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https://www.readbyqxmd.com/read/28533083/another-look-at-the-phylogenetic-relationships-and-intercontinental-biogeography-of-eastern-asian-north-american-rhus-gall-aphids-hemiptera-aphididae-eriosomatinae-evidence-from-mitogenome-sequences-via-genome-skimming
#1
Zhumei Ren, A J Harris, Rebecca B Dikow, Enbo Ma, Yang Zhong, Jun Wen
The Rhus gall aphids are sometimes referred to as subtribe Melaphidina (Aphididae: Eriosomatinae: Fordini) and comprise a unique group that forms galls on the primary host plants, Rhus. We examined the evolutionary relationships within the Melaphidina aphids using sequences of the complete mitochondrial genome and with samples of 11 of the 12 recognized species representing all six genera. Bayesian, maximum likelihood and parsimony analyses of the mitochondrial genome data support five well-supported clades within Melaphidina: (1) Nurudea (except N...
May 19, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28512060/characterization-and-phylogenetic-analysis-of-complete-mitochondrial-genomes-for-two-desert-cyprinodontoid-fishes-empetrichthys-latos-and-crenichthys-baileyi
#2
Miguel Jimenez, Shawn C Goodchild, Craig A Stockwell, Sean C Lema
The Pahrump poolfish (Empetrichthys latos) and White River springfish (Crenichthys baileyi) are small-bodied teleost fishes (order Cyprinodontiformes) endemic to the arid Great Basin and Mojave Desert regions of western North America. These taxa survive as small, isolated populations in remote streams and springs and evolved to tolerate extreme conditions of high temperature and low dissolved oxygen. Both species have experienced severe population declines over the last 50-60years that led to some subspecies being categorized with protected status under the U...
May 13, 2017: Gene
https://www.readbyqxmd.com/read/28510580/disease-associated-mitochondrial-mutations-and-the-evolution-of-primate-mitogenomes
#3
William Corrêa Tavares, Héctor N Seuánez
Several human diseases have been associated with mutations in mitochondrial genes comprising a set of confirmed and reported mutations according to the MITOMAP database. An analysis of complete mitogenomes across 139 primate species showed that most confirmed disease-associated mutations occurred in aligned codon positions and gene regions under strong purifying selection resulting in a strong evolutionary conservation. Only two confirmed variants (7.1%), coding for the same amino acids accounting for severe human diseases, were identified without apparent pathogenicity in non-human primates, like the closely related Bornean orangutan...
2017: PloS One
https://www.readbyqxmd.com/read/28500331/transcriptome-sequencing-and-phylogenetic-analysis-of-four-species-of-luminescent-beetles
#4
Kai Wang, Wei Hong, Hengwu Jiao, Huabin Zhao
The evolution of bioluminescence has prompted scientific attention to illuminate phylogenetic relationships of luminescent beetles. However, genomic resources are virtually lacking in rhagophthalmids (Rhagophthalmidae) and their related firefly beetles lampyrids (Lampyridae). Here, we employed the Illumina Hiseq 2000 platform and sequenced the whole-body transcriptomes of the four luminescent beetles: one rhagophthalmid (Rhagophthalmus sp.) and three fireflies (Asymmetricata circumdata, Aquatica ficta, and Pyrocoelia pectoralis)...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28487262/phylogenomic-analysis-of-a-rapid-radiation-of-misfit-fishes-syngnathiformes-using-ultraconserved-elements
#5
S J Longo, B C Faircloth, A Meyer, M W Westneat, M E Alfaro, P C Wainwright
Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders...
May 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28486518/complete-mitochondrial-genomes-of-two-blattid-cockroaches-periplaneta-australasiae-and-neostylopyga-rhombifolia-and-phylogenetic-relationships-within-the-blattaria
#6
Jinnan Ma, Chao Du, Chuang Zhou, Yongmei Sheng, Zhenxin Fan, Bisong Yue, Xiuyue Zhang
Complete mitochondrial genomes (mitogenomes) of two cockroach species, Periplaneta australasiae and Neostylopyga rhombifolia, 15,605 bp and 15,711 bp in length, respectively, were determined. As reported for other cockroach mitogenomes, the two mitogenomes possessed typical ancestral insect mitogenome gene composition and arrangement. Only several small intergenic spacers were found: one, which was common in all sequenced cockroach mitogenomes except for the genus Cryptocercus, was between tRNA-Ser (UCN) and ND1 and contained a 7bp highly conserved motif (WACTTAA)...
2017: PloS One
https://www.readbyqxmd.com/read/28484275/evolution-of-sex-dependent-mtdna-transmission-in-freshwater-mussels-bivalvia-unionida
#7
Davide Guerra, Federico Plazzi, Donald T Stewart, Arthur E Bogan, Walter R Hoeh, Sophie Breton
Doubly uniparental inheritance (DUI) describes a mode of mtDNA transmission widespread in gonochoric freshwater mussels (Bivalvia: Palaeoheterodonta: Unionida). In this system, both female- and male-transmitted mtDNAs, named F and M respectively, coexist in the same species. In unionids, DUI is strictly correlated to gonochorism and to the presence of the atypical open reading frames (ORFans) F-orf and M-orf, respectively inside F and M mtDNAs, which are hypothesized to participate in sex determination. However, DUI is not found in all three Unionida superfamilies (confirmed in Hyrioidea and Unionoidea but not in Etherioidea), raising the question of its origin in these bivalves...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28484268/the-first-two-complete-mitochondrial-genomes-for-the-family-triglidae-and-implications-for-the-higher-phylogeny-of-scorpaeniformes
#8
Lei Cui, Yuelei Dong, Fenghua Liu, Xingchen Gao, Hua Zhang, Li Li, Jingyi Cen, Songhui Lu
The mitochondrial genome (mitogenome) can provide useful information for analyzing phylogeny and molecular evolution. Scorpaeniformes is one of the most diverse teleostean orders and has great commercial importance. To develop mitogenome data for this important group, we determined the complete mitogenomes of two gurnards Chelidonichthys kumu and Lepidotrigla microptera of Triglidae within Scorpaeniformes for the first time. The mitogenomes are 16,495 bp long in C. kumu and 16,610 bp long in L. microptera...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28475163/first-mitochondrial-genome-from-nemouridae-plecoptera-reveals-novel-features-of-the-elongated-control-region-and-phylogenetic-implications
#9
Zhi-Teng Chen, Yu-Zhou Du
The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer (AGN), whose dihydrouridine (DHU) arm was reduced to a small loop...
May 5, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28460111/genetic-variation-for-mitochondrial-function-in-the-new-zealand-freshwater-snail-potamopyrgus-antipodarum
#10
Joel Sharbrough, Jennifer L Cruise, Megan Beetch, Nicole M Enright, Maurine Neiman
The proteins responsible for mitochondrial function are encoded by two different genomes with distinct inheritance regimes, rendering rigorous inference of genotype-phenotype connections intractable for all but a few model systems. Asexual organisms provide a powerful means to address these challenges because offspring produced without recombination inherit both nuclear and mitochondrial genomes from a single parent. As such, these offspring inherit mitonuclear genotypes that are identical to the mitonuclear genotypes of their parents and siblings and different from those of other asexual lineages...
April 29, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28456662/new-mitogenome-and-nuclear-evidence-on-the-phylogeny-and-taxonomy-of-the-highly-zoonotic-tapeworm-echinococcus-granulosus-sensu-stricto
#11
Liina Kinkar, Teivi Laurimäe, Mitra Sharbatkhori, Hossein Mirhendi, Eshrat Beigom Kia, Francisco Ponce-Gordo, Vanessa Andresiuk, Sami Simsek, Antti Lavikainen, Malik Irshadullah, Gérald Umhang, Myriam Oudni-M'rad, Gerardo Acosta-Jamett, Steffen Rehbein, Urmas Saarma
Cystic echinococcosis, a zoonotic disease caused by Echinococcus granulosus sensu lato (s. l.), is a significant global public health concern. Echinococcus granulosus s. l. is currently divided into numerous genotypes (G1-G8 and G10) of which G1-G3 are the most frequently implicated genotypes in human infections. Although it has been suggested that G1-G3 could be regarded as a distinct species E. granulosus sensu stricto (s. s.), the evidence to support this is inconclusive. Most importantly, data from nuclear DNA that provide means to investigate the exchange of genetic material between G1-G3 is lacking as none of the published nuclear DNA studies have explicitly included G2 or G3...
April 27, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28450228/mitogenomic-phylogeny-of-cone-snails-endemic-to-senegal
#12
Samuel Abalde, Manuel J Tenorio, Carlos M L Afonso, Rafael Zardoya
Cone snails attain in Senegal one of their highest peaks of species diversity throughout the continental coast of Western Africa. A total of 15 endemic species have been described, all placed in the genus Lautoconus. While there is ample data regarding the morphology of the shell and the radular tooth of these species, virtually nothing is known regarding the genetic diversity and phylogenetic relationships of one of the most endangered groups of cones. In this work, we determined the complete or near-complete (only lacking the control region) mitochondrial (mt) genomes of 17 specimens representing 11 endemic species (Lautoconus belairensis, Lautoconus bruguieresi, Lautoconus cacao, Lautoconus cloveri, Lautoconus cf...
April 24, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28448897/a-performance-evaluation-of-nextera-xt-and-kapa-hyperplus-for-rapid-illumina-library-preparation-of-long-range-mitogenome-amplicons
#13
Joseph D Ring, Kimberly Sturk-Andreaggi, Michelle A Peck, Charla Marshall
Next-generation sequencing (NGS) facilitates the rapid and high-throughput generation of human mitochondrial genome (mitogenome) data to build population and reference databases for forensic comparisons. To this end, long-range amplification provides an effective method of target enrichment that is amenable to library preparation assays employing DNA fragmentation. This study compared the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) and the KAPA HyperPlus Library Preparation Kit (Kapa Biosystems, Wilmington, MA) for enzymatic fragmentation and indexing of ∼8500bp mitogenome amplicons for Illumina sequencing...
April 5, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28435132/phylogenetic-position-of-the-rainbow-sardine-dussumieria-dussumieriidae-and-its-bearing-on-the-early-evolution-of-the-clupeoidei
#14
Sébastien Lavoué, Joris A M Bertrand, Wei-Jen Chen, Hsuan-Ching Hans Ho, Hiroyuki Motomura, Tetsuya Sado, Masaki Miya
The fish family Dussumieriidae (suborder Clupeoidei), commonly called round herrings, is traditionally considered to be a key taxon for understanding the evolution of the Clupeoidei because some of its morphological characteristics have been interpreted as being either derived or primitive, such as the nearly complete absence of abdominal scutes. Recent molecule-based studies showed that the Dussumieriidae is likely not a monophyletic group. None of those studies, however, included the genus Dussumieria (rainbow sardines) which is the type genus of the family Dussumieriidae...
April 20, 2017: Gene
https://www.readbyqxmd.com/read/28435087/the-complete-mitochondrial-genome-of-clostera-anachoreta-lepidoptera-notodontidae-and-phylogenetic-implications-for-noctuoidea-species
#15
Xiao-Yu Zhu, Zhao-Zhe Xin, Ying Wang, Hua-Bin Zhang, Dai-Zhen Zhang, Zheng-Fei Wang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
In this study, the complete mitochondrial genome (mitogenome) of Clostera anachoreta (Lepidoptera: Notodontidae) was sequenced. It comprises 15,456 base pairs (bp), including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNA), 22 transfer RNAs (tRNA) and one non-coding control region (CR), as found in other lepidopterans. Gene order is identical to that of typical lepidopterans. There are 15 intergenic spacers ranging from 1 to 49bp, and 9 overlapping regions ranging from 1 to 8bp, occurring throughout the genome...
April 20, 2017: Genomics
https://www.readbyqxmd.com/read/28408977/mitogenomes-of-giant-skipper-butterflies-reveal-an-ancient-split-between-deep-and-shallow-root-feeders
#16
Jing Zhang, Qian Cong, Xiao-Ling Fan, Rongjiang Wang, Min Wang, Nick V Grishin
Background: Giant-Skipper butterflies from the genus Megathymus are North American endemics. These large and thick-bodied Skippers resemble moths and are unique in their life cycles. Grub-like at the later stages of development, caterpillars of these species feed and live inside yucca roots. Adults do not feed and are mostly local, not straying far from the patches of yucca plants. Methods: Pieces of muscle were dissected from the thorax of specimens and genomic DNA was extracted (also from the abdomen of a specimen collected nearly 60 years ago)...
2017: F1000Research
https://www.readbyqxmd.com/read/28396681/evolution-of-nucleotide-punctuation-marks-from-structural-to-linear-signals
#17
Nawal El Houmami, Hervé Seligmann
We present an evolutionary hypothesis assuming that signals marking nucleotide synthesis (DNA replication and RNA transcription) evolved from multi- to unidimensional structures, and were carried over from transcription to translation. This evolutionary scenario presumes that signals combining secondary and primary nucleotide structures are evolutionary transitions. Mitochondrial replication initiation fits this scenario. Some observations reported in the literature corroborate that several signals for nucleotide synthesis function in translation, and vice versa...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28396619/the-complete-mitogenome-of-orcula-dolium-draparnaud-1801-ultra-deep-sequencing-from-a-single-long-range-pcr-using-the-ion-torrent-pgm
#18
D S J Groenenberg, J Harl, E Duijm, E Gittenberger
BACKGROUND: With the increasing capacity of present-day next-generation sequencers the field of mitogenomics is rapidly changing. Enrichment of the mitochondrial fraction, is no longer necessary for obtaining mitogenomic data. Despite the benefits, shotgun sequencing approaches also have disadvantages. They do not guarantee obtaining the complete mitogenome, generally require larger amounts of input DNA and coverage is low compared to sequencing with enrichment strategies. If the mitogenome could be amplified in a single amplification, additional time and costs for sample preparation might outweigh these disadvantages...
2017: Hereditas
https://www.readbyqxmd.com/read/28387361/origin-and-spread-of-human-mitochondrial-dna-haplogroup-u7
#19
Hovhannes Sahakyan, Baharak Hooshiar Kashani, Rakesh Tamang, Alena Kushniarevich, Amirtharaj Francis, Marta D Costa, Ajai Kumar Pathak, Zaruhi Khachatryan, Indu Sharma, Mannis van Oven, Jüri Parik, Hrant Hovhannisyan, Ene Metspalu, Erwan Pennarun, Monika Karmin, Erika Tamm, Kristiina Tambets, Ardeshir Bahmanimehr, Tuuli Reisberg, Maere Reidla, Alessandro Achilli, Anna Olivieri, Francesca Gandini, Ugo A Perego, Nadia Al-Zahery, Massoud Houshmand, Mohammad Hossein Sanati, Pedro Soares, Ekta Rai, Jelena Šarac, Tena Šarić, Varun Sharma, Luisa Pereira, Veronica Fernandes, Viktor Černý, Shirin Farjadian, Deepankar Pratap Singh, Hülya Azakli, Duran Üstek, Natalia Ekomasova Trofimova, Ildus Kutuev, Sergei Litvinov, Marina Bermisheva, Elza K Khusnutdinova, Niraj Rai, Manvendra Singh, Vijay Kumar Singh, Alla G Reddy, Helle-Viivi Tolk, Svjetlana Cvjetan, Lovorka Barac Lauc, Pavao Rudan, Emmanuel N Michalodimitrakis, Nicholas P Anagnou, Kalliopi I Pappa, Maria V Golubenko, Vladimir Orekhov, Svetlana A Borinskaya, Katrin Kaldma, Monica A Schauer, Maya Simionescu, Vladislava Gusar, Elena Grechanina, Periyasamy Govindaraj, Mikhail Voevoda, Larissa Damba, Swarkar Sharma, Lalji Singh, Ornella Semino, Doron M Behar, Levon Yepiskoposyan, Martin B Richards, Mait Metspalu, Toomas Kivisild, Kumarasamy Thangaraj, Phillip Endicott, Gyaneshwer Chaubey, Antonio Torroni, Richard Villems
Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16-19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28384231/the-mitochondrial-genome-of-pin-tailed-snipe-gallinago-stenura-and-its-implications-for-the-phylogeny-of-charadriiformes
#20
Chaochao Hu, Chenling Zhang, Lei Sun, Yi Zhang, Wenli Xie, Baowei Zhang, Qing Chang
The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1...
2017: PloS One
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