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https://www.readbyqxmd.com/read/28654082/a-mitogenomic-timetree-for-darwin-s-enigmatic-south-american-mammal-macrauchenia-patachonica
#1
Michael Westbury, Sina Baleka, Axel Barlow, Stefanie Hartmann, Johanna L A Paijmans, Alejandro Kramarz, Analía M Forasiepi, Mariano Bond, Javier N Gelfo, Marcelo A Reguero, Patricio López-Mendoza, Matias Taglioretti, Fernando Scaglia, Andrés Rinderknecht, Washington Jones, Francisco Mena, Guillaume Billet, Christian de Muizon, José Luis Aguilar, Ross D E MacPhee, Michael Hofreiter
The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of ∼66 Ma (95% credibility interval, 56...
June 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/28647620/the-mitogenome-phylogeny-of-adephaga-coleoptera
#2
Alejandro López-López, Alfried P Vogler
The beetle suborder Adephaga consists of several aquatic ('Hydradephaga') and terrestrial ('Geadephaga') families whose relationships remain poorly known. In particular, the position of Cicindelidae (tiger beetles) appears problematic, as recent studies have found them either within the Hydradephaga based on mitogenomes, or together with several unlikely relatives in Geadephaga based on 18S rRNA genes. We newly sequenced nine mitogenomes of representatives of Cicindelidae and three ground beetles (Carabidae), and conducted phylogenetic analyses together with 29 existing mitogenomes of Adephaga...
June 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28647499/complete-sequence-and-characterization-of-the-mitochondrial-genome-of-diphyllobothrium-stemmacephalum-the-type-species-of-genus-diphyllobothrium-cestoda-diphyllobothriidae-using-next-generation-sequencing
#3
Hiroshi Yamasaki, Shinji Izumiyama, Tomoyoshi Nozaki
We first constructed and characterized the complete mitochondrial genome (mitogenome) sequence of Diphyllobothrium stemmacephalum, the type species of genus Diphyllobothrium, using next generation sequencing (NGS). The mitogenome of D. stemmacephalum was 13,716bp, including 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 longer intergenic non-coding regions, and has features common to mitogenomes of other cestodes. Although it has been accepted that tRNA for serine (trnS2(UCN)) in Platyhelminthes lacks a D arm, the trnS2(UCN) of D...
June 21, 2017: Parasitology International
https://www.readbyqxmd.com/read/28646188/mitochondrial-haplotypes-influence-metabolic-traits-across-bovine-inter-and-intra-species-cybrids
#4
Jikun Wang, Hai Xiang, Langqing Liu, Minghua Kong, Tao Yin, Xingbo Zhao
In bovine species, mitochondrial DNA polymorphisms and their correlation to productive or reproductive performances have been widely reported across breeds and individuals. However, experimental evidence of this correlation has never been provided. In order to identify differences among bovine mtDNA haplotypes, transmitochondrial cybrids were generated, with the nucleus from MAC-T cell line, derived from a Holstein dairy cow (Bos taurus) and mitochondria from either primary cell line derived from a domestic Chinese native beef Luxi cattle breed or central Asian domestic yak (Bos grunniens)...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646134/complete-mitochondrial-genome-of-clistocoeloma-sinensis-brachyura-grapsoidea-gene-rearrangements-and-higher-level-phylogeny-of-the-brachyura
#5
Zhao-Zhe Xin, Yu Liu, Dai-Zhen Zhang, Xin-Yue Chai, Zheng-Fei Wang, Hua-Bin Zhang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
Deciphering the animal mitochondrial genome (mitogenome) is very important to understand their molecular evolution and phylogenetic relationships. In this study, the complete mitogenome of Clistocoeloma sinensis was determined. The mitogenome of C. sinensis was 15,706 bp long, and its A+T content was 75.7%. The A+T skew of the mitogenome of C. sinensis was slightly negative (-0.020). All the transfer RNA genes had the typical cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637530/characterization-of-the-complete-mitochondrial-genome-of-ortleppascaris-sinensis-nematoda-heterocheilidae-and-comparative-mitogenomic-analysis-of-eighteen-ascaridida-nematodes
#6
J H Zhao, G J Tu, X B Wu, C P Li
Ortleppascaris sinensis (Nematoda: Ascaridida) is a dominant intestinal nematode of the captive Chinese alligator. However, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. In this study, the complete mitochondrial (mt) genome sequence of O. sinensis was first determined using a polymerase chain reaction (PCR)-based primer-walking strategy, and this is also the first sequencing of the complete mitochondrial genome of a member of the genus Ortleppascaris...
June 22, 2017: Journal of Helminthology
https://www.readbyqxmd.com/read/28633069/mitogenomic-diversity-in-russians-and-poles
#7
Boris Malyarchuk, Andrey Litvinov, Miroslava Derenko, Katarzyna Skonieczna, Tomasz Grzybowski, Aleksandra Grosheva, Yuri Shneider, Sergei Rychkov, Olga Zhukova
Complete mtDNA genome sequencing improves molecular resolution for distinguishing variation between individuals and populations, but there is still deficiency of mitogenomic population data. To overcome this limitation, we used Sanger-based protocol to generate complete mtDNA sequences of 376 Russian individuals from six populations of European part of Russia and 100 Polish individuals from northern Poland. Nearly complete resolution of mtDNA haplotypes was achieved - about 97% of haplotypes were unique both in Russians and Poles, and no haplotypes overlapped between them when indels were considered...
June 15, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28623884/mitochondrial-rna-processing-in-absence-of-trna-punctuations-in-octocorals
#8
Gaurav G Shimpi, Sergio Vargas, Angelo Poliseno, Gert Wörheide
BACKGROUND: Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals...
June 17, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28622362/the-complete-mitochondrial-genome-of-sesarmops-sinensis-reveals-gene-rearrangements-and-phylogenetic-relationships-in-brachyura
#9
Bo-Ping Tang, Zhao-Zhe Xin, Yu Liu, Dai-Zhen Zhang, Zheng-Fei Wang, Hua-Bin Zhang, Xin-Yue Chai, Chun-Lin Zhou, Qiu-Ning Liu
Mitochondrial genome (mitogenome) is very important to understand molecular evolution and phylogenetics. Herein, in this study, the complete mitogenome of Sesarmops sinensis was reported. The mitogenome was 15,905 bp in size, and contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The AT skew and the GC skew are both negative in the mitogenomes of S. sinensis. The nucleotide composition of the S. sinensis mitogenome was also biased toward A + T nucleotides (75...
2017: PloS One
https://www.readbyqxmd.com/read/28610385/complete-mitochondrial-genome-and-taxonomic-revision-of-cardiodactylus-muiri-otte-2007-gryllidae-eneopterinae-lebinthini
#10
Jiajia Dong, Natallia Vicente, Ioana C Chintauan-Marquier, Cahyo Ramadi, Agnès Dettai, Tony Robillard
In the present study, we report the high-coverage complete mitochondrial genome (mitogenome) of the cricket Cardiodactylus muiri Otte, 2007. The mitogenome was sequenced using a long-PCR approach on an Ion Torrent Personal Genome Machine (PGM) for next generation sequencing technology. The total length of the amplified mitogenome is 16,328 bp, representing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one noncoding region (D-loop region). The new sets of long-PCR primers reported here are invaluable resources for future comparative evolutionary genomic studies in Orthopteran insects...
May 15, 2017: Zootaxa
https://www.readbyqxmd.com/read/28609941/mitochondrial-genome-of-i-abraxas-i-i-suspecta-i-lepidoptera-geometridae-%C3%A2-and-comparative-analysis-with-other-lepidopterans
#11
Y U Sun, Jiawei Zhang, Qingqing Li, Dan Liang, Muhammad Nadeem Abbas, Cen Qian, Lei Wang, Guoqing Wei, Bao-Jian Zhu, Chao-Liang Liu
In this study, a complete mitochondrial genome (mitogenome) sequence of Abraxas suspecta (Lepidoptera: Geometridae) is isolated and characterized. The complete DNA is 15,547 bp length and contains 2 ribosomal RNA genes, 23 putative transfer RNA (tRNA) genes including an extra tRNAAsn (AUU), 13 protein-coding genes and an adenine (A) + thymine (T)-rich region. The nucleotide composition and gene organization are identical to those of other lepidopteran, except for the presence of an extra copy of trnN (AUU)...
April 20, 2017: Zootaxa
https://www.readbyqxmd.com/read/28598968/comparative-mitochondrial-genome-analysis-of-daphnis-nerii-and-other-lepidopteran-insects-reveals-conserved-mitochondrial-genome-organization-and-phylogenetic-relationships
#12
Yu Sun, Chen Chen, Jin Gao, Muhammad Nadeem Abbas, Saima Kausar, Cen Qian, Lei Wang, Guoqing Wei, Bao-Jian Zhu, Chao-Liang Liu
In the present study, the complete sequence of the mitochondrial genome (mitogenome) of Daphnis nerii (Lepidoptera: Sphingidae) is described. The mitogenome (15,247 bp) of D.nerii encodes13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and an adenine (A) + thymine (T)-rich region. Its gene complement and order is similar to that of other sequenced lepidopterans. The 12 PCGs initiated by ATN codons except for cytochrome c oxidase subunit 1 (cox1) gene that is seemingly initiated by the CGA codon as documented in other insect mitogenomes...
2017: PloS One
https://www.readbyqxmd.com/read/28591857/adaptive-patterns-of-mitogenome-evolution-are-associated-with-the-loss-of-shell-scutes-in-turtles
#13
Tibisay Escalona, Cameron J Weadick, Agostinho Antunes
The mitochondrial genome encodes several protein components of the oxidative phosphorylation (OXPHOS) pathway and is critical for aerobic respiration. These proteins have evolved adaptively in many taxa, but linking molecular-level patterns with higher-level attributes (e.g., morphology, physiology) remains a challenge. Turtles are a promising system for exploring mitochondrial genome evolution as different species face distinct respiratory challenges and employ multiple strategies for ensuring efficient respiration...
June 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28567603/nearly-complete-mitogenome-of-hairy-sawfly-corynis-lateralis-brull%C3%A3-1832-hymenoptera-cimbicidae-rearrangements-in-the-iqm-and-arns1ef-gene-clusters
#14
Özgül Doğan, E Mahir Korkmaz
The Cimbicidae is a small family of the primitive and relatively less diverse suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genome (mitogenome) of hairy sawfly, Corynis lateralis (Hymenoptera: Cimbicidae) was sequenced using next generation sequencing and comparatively analysed with the mitogenome of Trichiosoma anthracinum. The sequenced length of C. lateralis mitogenome was 14,899 bp with an A+T content of 80.60%. All protein coding genes (PCGs) are initiated by ATN codons and all are terminated with TAR or T- stop codon...
May 31, 2017: Genetica
https://www.readbyqxmd.com/read/28546004/a-transfer-rna-gene-rearrangement-in-the-lepidopteran-mitochondrial-genome
#15
Qiu-Ning Liu, Zhao-Zhe Xin, Xiao-Yu Zhu, Xin-Yue Chai, Xiao-Ming Zhao, Chun-Lin Zhou, Bo-Ping Tang
Gene arrangements in the mitochondrial genomes (mitogenomes) of insects are conserved across the major lineages, but can be rearranged within derived groups and may provide valuable phylogenetic characters. In this study, we sequenced the entire mitogenome of Parasa consocia, a moth of the family Limacodidae (Lepidoptera: Zygaenoidea). Compared with other lepidopterans and ancestral insects, the P. consocia mitogenome features a transfer RNA gene arrangement novel among lepidopterans between the ND3 and ND5 genes: RANSEF (the underline signifies an inverted gene), which differs from the ARNSEF arrangement of ancestral insects...
May 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28545148/mitochondrial-genome-evolution-in-alismatales-size-reduction-and-extensive-loss-of-ribosomal-protein-genes
#16
Gitte Petersen, Argelia Cuenca, Athanasios Zervas, Gregory T Ross, Sean W Graham, Craig F Barrett, Jerrold I Davis, Ole Seberg
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant...
2017: PloS One
https://www.readbyqxmd.com/read/28539070/mitogenomics-data-reveal-effective-population-size-historical-bottlenecks-and-the-effects-of-hunting-on-new-zealand-fur-seals-arctocephalus-forsteri
#17
Arsalan Emami-Khoyi, Adrian M Paterson, David A Hartley, Laura J Boren, Robert H Cruickshank, James G Ross, Elaine C Murphy, Terry-Ann Else
The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0...
May 25, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28536079/the-complete-mitochondrial-genome-sequence-of-the-sichuan-digging-frog-kaloula-rugifera-anura-microhylidae-and-its-phylogenetic-implications
#18
Lichun Jiang, Li Zhao, Dongmei Cheng, Lilan Zhu, Min Zhang, Qiping Ruan, Wei Chen
The Sichuan Digging Frog (Kaloula rugifera) belongs to the family Dicroglossidae, which is endemic to northeastern Sichuan and southernmost Gansu provinces, in southwestern China. In this study, the complete mitochondrial genome of K. rugifera was sequenced. The mitogenome was 17,074bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand...
May 20, 2017: Gene
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
#19
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
#20
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
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