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Genome Génome / Conseil National de Recherches Canada

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https://www.readbyqxmd.com/read/28431212/dna-barcoding-and-traditional-taxonomy-an-integrated-approach-for-biodiversity-conservation
#1
Bhavisha P Sheth, Vrinda S Thaker
Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks...
April 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28355497/molecular-characterization-of-dihydroneopterin-aldolase-and-aminodeoxychorismate-synthase-in-common-bean-genes-coding-for-enzymes-in-the-folate-synthesis-pathway
#2
Weilong Xie, Gregory Perry, Christopher Joe Martin, Youn-Seb Shim, Alireza Navabi, Karl Peter Pauls
Common beans (Phaseolus vulgaris) are excellent sources of dietary folates, but different varieties contain different amounts of these compounds. Dihydroneopterin aldolase (DHNA) and aminodeoxychorismate synthase (ADCS) genes in the folate synthesis pathway, were characterized by PCR amplification, BAC clone sequencing, and whole genome sequencing. All DHNA and ADCS genes in the Mesoamerican cultivar OAC Rex were isolated and compared with those genes in the genome of Andean genotype G19833. Both genotypes have two functional DHNA genes and one pseudo gene...
March 29, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28355490/phylogenomic-inferences-from-reference-mapped-and-i-de-novo-i-assembled-short-read-sequence-data-using-radseq-sequencing-of-california-white-oaks-i-quercus-i-subgenus-i-quercus-i
#3
Sorel Fitz-Gibbon, Andrew L Hipp, Kasey Khanh Pham, Paul S Manos, Victoria Sork
The emergence of next generation sequencing has increased by several orders of magnitude the amount of data available for phylogenetics. Reduced representation approaches, such as restriction-site associated DNA sequencing (RADseq), have proven useful for phylogenetic studies of non-model species at a wide range of phylogenetic depths. However, analysis of these datasets is not uniform and we know little about the potential benefits and drawbacks of <i>de novo</i> assembly versus assembly by mapping to a reference genome...
March 29, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28340301/ten-years-of-barcoding-at-the-african-centre-for-dna-barcoding
#4
Simeon Bezeng Bezeng, T Jonathan Davies, Barnabas H Daru, Ronny Mukala Kabongo, Olivier Maurin, Kowiyou Yessoufou, Herman van der Bank, Michelle Van der Bank
The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that the two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants...
March 24, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28319670/identification-of-candidate-genes-for-the-seed-coat-colour-change-in-a-brachypodium-distachyon-mutant-induced-by-gamma-radiation-using-whole-genome-re-sequencing
#5
Man Bo Lee, Dae Yeon Kim, Yong Weon Seo
Brachypodium distachyon has been proposed as a model plant for agriculturally important cereal crops such as wheat and barley. Seed coat colour change from brown-red to yellow was observed in a mutant line (142-3) of B. distachyon, which was induced by chronic gamma radiation. In addition, dwarf phenotypes were observed in each of the lines 142-3, 421-2, and 1376-1. In order to identify causal mutations for the seed coat colour change, the three mutant lines and the wild type were subjected to whole-genome re-sequencing...
March 20, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28314115/genome-wide-identification-and-evolution-of-the-pin-formed-pin-gene-family-in-glycine-max
#6
Yuan Liu, Haichao Wei
Soybean is one of the most important crop plants, wild and cultivated soybean varieties have significant differences worth further investigation, such as plant morphology, seed size, seed coat development, these characters may be related to auxin biology. The PIN family is an essential auxin polar transport gene, but little research on soybean PINs (GmPINs) has been done, especially with respect to evolution and the differences between wild and cultivated soybean. In this study, we retrieved 23 GmPINs from the latest updated G...
March 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28314114/st-sub-2-sub-80-a-new-fish-marker-for-st-genome-and-genome-analysis-in-triticeae
#7
Long Wang, Qinghua Shi, Handong Su, Yi Wang, Sha Lina, Xing Fan, Kang Houyang, Zhang Haiqin, Yong-Hong Zhou
<b>St</b> genome is one of the most fundamental genomes in Triticeae. Repetitive sequences are widely used to distinguish different genomes or species. The primary objectives of this study are (1) to screen a new sequence that can easily distinguish the chromosome of <b>St</b> and other genome by fluorescence in situ hybridization (FISH); (2) to investigate the genome constitutions of some species remains uncertain and controversial. We used degenerated oligonucleotide primer PCR (Dop-PCR), Dot-blot and FISH to screen new marker for <b>St</b> genome and tested efficiency of this marker in detection <b>St</b> chromosome at different ploidy level...
March 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28314113/genome-wide-estimation-of-heritability-and-its-functional-components-for-flowering-defense-ionomics-and-developmental-traits-in-a-geographically-diverse-population-of-i-arabidopsis-thaliana-i
#8
Rong-Cai Yang
Narrow-sense heritability (portion of the total phenotypic variation due to additive genetic effect, <i>h</i><sup>2</sup>) is a critical parameter in plant breeding and genetics, but its estimation is difficult for populations with unknown pedigree information. This study applied a marker-based linear mixed model (LMM) analysis to estimate narrow-sense heritability and its seven functional components corresponding to SNPs in coding and noncoding regions for each of 107 flowering, defense, ionomics and developmental traits in an Arabidopsis (<i>Arabidopsis thaliana</i>) population of 199 inbred lines with unknown genetic relatedness...
March 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28314108/roegneria-alashanica-keng-a-species-with-the-ststst-y-st-y-genome-constitution
#9
Richard R-C Wang, Kevin B Jensen
The genome constitution of tetraploid Roegneria alashanica Keng has been in question for a long time. Most scientific studies have suggested that R. alashanica had two versions of the St genome, St1St2, similar to that of Pseudoroegneria elytrigioides (C. Yen & J.L. Yang) B.R. Lu. A study, however, concluded that R. alashanica had the StY genome formula typical for tetraploid species of Roegneria. For the present study, R. alashanica, Elymus longearistatus (Bioss.) Tzvelev (StY genomes), Pseudoroegneria strigosa (M...
March 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28235186/differential-transferability-of-est-ssr-primers-developed-from-the-diploid-species-pseudoroegneria-spicata-thinopyrum-bessarabicum-and-thinopyrum-elongatum
#10
Richard R-C Wang, Steve R Larson, Kevin B Jensen
Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid species of Triticeae, Pseudoroegneria spicata (Pursh) Á. Löve (having St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (J(b) = E(b) = J), and Thinopyrum elongatum (Host) D.R. Dewey (J(e) = E(e) = E), were used to produce amplicons in these three species to (i) assess relative transferability, (ii) identify polymorphic species-specific markers, and (iii) determine genome relationships among the three species...
February 24, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177825/enhancement-of-single-guide-rna-transcription-for-efficient-crispr-cas-based-genomic-engineering
#11
Kumiko Ui-Tei, Shohei Maruyama, Yuko Nakano
Genomic engineering using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein is a promising approach for targeting the genomic DNA of virtually any organism in a sequence-specific manner. Recent remarkable advances in CRISPR/Cas technology have made it a feasible system for use in therapeutic applications and biotechnology. In the CRISPR/Cas system, a guide RNA (gRNA), interacting with the Cas protein, recognizes a genomic region with sequence complementarity, and the double-stranded DNA at the target site is cleaved by the Cas protein...
January 26, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177846/nuclear-dna-content-correlates-with-depth-body-size-and-diversification-rate-in-amphipod-crustaceans-from-ancient-lake-baikal-russia
#12
Nicholas W Jeffery, Lev Yampolsky, T Ryan Gregory
Lake Baikal in Russia is a large, ancient lake that has been the site of a major radiation of amphipod crustaceans. Nearly 400 named species are known in this single lake, and it is thought that many more await description. The size and depth of Lake Baikal, in particular, may have contributed to the radiation of endemic amphipods by providing a large number of microhabitats for species to invade and subsequently experience reproductive isolation. Here we investigate the possibility that large-scale genomic changes have also accompanied diversification in these crustaceans...
April 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177845/analysis-of-the-oligopeptide-transporter-gene-family-in-ganoderma-lucidum-structure-phylogeny-and-expression-patterns
#13
Quanju Xiang, Keyu Shen, Xiumei Yu, Ke Zhao, Yunfu Gu, Xiaoping Zhang, Xiaoqiong Chen, Qiang Chen
Oligopeptide transporters (OPTs) are believed to transport broad ranges of substrates across the plasma membrane from the extracellular environment into the cell and are thought to contribute to various biological processes. In the present study, 13 putative OPTs (Gl-OPT1 to Gl-OPT13) were identified through extensive search of Ganoderma lucidum genome database. Phylogenetic analysis with OPTs from other fungi and plants indicates that these genes can be further divided into five groups. Motif compositions of OPT members are highly conserved in each group, indicative of functional conservation...
April 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177844/genome-wide-analysis-and-expression-characteristics-of-small-auxin-up-rna-saur-genes-in-moso-bamboo-phyllostachys-edulis
#14
Qingsong Bai, Dan Hou, Long Li, Zhanchao Cheng, Wei Ge, Jun Liu, Xueping Li, Shaohua Mu, Jian Gao
Moso bamboo (Phyllostachys edulis) is well known for its rapid shoot growth. Auxin exerts pleiotropic effects on plant growth. The small auxin-up RNA (SAUR) genes are early auxin-responsive genes involved in plant growth. In total, 38 SAUR genes were identified in P. edulis (PheSAUR). A comprehensive overview of the PheSAUR gene family is presented, including the gene structures, phylogeny, and subcellular location predictions. A transcriptome analysis indicated that 37 (except PheSAUR18) of the PheSAUR genes were expressed during shoot growth process and that the PheSAUR genes were differentially expressed...
April 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177843/estimation-of-long-terminal-repeat-element-content-in-the-helicoverpa-zea-genome-from-high-throughput-sequencing-of-bacterial-artificial-chromosome-pools
#15
Brad S Coates, Craig A Abel, Omaththage P Perera
The lepidopteran pest insect Helicoverpa zea feeds on cultivated corn and cotton across the Americas where control remains challenging owing to the evolution of resistance to chemical and transgenic insecticidal toxins, yet genomic resources remain scarce for this species. A bacterial artificial chromosome (BAC) library having a mean genomic insert size of 145 ± 20 kbp was created from a laboratory strain of H. zea, which provides ∼12.9-fold coverage of a 362.8 ± 8.8 Mbp (0.37 ± 0.09 pg) flow cytometry estimated haploid genome size...
April 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177841/dna-barcoding-as-an-aid-for-species-identification-in-austral-black-flies-insecta-diptera-simuliidae
#16
Luis M Hernández-Triana, Fernanda Montes De Oca, Sean W J Prosser, Paul D N Hebert, T Ryan Gregory, Shelley McMurtrie
In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha)...
April 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177838/testing-the-reliability-of-standard-and-complementary-dna-barcodes-for-the-monocot-subfamily-alooideae-from-south-africa
#17
Barnabas H Daru, Michelle van der Bank, Abubakar Bello, Kowiyou Yessoufou
Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar...
April 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177833/the-importance-of-molecular-markers-and-primer-design-when-characterizing-biodiversity-from-environmental-dna
#18
Joanna R Freeland
Environmental DNA (eDNA) comprises DNA fragments that have been shed into the environment by organisms, and which can be extracted from environmental samples such as water or soil. Characterization of eDNA can allow researchers to infer the presence or absence of species from a particular site without the need to locate and identify individuals, and therefore may provide an extremely valuable tool for quantifying biodiversity. However, as is often the case with relatively new protocols, methodological challenges remain...
April 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28121461/the-dynamic-evolutionary-history-of-genome-size-in-north-american-woodland-salamanders
#19
Catherine E Newman, T Ryan Gregory, Christopher C Austin
The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5-20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55)...
April 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177847/forensic-application-of-dna-barcoding-for-identification-of-illegally-traded-african-pangolin-scales
#20
Monica Mwale, Desire L Dalton, Raymond Jansen, Marli De Bruyn, Darren Pietersen, Prudent S Mokgokong, Antoinette Kotzé
The escalating growth in illegal wildlife trade and anthropogenic habitat changes threaten the survival of pangolin species worldwide. All eight extant species have experienced drastic population size reductions globally with a high extinction risk in Asia. Consequently, forensic services have become critical for law enforcement, with a need for standardised and validated genetic methods for reliable identifications. The seizure of three tonnes of pangolin scales, believed to have originated from Africa, by Hong Kong Customs Authorities provided an opportunity for the application of DNA barcoding in identifying scales...
March 2017: Genome Génome / Conseil National de Recherches Canada
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