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https://www.readbyqxmd.com/read/28204600/evolutionary-and-functional-mitogenomics-associated-with-the-genetic-restoration-of-the-florida-panther
#1
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
#2
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
#3
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
#4
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
#5
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...
February 8, 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
#6
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...
February 7, 2017: Gene
https://www.readbyqxmd.com/read/28177087/mitogenome-diversity-in-sardinians-a-genetic-window-onto-an-island-s-past
#7
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
#8
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
https://www.readbyqxmd.com/read/28160169/complete-mitochondrial-genome-from-south-american-catfish-pseudoplatystoma-reticulatum-eigenmann-eigenmann-and-its-impact-in-siluriformes-phylogenetic-tree
#9
Luciana Cristine Vasques Villela, Anderson Luis Alves, Eduardo Sousa Varela, Michel Eduardo Beleza Yamagishi, Poliana Fernanda Giachetto, Naiara Milagres Augusto da Silva, Josi Margarete Ponzetto, Samuel Rezende Paiva, Alexandre Rodrigues Caetano
The cachara (Pseudoplatystoma reticulatum) is a Neotropical freshwater catfish from family Pimelodidae (Siluriformes) native to Brazil. The species is of relative economic importance for local aquaculture production and basic biological information is under development to help boost efforts to domesticate and raise the species in commercial systems. The complete cachara mitochondrial genome was obtained by assembling Illumina RNA-seq data from pooled samples. The full mitogenome was found to be 16,576 bp in length, showing the same basic structure, order, and genetic organization observed in other Pimelodidae, with 13 protein-coding genes, 2 rNA genes, 22 trNAs, and a control region...
February 3, 2017: Genetica
https://www.readbyqxmd.com/read/28141957/mitochondrial-dna-sequence-of-ruffe-gymnocephalus-cernua
#10
Yan Zhang, Yun-Feng Li, Zi-Wei Shen, Hui-Jun Ru, Xiang-Xiang Wu, Xiao-Juan Liu, Zhao-Hui Ni
The complete mitochondrial genome (mitogenome) of the Gymnocephalus cernua has been studied. The genome sequence was 16,614 bp in length, including the typical structure of 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes, and the non-coding control region. The overall base composition of G. cernua mitogenome is 27.84% A, 27.60% T, 16.61% G, and 27.94% C, with a high A + T content of 55.45%. The complete mitochondrial genome of G. cernua provides basic genome data for relative studies on Perciformes...
January 31, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28140657/mitochondrial-super-haplogroup-u-diversity-in-serbians
#11
Slobodan Davidovic, Boris Malyarchuk, Jelena Aleksic, Miroslava Derenko, Vladanka Topalovic, Andrey Litvinov, Katarzyna Skonieczna, Urszula Rogalla, Tomasz Grzybowski, Milena Stevanovic, Natasa Kovacevic-Grujicic
BACKGROUND: Available mitochondrial (mtDNA) data demonstrate genetic differentiation among South Slavs inhabiting the Balkan Peninsula. However, their resolution is insufficient to elucidate the female-specific aspects of the genetic history of South Slavs, including the genetic impact of various migrations which were rather common within the Balkans, a region having a turbulent demographic history. AIM: Therefore, we thoroughly studied complete mitogenomes of Serbians, a population linking westward and eastward South Slavs...
January 31, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28129732/mitogenomics-phylogenetic-relationships-of-the-current-sloth-s-genera-and-species-bradypodidae-and-megalonychidae
#12
Manuel Ruiz-García, Diego Chacón, Tinka Plese, Ingrid Schuler, Joseph Mark Shostell
We sequenced the complete mitogenome of 39 sloths (19 Bradypus variegatus, 4 B. tridactylus, 1 B. pygmaeus, 1 B. torquatus, 4 Choloepus didactylus, and 10 C. hoffmanni). A Bayesian tree (BI) indicated a temporal split between Bradypus and Choloepus around 31 million years ago (MYA, Oligocene) and the other major splits within each genera during the Miocene and Pliocene. A haplotype network (MJN) estimated a lower temporal split between the sloth genera (around 23.5 MYA). Both methods detected the ancestor of B...
January 27, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28129721/mitogenomic-analysis-in-european-brown-hare-lepus-europaeus-proposes-genetic-and-functional-differentiation-between-the-distinct-lineages
#13
Themistoklis Giannoulis, Costas Stamatis, Andreas Tsipourlianos, Zissis Mamuris
European brown hare is a small game species spreading across Europe to Asia Minor, with important economic traits. Population genetics studies using mitochondrial DNA markers have revealed the existence of two major phylogeographic lineages, the European and the Anatolian. European lineage is further divided in the European type halpogroup and south-eastern European type halpogroup, while Anatolian consists only by the Anatolian/Middle Eastern type halpogroup. All three haplogroups show a discrete geographical distribution, with an overlapping zone forming in North-East Greece and Bulgaria, forming a contact zone...
January 27, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28116048/comparative-mitochondrial-and-chloroplast-genomics-of-a-genetically-distinct-form-of-sargassum-contributing-to-recent-golden-tides-in-the-western-atlantic
#14
Linda A Amaral-Zettler, Nicholas B Dragone, Jeffrey Schell, Beth Slikas, Leslie G Murphy, Clare E Morrall, Erik R Zettler
Over the past 5 years, massive accumulations of holopelagic species of the brown macroalga Sargassum in coastal areas of the Caribbean have created "golden tides" that threaten local biodiversity and trigger economic losses associated with beach deterioration and impact on fisheries and tourism. In 2015, the first report identifying the cause of these extreme events implicated a rare form of the holopelagic species Sargassum natans (form VIII). However, since the first mention of S. natans VIII in the 1930s, based solely on morphological characters, no molecular data have confirmed this identification...
January 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28097404/complete-mitochondrial-genome-of-the-endophytic-fungus-pestalotiopsis-fici-features-and-evolution
#15
Shu Zhang, Xiu-Na Wang, Xiao-Ling Zhang, Xing-Zhong Liu, Yong-Jie Zhang
Endophytic fungi (EF) live within plants and have profound impacts on plant communities. They are astonishingly diverse but poorly studied at the genome level. Herein, we assembled the mitochondrial genome (mitogenome) of the EF Pestalotiopsis fici, annotated and compared it with those of other relatives to better understand the evolution of the EF lineage. Except for standard fungal mitochondrial genes, the 69,529-bp circular mitogenome of P. fici harbors 18 introns acquired possibly through lateral transfer from other fungi and nine free-standing open reading frames with some scarcely seen in fungal mitogenomes...
January 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28094797/whole-genome-sequencing-data-and-de-novo-draft-assemblies-for-66-teleost-species
#16
Martin Malmstrøm, Michael Matschiner, Ole K Tørresen, Kjetill S Jakobsen, Sissel Jentoft
Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9-39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context...
January 17, 2017: Scientific Data
https://www.readbyqxmd.com/read/28089793/eggshell-palaeogenomics-palaeognath-evolutionary-history-revealed-through-ancient-nuclear-and-mitochondrial-dna-from-madagascan-elephant-bird-aepyornis-sp-eggshell
#17
Alicia Grealy, Matthew Phillips, Gifford Miller, M Thomas P Gilbert, Jean-Marie Rouillard, David Lambert, Michael Bunce, James Haile
Palaeognaths, the sister group of all other living birds (neognaths), were once considered to be vicariant relics from the breakup of the Gondwanan supercontinent. However, recent molecular studies instead argue for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing their evolutionary relationships and dating their divergences, which often relies on phylogenetic information from extinct relatives and nuclear genomes. Mitogenomes from the extinct elephant birds of Madagascar have helped inform the palaeognath phylogeny; however, nuclear information has remained unavailable...
January 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28088402/historical-relationships-of-three-enigmatic-phasianid-genera-aves-galliformes-inferred-using-phylogenomic-and-mitogenomic-data
#18
Ning Wang, Peter A Hosner, Bin Liang, Edward L Braun, Rebecca T Kimball
The phylogeny of the Phasianidae (pheasants, partridges, and allies) has been studied extensively. However, these studies have largely ignored three enigmatic genera because of scarce DNA source material and limited overlapping phylogenetic data: blood pheasants (Ithaginis), snow partridges (Lerwa), and long-billed partridges (Rhizothera). Thus, phylogenetic positions of these three genera remain uncertain in what is otherwise a well-resolved phylogeny. Previous studies using different data types place Lerwa and Ithaginis in similar positions, but the absence of overlapping data means the relationship between them could not be inferred...
January 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28070758/phylogeography-of-the-asian-rice-gall-midge-orseolia-oryzae-wood-mason-diptera-cecidomyiidae-in-thailand
#19
Solene Janique, Wantana Sriratanasak, Kulchana Ketsuwan, Jirapong Jairin, Ekgachai Jeratthitikul
The Asian rice gall midge (RGM) Orseolia oryzae (Wood Mason) (Diptera: Cecidomyiidae) is a major pest of rice, leading to yield losses in Thailand and many Asian countries. Despite an increasing number of reported midge outbreaks and the presence of many susceptible rice varieties, only a few studies have focused on the genetic variation of the midges. Therefore, we analyzed the phylogeography among Thai RGM populations covering north, northeast and central Thailand. Two mitochondrial DNA genes, cytochrome C oxidase I (COI) and 12S, and a non-coding repeat region (RR) situated just before COI were amplified...
January 9, 2017: Genetica
https://www.readbyqxmd.com/read/28068380/the-complete-maternally-and-paternally-inherited-mitochondrial-genomes-of-a-freshwater-mussel-potamilus-alatus-bivalvia-unionidae
#20
Hai B Wen, Zhe M Cao, Dan Hua, Pao Xu, Xue Y Ma, Wu Jin, Xin H Yuan, Ruo B Gu
Doubly uniparental inheritance (DUI) of mitochondrial DNA, found only in some bivalve families and characterized by the existence of gender-associated mtDNA lineages that are inherited through males (M-type) or females (F-type), is one of the very few exceptions to the general rule of strict maternal mtDNA inheritance in animals. M-type sequences are often undetected and hence still underrepresented in the GenBank, which hinders the progress of the understanding of the DUI phenomenon. We have sequenced and analyzed the complete M and F mitogenomes of a freshwater mussel, Potamilus alatus...
2017: PloS One
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