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https://www.readbyqxmd.com/read/29782829/global-phylogeography-and-genetic-diversity-of-the-zoonotic-tapeworm-echinococcus-granulosus-sensu-stricto-genotype-g11
#1
Liina Kinkar, Teivi Laurimäe, Gerardo Acosta-Jamett, Vanessa Andresiuk, Ibrahim Balkaya, Adriano Casulli, Robin B Gasser, Joke van der Giessen, Luis Miguel González, Karen L Haag, Houria Zait, Malik Irshadullah, Abdul Jabbar, David J Jenkins, Eshrat Beigom Kia, Maria Teresa Manfredi, Hossein Mirhendi, Selim M'rad, Mohammad Rostami-Nejad, Myriam Oudni-M'rad, Nora Beatriz Pierangeli, Francisco Ponce-Gordo, Steffen Rehbein, Mitra Sharbatkhori, Sami Simsek, Silvia Viviana Soriano, Hein Sprong, Viliam Šnábel, Gérald Umhang, Antonio Varcasia, Urmas Saarma
Echinococcus granulosus sensu stricto (s.s.) is the major cause of human cystic echinococcosis worldwide and is listed among the most severe parasitic diseases of humans. To date, numerous studies have investigated the genetic diversity and population structure of E. granulosus s.s. in various geographic regions. However, there has been no global study. Recently, using mitochondrial DNA, it was shown that E. granulosus s.s. G1 and G3 are distinct genotypes, but a larger dataset is required to confirm the distinction of these genotypes...
May 18, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29777385/changes-in-selection-intensity-on-the-mitogenome-of-subterranean-and-fossorial-rodents-respective-to-aboveground-species
#2
William Corrêa Tavares, Hector N Seuánez
Several rodent lineages independently acquired the ability to dig complex networks of tunnels where fossorial and subterranean species spend part or their whole life, respectively. Their underground lifestyles imposed harsh physiological demands, presumably triggering strong selective pressures on genes involved in energy metabolism like those coding for mitochondrial proteins. Moreover, underground lifestyles must have increased inbreeding and susceptibility to population bottlenecks as well as restricted migration, leading to small effective population size (Ne ) that, in turn, must have reduced the effectiveness of selection...
May 18, 2018: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29769358/resolving-the-phylogenetic-position-of-darwin-s-extinct-ground-sloth-mylodon-darwinii-using-mitogenomic-and-nuclear-exon-data
#3
Frédéric Delsuc, Melanie Kuch, Gillian C Gibb, Jonathan Hughes, Paul Szpak, John Southon, Jacob Enk, Ana T Duggan, Hendrik N Poinar
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12 880-year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient subfossil, probably the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra...
May 16, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29769015/a-comparison-of-methods-for-estimating-substitution-rates-from-ancient-dna-sequence-data
#4
K Jun Tong, David A Duchêne, Sebastián Duchêne, Jemma L Geoghegan, Simon Y W Ho
BACKGROUND: Phylogenetic analysis of DNA from modern and ancient samples allows the reconstruction of important demographic and evolutionary processes. A critical component of these analyses is the estimation of evolutionary rates, which can be calibrated using information about the ages of the samples. However, the reliability of these rate estimates can be negatively affected by among-lineage rate variation and non-random sampling. Using a simulation study, we compared the performance of three phylogenetic methods for inferring evolutionary rates from time-structured data sets: regression of root-to-tip distances, least-squares dating, and Bayesian inference...
May 16, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29768482/sequencing-of-complete-mitochondrial-genomes-confirms-synonymization-of-hyalomma-asiaticum-asiaticum-and-kozlovi-and-advances-phylogenetic-hypotheses-for-the-ixodidae
#5
Zhi-Qiang Liu, Yan-Feng Liu, Nuer Kuermanali, Deng-Feng Wang, Shi-Jun Chen, Hui-Ling Guo, Li Zhao, Jun-Wei Wang, Tao Han, Yuan-Zhi Wang, Jie Wang, Chen-Feng Shen, Zhuang-Zhi Zhang, Chuang-Fu Chen
Phylogeny of hard ticks (Ixodidae) remains unresolved. Mitochondrial genomes (mitogenomes) are increasingly used to resolve phylogenetic controversies, but remain unavailable for the entire large Hyalomma genus. Hyalomma asiaticum is a parasitic tick distributed throughout the Asia. As a result of great morphological variability, two subspecies have been recognised historically; until a morphological data-based synonymization was proposed. However, this hypothesis was never tested using molecular data. Therefore, objectives of this study were to: 1...
2018: PloS One
https://www.readbyqxmd.com/read/29765106/the-mitochondrial-genome-of-the-oribatid-mite-paraleius-leontonychus-new-insights-into-trna-evolution-and-phylogenetic-relationships-in-acariform-mites
#6
Sylvia Schäffer, Stephan Koblmüller, Ingeborg Klymiuk, Gerhard G Thallinger
Bilaterian mitochondrial (mt) genomes are circular molecules that typically contain 37 genes. To date, only a single complete mitogenome sequence is available for the species-rich sarcoptiform mite order Oribatida. We sequenced the mitogenome of Paraleius leontonychus, another species of this suborder. It is 14,186 bp long and contains 35 genes, including only 20 tRNAs, lacking tRNA Gly and tRNA Tyr . Re-annotation of the mitogenome of Steganacarus magnus increased the number of mt tRNAs for this species to 12...
May 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29760889/measuring-inferential-importance-of-taxa-using-taxon-influence-indices
#7
John S S Denton, Eric W Goolsby
Assessing the importance of different taxa for inferring evolutionary history is a critical, but underutilized, aspect of systematics. Quantifying the importance of all taxa within a dataset provides an empirical measurement that can establish a ranking of extant taxa for ecological study and/or quantify the relative importance of newly announced or redescribed specimens to enable the disentangling of novelty and inferential influence. Here, we illustrate the use of taxon influence indices through analysis of both molecular and morphological datasets, introducing a modified Bayesian approach to the taxon influence index that accounts for model and topological uncertainty...
May 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29760079/selection-and-environmental-adaptation-along-a-path-to-speciation-in-the-tibetan-frog-nanorana-parkeri
#8
Guo-Dong Wang, Bao-Lin Zhang, Wei-Wei Zhou, Yong-Xin Li, Jie-Qiong Jin, Yong Shao, He-Chuan Yang, Yan-Hu Liu, Fang Yan, Hong-Man Chen, Li Jin, Feng Gao, Yaoguang Zhang, Haipeng Li, Bingyu Mao, Robert W Murphy, David B Wake, Ya-Ping Zhang, Jing Che
Tibetan frogs, Nanorana parkeri , are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29755486/organelle-genome-inheritance-in-deparia-ferns-athyriaceae-aspleniineae-polypodiales
#9
Li-Yaung Kuo, Te-Yen Tang, Fay-Wei Li, Huei-Jiun Su, Wen-Liang Chiou, Yao-Moan Huang, Chun-Neng Wang
Organelle genomes of land plants are predominately inherited maternally but in some cases can also be transmitted paternally or biparentally. Compared to seed plants (>83% genera of angiosperms and >12% genera of gymnosperms), plastid genome (plastome) inheritance has only been investigated in fewer than 2% of fern genera, and mitochondrial genome (mitogenome) from only one fern genus. We developed a new and efficient method to examine plastome and mitogenome inheritance in a fern species- Deparia lancea (Athyriaceae, Aspleniineae, Polypodiales), and found that plastid and mitochondrial DNAs were transmitted from only the maternal parentage to a next generation...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29755260/characterization-of-the-complete-mitochondrial-dna-of-theretra-japonica-and-its-phylogenetic-position-within-the-sphingidae-lepidoptera-sphingidae
#10
Jun Li, Rui-Rui Lin, Yao-Yao Zhang, Kun-Jie Hu, Ya-Qi Zhao, Yan Li, Zhuo-Ran Huang, Xu Zhang, Xue-Xia Geng, Jian-Hua Ding
In the present study, the complete mitogenome of Theretra japonica was sequenced and compared with other sequenced mitogenomes of Sphingidae species. The mitogenome of T. japonica , containing 37 genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) and a region rich in adenine and thymine (AT-rich region), is a circular molecule with 15,399 base pairs (bp) in length. The order and orientation of the genes in the mitogenome are similar to those of other sequenced mitogenomes of Sphingidae species...
2018: ZooKeys
https://www.readbyqxmd.com/read/29752988/the-complete-mitochondrial-genome-of-parasesarma-pictum-brachyura-grapsoidea-sesarmidae-and-comparison-with-other-brachyuran-crabs
#11
Zhengfei Wang, Xuejia Shi, Yitao Tao, Qiong Wu, Yuze Bai, Huayun Guo, Dan Tang
Mitochondrial DNA (mtDNA) is an extrachromosomal genome which can provide important information for evolution and phylogenetic analysis. In this study, we assembled a complete mitogenome of a crab Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) from next generation sequencing reads at the first time. P. pictum is a mudflat crab, belonging to the Sesarmidae family (subfamily Sesarminae), which is perched on East Asia. The 15,716 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (CR)...
May 9, 2018: Genomics
https://www.readbyqxmd.com/read/29748765/de-novo-assembly-of-mitochondrial-genomes-provides-insights-into-genetic-diversity-and-molecular-evolution-in-wild-boars-and-domestic-pigs
#12
Pan Ni, Ali Akbar Bhuiyan, Jian-Hai Chen, Jingjin Li, Cheng Zhang, Shuhong Zhao, Xiaoyong Du, Hua Li, Hui Yu, Xiangdong Liu, Kui Li
Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression...
May 10, 2018: Genetica
https://www.readbyqxmd.com/read/29747572/multiple-independent-structural-dynamic-events-in-the-evolution-of-snake-mitochondrial-genomes
#13
Lifu Qian, Hui Wang, Jie Yan, Tao Pan, Shanqun Jiang, Dingqi Rao, Baowei Zhang
BACKGROUND: Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes...
May 10, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29743928/genome-sequencing-of-rhinorhipus-lawrence-exposes-an-early-branch-of-the-coleoptera
#14
Dominik Kusy, Michal Motyka, Carmelo Andujar, Matej Bocek, Michal Masek, Katerina Sklenarova, Filip Kokas, Milada Bocakova, Alfried P Vogler, Ladislav Bocak
Background: Rhinorhipidae Lawrence, 1988 is an enigmatic beetle family represented by a single species, Rhinorhipus tamborinensis Lawrence, 1988, from Australia, with poorly established affinities near the superfamily Elateroidea (click beetles, soldier beetles and fireflies) or the more inclusive series (infraorder) Elateriformia. Its evolutionary position may inform the basal relationships of the suborder Polyphaga, the largest clade of Coleoptera. Results: We analyzed four densely sampled DNA datasets of major coleopteran lineages for mitogenomes, rRNA genes and single copy nuclear genes...
2018: Frontiers in Zoology
https://www.readbyqxmd.com/read/29743617/complete-mitochondrial-and-rdna-complex-sequences-of-important-vector-species-of-biomphalaria-obligatory-hosts-of-the-human-infecting-blood-fluke-schistosoma-mansoni
#15
Si-Ming Zhang, Lijing Bu, Martina R Laidemitt, Lijun Lu, Martin W Mutuku, Gerald M Mkoji, Eric S Loker
Using high throughput Illumina sequencing technology, we determined complete sequences for the mitochondrial genome (mitogenome) and nuclear ribosomal DNA (rDNA) complex for three African freshwater snail taxa within the genus Biomphalaria, B. pfeifferi, B. sudanica and B. choanomphala, and for two laboratory strains of B. glabrata originating from the Neotropics. Biomphalaria snails are obligate vectors of the blood fluke Schistosoma mansoni, a major etiologic agent of human intestinal schistosomiasis. Our data show that mitogenomes from African and Neotropical Biomphalaria are highly conserved...
May 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29731304/absence-of-complex-i-is-associated-with-diminished-respiratory-chain-function-in-european-mistletoe
#16
Andrew E Maclean, Alexander P Hertle, Joanna Ligas, Ralph Bock, Janneke Balk, Etienne H Meyer
Parasitism is a life history strategy found across all domains of life whereby nutrition is obtained from a host. It is often associated with reductive evolution of the genome, including loss of genes from the organellar genomes [1, 2]. In some unicellular parasites, the mitochondrial genome (mitogenome) has been lost entirely, with far-reaching consequences for the physiology of the organism [3, 4]. Recently, mitogenome sequences of several species of the hemiparasitic plant mistletoe (Viscum sp.) have been reported [5, 6], revealing a striking loss of genes not seen in any other multicellular eukaryotes...
April 26, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29721275/a-new-strategy-to-infer-circularity-applied-to-four-new-complete-frog-mitogenomes
#17
Denis Jacob Machado, Daniel Janies, Cory Brouwer, Taran Grant
We applied a novel strategy to infer sequence circularity and complete assembly of four mitochondrial genomes (mitogenomes) of the frog families Bufonidae ( Melanophryniscus moreirae ), Dendrobatidae ( Hyloxalus subpunctatus and Phyllobates terribilis ), and Scaphiopodidae ( Scaphiopus holbrookii ). These are the first complete mitogenomes of these four genera and Scaphiopodidae. We assembled mitogenomes from short genomic sequence reads using a baiting and iterative mapping strategy followed by a new ad hoc mapping strategy developed to test for assembly circularization...
April 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29718949/comparative-analyses-of-the-complete-mitochondrial-genomes-of-dosinia-clams-and-their-phylogenetic-position-within-veneridae
#18
Changda Lv, Qi Li, Lingfeng Kong
Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions...
2018: PloS One
https://www.readbyqxmd.com/read/29718506/complete-mitochondrial-genome-of-dinorhynchus-dybowskyi-hemiptera-pentatomidae-asopinae-and-phylogenetic-analysis-of-pentatomomorpha-species
#19
Qing Zhao, Juan Wang, Meng-Qing Wang, Bo Cai, Hu-Fang Zhang, Jiu-Feng Wei
Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) is used as a biological control agent against various insect pests for its predatory. In the present study, the complete mitochondrial genome (mitogenome) of the species was sequenced using the next-generation sequencing technology. The results showed that the mitogenome is 15,952 bp long, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a control region. Furthermore, the gene order and orientation of this mitogenome are identical to those of most heteropterans...
March 1, 2018: Journal of Insect Science
https://www.readbyqxmd.com/read/29718488/the-complete-mitochondrial-genome-of-coptotermes-suzhouensis-syn-coptotermes-formosanus-isoptera-rhinotermitidae-and-molecular-phylogeny-analysis
#20
Juan Li, Jin-Long Zhu, Shi-di Lou, Ping Wang, You-Sen Zhang, Lin Wang, Ruo-Chun Yin, Ping-Ping Zhang
Coptotermes suzhouensis (Isoptera: Rhinotermitidae) is a significant subterranean termite pest of wooden structures and is widely distributed in southeastern China. The complete mitochondrial DNA sequence of C. suzhouensis was analyzed in this study. The mitogenome was a circular molecule of 15,764 bp in length, which contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A+T-rich region with a gene arrangement typical of Isoptera mitogenomes. All PCGs were initiated by ATN codons and terminated by complete termination codons (TAA), except COX2, ND5, and Cytb, which ended with an incomplete termination codon T...
March 1, 2018: Journal of Insect Science
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