while few studies have focused on insects. Gynaephora species (Lepidoptera: Lymantriinae) are endemic to the Qinghai-Tibetan Plateau (QTP) and represent an important insect pest of alpine meadows. Here, we present a detailed comparative analysis of the mitochondrial genomes (mitogenomes) of two Gynaephora species inhabiting different high-elevation environments: G. alpherakii and G. menyuanensis. The results indicated that the general mitogenomic features (genome size, nucleotide composition, codon usage and secondary structures of tRNAs) were well conserved between the two species...
April 30, 2017: Gene
https://www.readbyqxmd.com/read/28177087/mitogenome-diversity-in-sardinians-a-genetic-window-onto-an-island-s-past
#19
Anna Olivieri, Carlo Sidore, Alessandro Achilli, Andrea Angius, Cosimo Posth, Anja Furtwängler, Stefania Brandini, Marco Rosario Capodiferro, Francesca Gandini, Magdalena Zoledziewska, Maristella Pitzalis, Andrea Maschio, Fabio Busonero, Luca Lai, Robin Skeates, Maria Giuseppina Gradoli, Jessica Beckett, Michele Marongiu, Vittorio Mazzarello, Patrizia Marongiu, Salvatore Rubino, Teresa Rito, Vincent Macaulay, Ornella Semino, Maria Pala, Gonçalo R Abecasis, David Schlessinger, Eduardo Conde-Sousa, Pedro Soares, Martin B Richards, Francesco Cucca, Antonio Torroni
No abstract text is available yet for this article.
February 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28173059/phylogenomic-reconstruction-of-sportive-lemurs-genus-lepilemur-recovered-from-mitogenomes-with-inferences-for-madagascar-biogeography
#20
Runhua Lei, Cynthia L Frasier, Melissa T R Hawkins, Shannon E Engberg, Carolyn A Bailey, Steig E Johnson, Adam T McLain, Colin P Groves, George H Perry, Stephen D Nash, Russell A Mittermeier, Edward E Louis
No abstract text is available yet for this article.
March 1, 2017: Journal of Heredity
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