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https://www.readbyqxmd.com/read/28725363/bridging-two-scholarly-islands-enriches-both-coi-dna-barcodes-for-species-identification-versus-human-mitochondrial-variation-for-the-study-of-migrations-and-pathologies
#1
David S Thaler, Mark Y Stoeckle
DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648-bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28717152/effects-of-population-bottleneck-and-balancing-selection-on-the-chinese-alligator-are-revealed-by-locus-specific-characterization-of-mhc-genes
#2
Teng Zhai, Hai-Qiong Yang, Rui-Can Zhang, Li-Ming Fang, Guo-Heng Zhong, Sheng-Guo Fang
Chinese alligator (Alligator sinensis) is an endangered freshwater crocodilian endemic to China, which experienced a severe bottleneck about 30 years ago. In this study, we developed locus-specific primers to investigate the polymorphism of 3 major histocompatibility complex (MHC) loci in 3 Chinese alligator populations, in combination with 6 neutral microsatellite markers as a contrast. We found the genetic trace for the bottleneck effect on the endangered Chinese alligator: the low allelic diversity (2 alleles at each locus), the low nucleotide substitution rate (no more than 0...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28711653/highly-conserved-intragenic-hsv-2-sequences-results-from-next-generation-sequencing-of-hsv-2-ul-and-us-regions-from-genital-swabs-collected-from-3-continents
#3
Christine Johnston, Amalia Magaret, Pavitra Roychoudhury, Alexander L Greninger, Anqi Cheng, Kurt Diem, Matthew P Fitzgibbon, Meei-Li Huang, Stacy Selke, Jairam R Lingappa, Connie Celum, Keith R Jerome, Anna Wald, David M Koelle
INTRODUCTION: Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines. METHODS: Genital lesion swabs containing ≥ 10(7)log10 copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (UL_US) regions were identified...
July 13, 2017: Virology
https://www.readbyqxmd.com/read/28711373/comparative-genomic-and-phylogenetic-analysis-of-a-toxigenic-clinical-isolate-of-corynebacterium-diphtheriae-strain-b-d-16-78-from-malaysia
#4
Kar-Wai Hong, A W Asmah Hani, C A Nurul Aina Murni, R R Pusparani, Chee Kheong Chong, Khebir Verasahib, Wan Noraini W Yusoff, Noorliza M Noordin, Kok Keng Tee, Wai-Fong Yin, Choo Yee Yu, Geik Yong Ang, Kok-Gan Chan
In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile...
July 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28696392/comparative-transcriptome-analysis-reveals-adaptive-evolution-of-notopterygium-incisum-and-notopterygium-franchetii-two-high-alpine-herbal-species-endemic-to-china
#5
Yun Jia, Mi-Li Liu, Ming Yue, Zhe Zhao, Gui-Fang Zhao, Zhong-Hu Li
The extreme conditions (e.g., cold, low oxygen, and strong ultraviolet radiation) of the high mountains provide an ideal natural laboratory for studies on speciation and the adaptive evolution of organisms. Up to now, few genome/transcriptome-based studies have been carried out on how plants adapt to conditions at extremely high altitudes. Notopterygium incisum and Notopterygium franchetii (Notopterygium, Apiaceae) are two endangered high-alpine herbal plants endemic to China. To explore the molecular genetic mechanisms of adaptation to high altitudes, we performed high-throughput RNA sequencing (RNA-seq) to characterize the transcriptomes of the two species...
July 11, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28690785/rates-and-relations-of-mitochondrial-genome-evolution-across-the-echinoidea-with-special-focus-on-the-superfamily-odontophora
#6
Áki Jarl Láruson
In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular-clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28690071/plasmodium-vivax-rhomboid-like-protease-1-gene-diversity-in-thailand
#7
Touchchapol Mataradchakul, Chairat Uthaipibull, Francois Nosten, Joel Vega-Rodriguez, Marcelo Jacobs-Lorena, Usa Lek-Uthai
BACKGROUND: Plasmodium vivax infection remains a major public health problem, especially along the Thailand border regions. We examined the genetic diversity of this parasite by analyzing single-nucleotide polymorphisms (SNPs) of the P. vivax rhomboid-like protease 1 gene (Pvrom1) in parasites collected from western (Tak province, Thai-Myanmar border) and eastern (Chanthaburi province, Thai-Cambodia border) regions. METHODS: Data were collected by a cross-sectional survey, consisting of 47 and 45 P...
July 6, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28687708/germline-loss-of-function-mutations-in-ephb4-cause-a-second-form-of-capillary-malformation-arteriovenous-malformation-cm-avm2-deregulating-ras-mapk-signaling
#8
Mustapha Amyere, Nicole Revencu, Raphaël Helaers, Eleonore Pairet, Eulalia Baselga, Maria R Cordisco, Wendy K Chung, Josée Dubois, Jean-Philippe Lacour, Loreto Martorell, Juliette Mazereeuw-Hautier, Reed E Pyeritz, David J Amor, Annouk Bisdorff, Francine Blei, Hannah Bombei, Anne Dompmartin, David G Brooks, Juliette Dupont, Maria A González-Enseñat, Ilona J Frieden, Marion Gérard, Malin Kvarnung, Andrea Kwan Hanson-Kahn, Louanne Hudgins, Christine Léauté-Labrèze, Catherine McCuaig, Denise Metry, Philippe Parent, Carle Paul, Florence Petit, Alice Phan, Isabelle Quéré, Aicha Salhi, Anne M Turner, Pierre Vabres, Asuncion Vicente, Orli Wargon, Shoji Watanabe, Lisa Weibel, Ashley Wilson, Marcia Willing, John B Mulliken, Laurence M Boon, Miikka Vikkula
Background -Most AVMs are localized and occur sporadically; however they also can be multifocal in autosomal dominant disorders, such as Hereditary Hemorrhagic Telangiectasia (HHT) and Capillary Malformation-Arteriovenous Malformation (CM-AVM). Previously, we identified RASA1 mutations in 50% of patients with CM-AVM. Herein we studied non-RASA1 patients to further elucidate the pathogenicity of CMs and AVMs. Methods -We conducted a genome-wide linkage study on a CM-AVM family. Whole exome sequencing was also performed on 9 unrelated CM-AVM families...
July 7, 2017: Circulation
https://www.readbyqxmd.com/read/28669524/from-genetic-variability-to-phenotypic-expression-of-blood-group-systems
#9
L Raud, C Férec, Y Fichou
More than 300 red blood cell (RBC) antigens belonging to 36 blood group systems have been officially reported in humans by the International Society of Blood Transfusion (ISBT). Phenotypic variability is directly linked to the expression of the 41 blood group genes. The Rh blood group system, which is composed of 54 antigens, is the most complex and polymorphic system. Many rare genetic variants within the RH (RHD and RHCE) genes, involving various mutational mechanisms (single-nucleotide substitutions, short insertions/deletions, rearrangements, large deletions), have been reported in the literature and reference databases...
June 29, 2017: Transfusion Clinique et Biologique: Journal de la Société Française de Transfusion Sanguine
https://www.readbyqxmd.com/read/28665990/molecular-evolutionary-analysis-of-a-gender-limited-mid-ortholog-from-the-homothallic-species-volvox-africanus-with-male-and-monoecious-spheroids
#10
Kayoko Yamamoto, Hiroko Kawai-Toyooka, Takashi Hamaji, Yuki Tsuchikane, Toshiyuki Mori, Fumio Takahashi, Hiroyuki Sekimoto, Patrick J Ferris, Hisayoshi Nozaki
Volvox is a very interesting oogamous organism that exhibits various types of sexuality and/or sexual spheroids depending upon species or strains. However, molecular bases of such sexual reproduction characteristics have not been studied in this genus. In the model species V. carteri, an ortholog of the minus mating type-determining or minus dominance gene (MID) of isogamous Chlamydomonas reinhardtii is male-specific and determines the sperm formation. Male and female genders are genetically determined (heterothallism) in V...
2017: PloS One
https://www.readbyqxmd.com/read/28662630/sequence-differences-in-the-seed-dormancy-gene-qsd1-among-various-wheat-genomes
#11
Kazumitsu Onishi, Miki Yamane, Nami Yamaji, Mayumi Tokui, Hiroyuki Kanamori, Jianzhong Wu, Takao Komatsuda, Kazuhiro Sato
BACKGROUND: Pre-harvest sprouting frequently occurs in Triticum aestivum (wheat) and Hordeum vulgare (barley) at the end of the maturity period due to high rainfall, particularly in Asian monsoon areas. Seed dormancy is a major mechanism preventing pre-harvest sprouting in these crops. RESULTS: We identified orthologous sequences of the major Hordeum vulgare (barley) seed dormancy gene Qsd1 in hexaploid wheat cv. Chinese Spring by performing genomic clone sequencing, followed by transcript sequencing...
June 29, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28651519/analysis-of-the-genetic-variation-in-mitochondrial-dna-y-chromosome-sequences-and-mc1r-sheds-light-on-the-ancestry-of-nigerian-indigenous-pigs
#12
Adeniyi C Adeola, Olufunke O Oluwole, Bukola M Oladele, Temilola O Olorungbounmi, Bamidele Boladuro, Sunday C Olaogun, Lotanna M Nneji, Oscar J Sanke, Philip M Dawuda, Ofelia G Omitogun, Laurent Frantz, Robert W Murphy, Hai-Bing Xie, Min-Sheng Peng, Ya-Ping Zhang
BACKGROUND: The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved in the determination of coat color. We investigated the genetic diversity of Nigerian indigenous pigs (NIP) by simultaneously analyzing variation in mitochondrial DNA (mtDNA), Y-chromosome sequence and the melanocortin receptor 1 (MC1R) gene. RESULTS: Median-joining network analysis of mtDNA D-loop sequences from 201 NIP and previously characterized loci clustered NIP with populations from the West (Europe/North Africa) and East/Southeast Asia...
June 26, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28650169/increasing-protein-production-rates-can-decrease-the-rate-at-which-functional-protein-is-produced-and-their-steady-state-levels
#13
Ajeet K Sharma, Edward P O'Brien
The rate at which soluble, functional protein is produced by the ribosome has recently been found to vary in complex and unexplained ways as various translation-associated rates are altered through synonymous codon substitutions. To understand this phenomenon, here, we combine a well-established ribosome-traffic model with a master-equation model of cotranslational domain folding to explore the scenarios that are possible for the protein production rate, J, and the functional-nascent protein production rate, F, as the rates of various translation processes are altered for five different E...
July 7, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28649259/the-cbl-and-cipk-gene-family-in-grapevine-vitis-vinifera-genome-wide-analysis-and-expression-profiles-in-response-to-various-abiotic-stresses
#14
Yue Xi, Jinyi Liu, Chao Dong, Zong-Ming Max Cheng
Calcium plays a central role in regulating signal transduction pathways. Calcineurin B-like proteins (CBLs), which harbor a crucial region consisting of EF hands that capture Ca(2+), interact in a specific manner with CBL-interacting protein kinases (CIPKs). This two gene families or their interacting-complex widely respond to various environment stimuli and development processes. The genome-wide annotation and specific expression patterns of CBLs and CIPKs, however, in grapevine remain unclear. In the present study, eight CBL and 20 CIPK genes were identified in grapevine genome, and divided into four and five subfamilies, respectively, based on phylogenetic analysis, and validated by gene structure and the distribution of conserved protein motifs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28648850/complete-genome-analysis-of-dengue-virus-type-3-isolated-from-the-2013-dengue-outbreak-in-yunnan-china
#15
Xiaodan Wang, Dehong Ma, Xinwei Huang, Lihua Li, Duo Li, Yujiao Zhao, Lijuan Qiu, Yue Pan, Junying Chen, Juemin Xi, Xiyun Shan, Qiangming Sun
In the past few decades, dengue has spread rapidly and is an emerging disease in China. An unexpected dengue outbreak occurred in Xishuangbanna, Yunnan, China, resulting in 1331 patients in 2013. In order to obtain the complete genome information and perform mutation and evolutionary analysis of causative agent related to this largest outbreak of dengue fever. The viruses were isolated by cell culture and evaluated by genome sequence analysis. Phylogenetic trees were then constructed by Neighbor-Joining methods (MEGA6...
June 23, 2017: Virus Research
https://www.readbyqxmd.com/read/28642787/mutational-signatures-are-critical-for-proper-estimation-of-purifying-selection-pressures-in-cancer-somatic-mutation-data-when-using-the-dn-ds-metric
#16
Jimmy Van den Eynden, Erik Larsson
Large cancer genome sequencing initiatives have led to the identification of cancer driver genes based on signals of positive selection in somatic mutation data. Additionally, the identification of purifying (negative) selection has the potential to identify essential genes that may be of therapeutic interest. The most widely used way of quantifying selection pressures in protein-coding genes is the dN/dS metric, which compares non-synonymous to synonymous substitution rates. In this study, we examine whether and how this metric is influenced by the mutational processes that have been active during tumor evolution...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28642169/a-novel-method-to-quantify-base-substitution-mutations-at-the-10-6-per-bp-level-in-dna-samples
#17
Satoshi Yamashita, Naoko Iida, Hideyuki Takeshima, Naoko Hattori, Masahiro Maeda, Takayoshi Kishino, Reiko Nagano, Taichi Shimazu, Shoichiro Tsugane, Toshikazu Ushijima
Somatic base substitution mutations of frequencies at the 10(-6)/bp level are expected to be present in many biomedical samples, such as tissues exposed to carcinogenic factors and exhausted stem cells. However, measurement of such rare mutations has been very difficult in human DNA samples. Here, we invented the use of 100 copies of genomic DNA as a template for amplicon deep sequencing so that a real mutation in a single DNA molecule would be detected at a variant allele frequency of 1% while sequencing errors have less frequency...
June 19, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28637758/genome-wide-analysis-of-eighteen-epstein-barr-viruses-isolated-from-primary-nasopharyngeal-carcinoma-biopsies
#18
Chaofeng Tu, Zhaoyang Zeng, Peng Qi, Xiayu Li, Zhengyuan Yu, Can Guo, Fang Xiong, Bo Xiang, Ming Zhou, Zhaojian Gong, Qianjin Liao, Jianjun Yu, Yi He, Wenling Zhang, Xiaoling Li, Yong Li, Guiyuan Li, Wei Xiong
Epstein-Barr virus (EBV) is a ubiquitous gamma-herpesvirus that is highly prevalent in almost all human populations, and is associated with many human cancers such as nasopharyngeal carcinoma (NPC), Hodgkin's disease, and gastric carcinoma. However, in these EBV-associated cancers, only NPC exhibits remarkable ethnic and geographic distribution. We hypothesized that EBV genomic variations might contribute to the pathogenesis of different human cancers in different geographic areas. In this study, we collected 18 NPC biopsies from the Hunan Province in Southern China and de novo assembled 18 NPC biopsy specimen-derived EBV (NPC-EBV) genomes, designated as HN1 to HN18...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28635965/identification-genealogical-structure-and-population-genetics-of-s-alleles-in-malus-sieversii-the-wild-ancestor-of-domesticated-apple
#19
X Ma, Z Cai, W Liu, S Ge, L Tang
The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris...
June 21, 2017: Heredity
https://www.readbyqxmd.com/read/28634105/genetic-diversity-in-the-c-terminus-of-merozoite-surface-protein-1-among-plasmodium-knowlesi-isolates-from-selangor-and-sabah-borneo-malaysia
#20
Nan Jiun Yap, Xiang Ting Goh, Anson V Koehler, Timothy William, Tsin Wen Yeo, Indra Vythilingam, Robin B Gasser, Yvonne A L Lim
Plasmodium knowlesi, a malaria parasite of macaques, has emerged as an important parasite of humans. Despite the significance of P. knowlesi malaria in parts of Southeast Asia, very little is known about the genetic variation in this parasite. Our aim here was to explore sequence variation in a molecule called the 42kDa merozoite surface protein-1 (MSP-1), which is found on the surface of blood stages of Plasmodium spp. and plays a key role in erythrocyte invasion. Several studies of P. falciparum have reported that the C-terminus (a 42kDa fragment) of merozoite surface protein-1 (MSP-142; consisting of MSP-119 and MSP-133) is a potential candidate for a malaria vaccine...
June 17, 2017: Infection, Genetics and Evolution
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