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Genome Génome / Conseil National de Recherches Canada

Sundar Poovitha, Nithaniyal Stalin, Raju Balaji, Madasamy Parani
The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2...
September 14, 2016: Genome Génome / Conseil National de Recherches Canada
Joanne E Littlefair, Elizabeth L Clare
Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding)...
September 2, 2016: Genome Génome / Conseil National de Recherches Canada
Muhammad Ashfaq, Paul D N Hebert
Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases...
August 30, 2016: Genome Génome / Conseil National de Recherches Canada
T Fatima Mitterboeck, Jinzhong Fu, Sarah J Adamowicz
Insect lineages have crossed between terrestrial and aquatic habitats many times, for both immature and adult life stages. We explore patterns in molecular evolutionary rates between 42 sister pairs of related terrestrial and freshwater insect clades using publicly available protein-coding DNA sequence data from the orders Coleoptera, Diptera, Lepidoptera, Hemiptera, Mecoptera, Trichoptera, and Neuroptera. We furthermore test for habitat-associated convergent molecular evolution in the cytochrome c oxidase subunit I (COI) gene in general and at a particular amino acid site previously reported to exhibit habitat-linked convergence within an aquatic beetle group...
August 19, 2016: Genome Génome / Conseil National de Recherches Canada
Dong Yu, Zhiqiu Yin, Beiping Li, Yuan Jin, Hongguang Ren, Jing Zhou, Wei Zhou, Long Liang, Junjie Yue
Stenotrophomonas maltophilia is a global multidrug-resistant human opportunistic pathogen in clinical environments. Stenotrophomonas maltophilia is also ubiquitous in aqueous environments, soil, and plants. Various molecular typing methods have revealed that S. maltophilia exhibits high levels of phenotypic and genotypic diversity. However, information regarding the genomic diversity within S. maltophilia and the corresponding genetic mechanisms resulting in said diversity remain scarce. The genome sequences of 17 S...
August 6, 2016: Genome Génome / Conseil National de Recherches Canada
Rocío Ana González-Vaquero, Arturo Roig-Alsina, Laurence Packer
Special care is needed in the delimitation and identification of halictid bee species, which are renowned for being morphologically monotonous. Corynura Spinola and Halictillus Moure (Halictidae: Augochlorini) contain species that are key elements in southern South American ecosystems. These bees are very difficult to identify due to close morphological similarity among species and high sexual dimorphism. We analyzed 170 barcode-compliant COI sequences from 19 species. DNA barcodes were useful to confirm gender associations and to detect two new cryptic species...
October 2016: Genome Génome / Conseil National de Recherches Canada
Chonticha Kunprom, Pairot Pramual
The objectives of this study were to examine the genetic variation in fruit flies (Diptera: Tephritidae) in Thailand and to test the efficiency of the mitochondrial cytochrome c oxidase subunit I (COI) barcoding region for species-level identification. Twelve fruit fly species were collected from 24 host plant species of 13 families. The number of host plant species for each fruit fly species ranged between 1 and 11, with Bactrocera correcta found in the most diverse host plants. A total of 123 COI sequences were obtained from these fruit fly species...
October 2016: Genome Génome / Conseil National de Recherches Canada
Kaihui Huang, Yan Zhong, Yingjun Li, Dan Zheng, Zong-Ming Cheng
The ABA/water stress/ripening-induced (ASR) gene family exists universally in higher plants, and many ASR genes are up-regulated during periods of environmental stress and fruit ripening. Although a considerable amount of research has been performed investigating ASR gene response to abiotic stresses, relatively little is known about their roles in response to biotic stresses. In this report, we identified five ASR genes in apple (Malus × domestica) and explored their phylogenetic relationship, duplication events, and selective pressure...
October 2016: Genome Génome / Conseil National de Recherches Canada
Junshuang Jia, Xiaolin Lin, Xia Lin, Taoyan Lin, Bangzhu Chen, Weichao Hao, Yushuang Cheng, Yu Liu, Meijuan Dian, Kaitai Yao, Dong Xiao, Weiwang Gu
The Cre/loxP system has become an important tool for the conditional gene knockout and conditional gene expression in genetically engineered mice. The applications of this system depend on transgenic reporter mouse lines that provide Cre recombinase activity with a defined cell type-, tissue-, or developmental stage-specificity. To develop a sensitive assay for monitoring Cre-mediated DNA excisions in mice, we generated Cre-mediated excision reporter mice, designated R/L mice (R/L: mRFP(monomeric red fluorescent protein)/luciferase), express mRFP throughout embryonic development and adult stages, while Cre-mediated excision deletes a loxP-flanked mRFP reporter gene and STOP sequence, thereby activating the expression of the second reporter gene luciferase, as assayed by in vivo and ex vivo bioluminescence imaging...
October 2016: Genome Génome / Conseil National de Recherches Canada
Liqiang Song, Yuqing Lu, Jinpeng Zhang, Cuili Pan, Xinming Yang, Xiuquan Li, Weihua Liu, Lihui Li
Agropyron cristatum (2n = 4x = 28, PPPP) is a wild relative of common wheat and confers several desirable agronomic traits to wheat, such as high grain number per spike and enhanced resistance to certain diseases. Development of wheat - A. cristatum 6P translocation lines facilitates its utilization in wheat improvement. In this study, 26 wheat - A. cristatum 6P translocation lines were characterized by in situ hybridization (ISH) and 6P-specific sequence-tagged-site (STS) markers. These translocation lines carried different 6P chromosomal segments, which covered the whole 6P chromosome...
October 2016: Genome Génome / Conseil National de Recherches Canada
Silvia Britto Barreto, Lorena Andrade Nunes, André Teixeira da Silva, Ricardo Jucá-Chagas, Débora Diniz, Iracilda Sampaio, Horacio Schneider, Paulo Roberto Antunes de Mello Affonso
The combination of DNA barcodes and geometric morphometrics is useful to discriminate taxonomically controversial species, providing more precise estimates of biodiversity. Therefore, our goal was to assess the genetic and morphometric diversity in Nematocharax, a controversial monotypic and sexually dimorphic genus of Neotropical fish, based on sequencing of cytochrome c oxidase subunit I (COI) and morphometric analyses in seven populations of N. venustus from coastal rivers in Brazil. The average pairwise intrapopulation divergence in COI ranged from 0 to 2...
October 2016: Genome Génome / Conseil National de Recherches Canada
Markus J Ankenbrand, Alexander Keller
The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history...
October 2016: Genome Génome / Conseil National de Recherches Canada
Muhammad Jakir Hasan, Habibur Rahman
Clubroot disease, caused by Plasmodiophora brassicae, is a threat to the production of Brassica crops including oilseed B. napus. In Canada, several pathotypes of this pathogen, such as pathotypes 2, 3, 5, 6, and 8, were identified, and resistance to these pathotypes was found in a rutabaga (B. napus var. napobrassica) genotype. In this paper, we report the genetic basis and molecular mapping of this resistance by use of F2, backcross (BC1), and doubled haploid (DH) populations generated from crossing of this rutabaga line to a susceptible spring B...
October 2016: Genome Génome / Conseil National de Recherches Canada
Sarah J Adamowicz, Frédéric J J Chain, Elizabeth L Clare, Kristy Deiner, Vlad Dincă, Manuel Elías-Gutiérrez, Axel Hausmann, Ian D Hogg, Mari Kekkonen, Darío A Lijtmaer, Amanda Naaum, Dirk Steinke, Martha Valdez-Moreno, Michelle Van der Bank, John-James Wilson, Jianping Xu
No abstract text is available yet for this article.
September 2016: Genome Génome / Conseil National de Recherches Canada
(no author information available yet)
No abstract text is available yet for this article.
September 2016: Genome Génome / Conseil National de Recherches Canada
Seikoh Saitoh, Hiroaki Aoyama, Saori Fujii, Haruki Sunagawa, Hideki Nagahama, Masako Akutsu, Naoya Shinzato, Nobuhiro Kaneko, Taizo Nakamori
We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species)...
September 2016: Genome Génome / Conseil National de Recherches Canada
J Williamson, O Maurin, S N S Shiba, H van der Bank, M Pfab, M Pilusa, R M Kabongo, M van der Bank
Species in the cycad genus Encephalartos are listed in CITES Appendix I and as Threatened or Protected Species in terms of South Africa's National Environmental Management: Biodiversity Act (NEM:BA) of 2004. Despite regulations, illegal plant harvesting for medicinal trade has continued in South Africa and resulted in declines in cycad populations and even complete loss of sub-populations. Encephalartos is traded at traditional medicine markets in South Africa in the form of bark strips and stem sections; thus, determining the species traded presents a major challenge due to a lack of characteristic plant parts...
September 2016: Genome Génome / Conseil National de Recherches Canada
Mamoon M D Al-Rshaidat, Allison Snider, Sydney Rosebraugh, Amanda M Devine, Thomas D Devine, Laetitia Plaisance, Nancy Knowlton, Matthieu Leray
High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months...
September 2016: Genome Génome / Conseil National de Recherches Canada
Daniel H Janzen, Winnie Hallwachs
The 37-year ongoing inventory of the estimated 15 000 species of Lepidoptera living in the 125 000 terrestrial hectares of Area de Conservacion Guanacaste, northwestern Costa Rica, has DNA barcode documented 11 000+ species, and the simultaneous inventory of at least 6000+ species of wild-caught caterpillars, plus 2700+ species of parasitoids. The inventory began with Victorian methodologies and species-level perceptions, but it was transformed in 2004 by the full application of DNA barcoding for specimen identification and species discovery...
September 2016: Genome Génome / Conseil National de Recherches Canada
Kristiina Mark, Carolina Cornejo, Christine Keller, Daniela Flück, Christoph Scheidegger
Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS)...
September 2016: Genome Génome / Conseil National de Recherches Canada
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