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Shao'e Sun, Ming Hui, Minxiao Wang, Zhongli Sha
Deep-sea hydrothermal vent is one of the most extreme environments on Earth with low oxygen and high levels of toxins. Decapod species from the family Alvinocarididae have colonized and successfully adapted to this extremely harsh environment. Mitochondria plays a vital role in oxygen usage and energy metabolism, thus it may be under selection in the adaptive evolution of the hydrothermal vent shrimps. In this study, the mitochondrial genome (mitogenome) of alvinocaridid shrimp Shinkaicaris leurokolos (Kikuchi & Hashimoto, 2000) was determined through Illumina sequencing...
November 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
P Xiao, L L Niu, Q J Zhao, X Y Chen, L J Wang, L Li, H P Zhang, J Z Guo, H Y Xu, T Zhong
The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0...
November 16, 2017: Animal: An International Journal of Animal Bioscience
Deepika Singh, Debajyoti Kabiraj, Pragya Sharma, Hasnahana Chetia, Ponnala Vimal Mosahari, Kartik Neog, Utpal Bora
Muga (Antheraea assamensis) is an economically important silkmoth endemic to the states of Assam and Meghalaya in India and is the producer of the strongest known commercial silk. However, there is a scarcity of genomic and proteomic data for understanding the organism at a molecular level. Our present study is on decoding the complete mitochondrial genome (mitogenome) of A. assamensis using next generation sequencing technology and comparing it with other available lepidopteran mitogenomes. Mitogenome of A...
2017: PloS One
Philippe Gaubert, Agostinho Antunes, Hao Meng, Lin Miao, Stéphane Peigné, Fabienne Justy, Flobert Njiokou, Sylvain Dufour, Emmanuel Danquah, Jayanthi Alahakoon, Erik Verheyen, William T Stanley, Stephen J O'Brien, Warren E Johnson, Shu-Jin Luo
Pangolins, considered the most-trafficked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships remain largely unexplored. Here we present the most comprehensive phylogenetic assessment of pangolins, based on genetic variation of complete mitogenomes and nine nuclear genes. We confirm deep divergence among Asian and African pangolins occurring not later than the Oligocene-Miocene boundary ca...
November 13, 2017: Journal of Heredity
Li-Shang Dai, Xu-Dong Zhou, Saima Kausar, Muhammad Nadeem Abbas, Liang Wu, Hai-Ling Zhou
The cucumber moth, Diaphania indica (Saunders) (Lepipdoptera: Pyralidae) is an economically important insect pest of cucurbits and is widely distributed in tropical and sub-tropical regions. Herein, we obtained entire mitochondrial genome (mitogenome) sequence of D. indica using polymerase chain reaction amplification and sequencing method. The complete mitogenome of D. indica is 15,367bp long, including 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and an A+T rich element...
November 11, 2017: International Journal of Biological Macromolecules
Weijun Li, Zongqing Wang, Yanli Che
In this study, the complete mitochondrial genome of Cryptocercus meridianus was sequenced. The circular mitochondrial genome is 15,322 bp in size and contains 13 protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes, and one D-loop region. We compare the mitogenome of C. meridianus with that of C. relictus and C. kyebangensis. The base composition of the whole genome was 45.20%, 9.74%, 16.06%, and 29.00% for A, G, C, and T, respectively; it shows a high AT content (74...
November 12, 2017: International Journal of Molecular Sciences
Zhiwen Chen, Hushuai Nie, Yumei Wang, Haili Pei, Shuangshuang Li, Lida Zhang, Jinping Hua
BACKGROUND: Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD1), G. barbadense (AD2), G. raimondii (D5) and G. arboreum (A2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium...
November 13, 2017: BMC Genomics
Shujie Xiao, Duong T Nguyen, Baojun Wu, Weilong Hao
Mitochondrial genomes (mitogenomes) are remarkably diverse in genome size and organization, but the origins of dynamic mitogenome architectures are still poorly understood. For instance, the mutational burden hypothesis postulates that the drastic difference between large plant mitogenomes and streamlined animal mitogenomes can be driven by their different mutation rates. However, inconsistent trends between mitogenome sizes and mutation rates have been documented in several lineages. These conflicting results highlight the need of systematic and sophisticated investigations on the evolution and diversity of mitogenome architecture...
November 8, 2017: Genome Biology and Evolution
Xing Yuhui, Zhou Lijun, Hou Yue, Wang Xiaoqi, Zhang Chen, Zhang Huilun, Wang Ruoran, Pan Da, Sun Hongying
Recent morphological and molecular evidence has challenged classical interpretations of eubrachyuran phylogeny and evolution. Complete mitochondrial genomes of two species of potamid freshwater crabs, Sinopotamon yaanense and Sinopotamon yangtsekiense were obtained using next-generation sequencing. The results revealed a novel gene order with translocations of a five-gene block and a tRNA gene in comparison to available brachyuran mitochondrial genomes. DNA sequence comparisons position the Potamidae, a primary freshwater crab family, outside of the clade for the traditional heterotreme families, and closer to the clade that includes the thoracotreme families of grapsoid and ocypodoid crabs...
2017: ZooKeys
Ana C Conrado, Hugo Arruda, David W G Stanton, Samuel W James, Peter Kille, George Brown, Elodie Silva, Lise Dupont, Shabnam Taheri, Andrew J Morgan, Nelson Simões, Armindo Rodrigues, Rafael Montiel, Luis Cunha
Pontoscolex corethrurus (Müller, 1857) plays an important role in tropical soil ecosystems and has been widely used as an animal model for a large variety of ecological studies in particular due to its common presence and generally high abundance in human-disturbed tropical soils. In this study we describe the complete mitochondrial genome of the peregrine earthworm P. corethrurus. This is the first record of a mitochondrial genome within the Rhinodrilidae family. Its mitochondrial genome is 14 835 bp in length containing 37 genes (13 protein-coding genes (PCG) 2 rRNA genes and 22 tRNA genes)...
2017: ZooKeys
Jihyun Yu, Bo-Hye Nam, Joon Yoon, Eun Bae Kim, Jung Youn Park, Heebal Kim, Sook Hee Yoon
To explore the spatio-temporal dynamics of endangered fin whales (Balaenoptera physalus) within the baleen whale (Mysticeti) lineages, we analyzed 148 published mitochondrial genome sequences of baleen whales. We used a Bayesian coalescent approach as well as Bayesian inferences and maximum likelihood methods. The results showed that the fin whales had a single maternal origin, and that there is a significant correlation between geographic location and evolution of global fin whales. The most recent common female ancestor of this species lived approximately 9...
November 4, 2017: Genetica
Charla Marshall, Kimberly Sturk-Andreaggi, Jennifer Daniels-Higginbotham, Robert Sean Oliver, Suzanne Barritt-Ross, Timothy P McMahon
Next-generation ancient DNA technologies have the potential to assist in the analysis of degraded DNA extracted from forensic specimens. Mitochondrial genome (mitogenome) sequencing, specifically, may be of benefit to samples that fail to yield forensically relevant genetic information using conventional PCR-based techniques. This report summarizes the Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory's (AFMES-AFDIL) performance evaluation of a Next-Generation Sequencing protocol for degraded and chemically treated past accounting samples...
September 8, 2017: Forensic Science International. Genetics
Stefania Brandini, Paola Bergamaschi, Marco Fernando Cerna, Francesca Gandini, Francesca Bastaroli, Emilie Bertolini, Cristina Cereda, Luca Ferretti, Alberto Gómez-Carballa, Vincenza Battaglia, Antonio Salas, Ornella Semino, Alessandro Achilli, Anna Olivieri, Antonio Torroni
Recent and compelling archaeological evidence attests to human presence ∼14.5 thousand years ago (Kya) at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 Kya, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent...
October 31, 2017: Molecular Biology and Evolution
Hong Zou, Ivan Jakovlić, Rong Chen, Dong Zhang, Jin Zhang, Wen-Xiang Li, Gui-Tang Wang
BACKGROUND: Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order...
November 2, 2017: BMC Genomics
Arild Johnsen, Anna M Kearns, Kevin E Omland, Jarl Andreas Anmarkrud
Previous studies based on single mitochondrial markers have shown that the common raven (Corvus corax) consists of two highly diverged lineages that are hypothesised to have undergone speciation reversal upon secondary contact. Furthermore, common ravens are paraphyletic with respect to the Chihuahuan raven (C. cryptoleucus) based on mitochondrial DNA (mtDNA). Here we explore the causes of mtDNA paraphyly by sequencing whole mitochondrial genomes of 12 common ravens from across the Northern Hemisphere, in addition to three Chihuahuan ravens and one closely related brown-necked raven (C...
2017: PloS One
Paulo Henrique Costa de Lima, Rafael Mazioli Barcelos, Raphael Contelli Klein, Pedro Marcus Pereira Vidigal, Carlos Emmanuel Montandon, Mary Hellen Fabres-Klein, Jorge Abdala Dergam, Cláudio Mafra
The mitogenome of Amblyomma sculptum was sequenced, providing important information for understanding the evolutionary relationships among species of the A. cajennense complex. The mitochondrial genome has a circular structure with 37 genes, including 13 coding DNA sequences, two ribosomal RNA genes (12S rRNA and 16S rRNA) and 22 tRNA genes. Comparative analysis with the mitogenomes of six reference species of the genus Amblyomma revealed that the ND5 gene, which is related to energy metabolism, and control regions 1 and 2 of the mitogenomes have polymorphisms that can be exploited as molecular markers to differentiate A...
November 30, 2017: Veterinary Parasitology
Kimberly Sturk-Andreaggi, Michelle A Peck, Cecilie Boysen, Patrick Dekker, Timothy P McMahon, Charla K Marshall
The feasibility of generating mitochondrial DNA (mtDNA) data has expanded considerably with the advent of next-generation sequencing (NGS), specifically in the generation of entire mtDNA genome (mitogenome) sequences. However, the analysis of these data has emerged as the greatest challenge to implementation in forensics. To address this need, a custom toolkit for use in the CLC Genomics Workbench (QIAGEN, Hilden, Germany) was developed through a collaborative effort between the Armed Forces Medical Examiner System - Armed Forces DNA Identification Laboratory (AFMES-AFDIL) and QIAGEN Bioinformatics...
September 19, 2017: Forensic Science International. Genetics
Abdelmadjid Djoumad, Audrey Nisole, Reza Zahiri, Luca Freschi, Sandrine Picq, Dawn E Gundersen-Rindal, Michael E Sparks, Ken Dewar, Don Stewart, Halim Maaroufi, Roger C Levesque, Richard C Hamelin, Michel Cusson
The gypsy moth, Lymantria dispar L., is one of the most destructive forest pests in the world. While the subspecies established in North America is the European gypsy moth (L. dispar dispar), whose females are flightless, the two Asian subspecies, L. dispar asiatica and L. dispar japonica, have flight-capable females, enhancing their invasiveness and warranting precautionary measures to prevent their permanent establishment in North America. Various molecular tools have been developed to help distinguish European from Asian subspecies, several of which are based on the mitochondrial barcode region...
October 27, 2017: Scientific Reports
Yimin Du, Chunni Zhang, Christopher H Dietrich, Yalin Zhang, Wu Dai
Only six mitochondrial genomes (mitogenomes) have been previously published for Cicadellidae, the largest family of Hemiptera. This study provides complete, annotated mitogenomes of two additional cicadellid, species Maiestas dorsalis and Japananus hyalinus, and the first comparative mitogenome analysis across the superfamily Membracoidea. The mitogenomes of both sequenced species are similar to those of other studied hemipteran mitogenomes in organization and the lengths are 15,352 and 15,364 bp with an A + T content of 78...
October 27, 2017: Scientific Reports
Xiao-Long Yuan, Xin-Xin Mao, Xin-Min Liu, Sen Cheng, Peng Zhang, Zhong-Feng Zhang
Engyodontium album is a widespread pathogen that causes different kinds of dermatoses and respiratory tract diseases in humans and animals. In spite of its perniciousness, the basic genetic and molecular background of this species remains poorly understood. In this study, the mitochondrial genome sequence of E. album was determined using a high-throughput sequencing platform. The circular mitogenome was found to be 28,081 nucleotides in length and comprised of 17 protein-coding genes, 24 tRNA genes, and 2 rRNA genes...
October 23, 2017: Genetics and Molecular Biology
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