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Genome Génome / Conseil National de Recherches Canada

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https://www.readbyqxmd.com/read/28340301/ten-years-of-barcoding-at-the-african-centre-for-dna-barcoding
#1
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
#2
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
#3
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
#4
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
#5
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/-i-roegneria-alashanica-i-keng-a-species-with-the-b-ststst-sup-y-sup-st-sup-y-sup-b-genome-constitution
#6
Richard R-C Wang, Kevin B Jensen
The genome constitution of tetraploid <i>Roegneria alashanica</I> Keng has been in question for a long time. Most scientific studies have suggested that <i>R. alashanica</I> had two versions of the <b>St</b> genome, <b>St<sub>1</sub>St<sub>2</sub></b>, similar to that of <i>Pseudoroegneria elytrigioides</I> (C. Yen et J. L. Yang) B. R. Lu. A study, however, concluded that <i>R. alashanica</I> had the <b>StY</b> genome formula typical for tetraploid <i>Roegneria</I> species...
March 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28235186/differential-transferability-of-est-ssr-primers-developed-from-diploid-species-i-pseudoroegneria-spicata-i-i-thinopyrum-bessarabicum-i-and-i-th-elongatum-i
#7
Richard R-C Wang, Steven 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 Triticeae species, <i>Pseudoroegneria spicata</I> (Pursh) Á. Löve (having <b>St</b> genome), <i>Thinopyrum bessarabicum</I> (Savul. & Rayss) Á. Löve (<b>J<sup>b</sup></b> = <b>E<sup>b</sup></b> = <b>J</b>), and <i>Th...
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
#8
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/28177827/genomic-constitution-and-intergenomic-translocations-in-elymus-dahuricus-complex-revealed-by-multicolor-gish
#9
Cairong Yang, Zhang Haiqin, Weihuan Chen, Houyang Kang, Yi Wang, Sha Lina, Xing Fan, Jian Zeng, Yong-Hong Zhou
Multicolor genomic in situ hybridization was used to investigate genomic constitution and intergenomic translocations in Elymus dahuricus complex. The genomic constitution of species in E. dahuricus complex was confirmed as StYH. H/Y and H/St intergenomic translocations were identified in the present study with 7H and 1Y chromosomes involved in reciprocal translocations for all the accessions investigated in the complex. We propose that the translocations are species-specific in the E. dahuricus complex, are associated with allopolyploidy and may serve as important structural alterations for allopolyploid stability...
January 11, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177826/phylogenetic-analysis-of-two-single-copy-nuclear-genes-revealed-origin-and-complex-relationships-of-hordeum-polyploids-in-triticeae-poaceae
#10
Qianni Hu, Genlou Sun
Two single copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and thioredoxin-like gene (HTL), were used to explore the phylogeny and origin of polyploid species in Hordeum. Our results were partly in accord with previous studies, but disclosed additional complexity. Both RPB2 and HTL trees confirmed the presence of Xa genome in H. capense and H. secalinum, and that H. depressum originated from H. californicum together with other American diploids, either H. intercedens or H. pusillum...
January 11, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177829/genomic-and-metabolic-characterisation-of-alkaloid-biosynthesis-by-asexual-epichlo%C3%A3-fungal-endophytes-of-tall-fescue-pasture-grasses
#11
Piyumi Ekanayake, Jatinder Kaur, Pei Tian, Simone Rochfort, Kathryn Guthridge, Tim Sawbridge, German Spangenberg, John Forster
Symbiotic associations between tall fescue grasses and asexual Epichloë fungal endophytes exhibit biosynthesis of alkaloid compounds causing both beneficial and detrimental effects. Candidate novel endophytes with favourable chemotypic profiles have been identified in germplasm collections by screening for genetic diversity, followed by metabolite profile analysis in endogenous genetic backgrounds. A sub-set of candidates was subjected to genome survey sequencing to detect the presence or absence and structural status of known genes for biosynthesis of the major alkaloid classes...
January 4, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177828/isolation-and-characterization-of-a-novel-pollen-specific-promoter-in-maize%C3%AF-i-zea-mays-l-i-%C3%AF
#12
He Wang, Mingxia Fan, Guohong Wang, Chunyu Zhang, Lei Shi, Zhengyi Wei, Wenjuan Ma, Jing Chang, Senxin Huang, Feng Lin
<i>ZmSTK2_USP</i>, located on the long arm of chromosome 4, belongs to the serine/threonine kinase gene in maize. The sequence analysis of 2,100 bp upstream from the start codon ATG has shown that it contains <i>cis</i>-element motifs and two types of anther/pollen-specific promoter elements (GTGA and AGAAA), suggesting that it is the pollen-specific promoter. To investigate the function of <i>ZmSTK2_USP</i> promoter, the GUS gene fusion system was employed. In pro<i>ZmSTK2_USP-GUS</i> genetically modified plants, GUS activity was detected in mature pollen grains and pollen tubes but not found in other floral and vegetable tissues...
January 4, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28177830/analysis-of-codon-usage-patterns-in-morus-notabilis-based-on-genome-and-transcriptome-data
#13
Yan Wen, Ziliang Zou, Hongshun Li, Zhonghuai Xiang, Ningjia He
Codons play important roles in regulating gene expression levels and mRNA half-lives. However, codon usage and related studies in multicellular organisms still lag far behind those in unicellular organisms. In this study, we describe for the first time genome-wide patterns of codon bias in Morus notabilis (mulberry tree), and analyze genome-wide codon usage in 12 other Rosales species. The codon usage of M. notabilis was affected by nucleotide composition, mutation pressure, nature selection, and gene expression level...
January 3, 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
#14
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
https://www.readbyqxmd.com/read/28169563/collinearity-between-potato-solanum-tuberosum-l-and-wild-relatives-assessed-by-comparative-cytogenetic-mapping
#15
Paola Gaiero, José van de Belt, Francisco Vilaró, M Eric Schranz, Pablo Speranza, Hans de Jong
A major bottleneck to introgressive hybridization is the lack of genome collinearity between the donor (alien) genome and the recipient crop genome. Structural differences between the homeologs may create unbalanced segregation of chromosomes or cause linkage drag. To assess large-scale collinearity between potato and two of its wild relatives (Solanum commersonii and Solanum chacoense), we used BAC-FISH mapping of sequences with known positions on the RH potato map. BAC probes could successfully be hybridized to the S...
March 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28156137/chromosomal-distribution-patterns-of-the-ac-10-microsatellite-and-other-repetitive-sequences-and-their-use-in-chromosome-rearrangement-analysis-of-species-of-the-genus-avena
#16
Araceli Fominaya, Yolanda Loarce, Alexander Montes, Esther Ferrer
Fluorescence in situ hybridization (FISH) was used to determine the physical location of the (AC)10 microsatellite in metaphase chromosomes of six diploid species (AA or CC genomes), two tetraploid species (AACC genome), and five cultivars of two hexaploid species (AACCDD genome) of the genus Avena, a genus in which genomic relationships remain obscure. A preferential distribution of the (AC)10 microsatellite in the pericentromeric and interstitial regions was seen in both the A- and D-genome chromosomes, while in C-genome chromosomes the majority of signals were located in the pericentromeric heterochromatic regions...
March 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28145743/priming-of-a-dna-metabarcoding-approach-for-species-identification-and-inventory-in-marine-macrobenthic-communities
#17
Claudia Hollatz, Barbara R Leite, Jorge Lobo, Hugo Froufe, Conceição Egas, Filipe O Costa
In marine and estuarine benthic communities, the inventory and estimation of species richness are often hampered by the need for broad taxonomic expertise across several phyla. The use of DNA metabarcoding has emerged as a powerful tool for the fast assessment of species composition in a diversity of ecological communities. Here, we tested the amplification success of five primer sets targeting different COI-5P regions by 454 pyrosequencing to maximize the recovery of two simulated macrobenthic communities containing 21 species (SimCom1 and SimCom 2)...
March 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28106473/overexpression-of-buffy-enhances-the-loss-of-parkin-and-suppresses-the-loss-of-pink1-phenotypes-in-drosophila
#18
P Githure M'Angale, Brian E Staveley
Mutations in parkin (PARK2) and Pink1 (PARK6) are responsible for autosomal recessive forms of early onset Parkinson's disease (PD). Attributed to the failure of neurons to clear dysfunctional mitochondria, loss of gene expression leads to loss of nigrostriatal neurons. The Pink1/parkin pathway plays a role in the quality control mechanism aimed at eliminating defective mitochondria, and the failure of this mechanism results in a reduced lifespan and impaired locomotor ability, among other phenotypes. Inhibition of parkin or Pink1 through the induction of stable RNAi transgene in the Ddc-Gal4-expressing neurons results in such phenotypes to model PD...
March 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28106469/building-a-dna-barcode-library-of-alaska-s-non-marine-arthropods
#19
Derek S Sikes, Matthew Bowser, John M Morton, Casey Bickford, Sarah Meierotto, Kyndall Hildebrandt
Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection...
March 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28098486/identification-and-characterization-of-genes-on-a-single-subgenome-in-the-hexaploid-wheat-triticum-aestivum-l-genotype-chinese-spring
#20
Jian Ma, Zhi Zheng, Jiri Stiller, Xiu-Jin Lan, Yaxi Liu, Mei Deng, Penghao Wang, Zhien Pu, Guangdeng Chen, Qian-Tao Jiang, Yuming Wei, You-Liang Zheng
Gene loss during the formation of hexaploid bread wheat has been repeatedly reported. However, our knowledge on genome-wide analysis of the genes present on a single subgenome (SSG) in bread wheat is still limited. In this study, by analysing the 'Chinese Spring' chromosome arm shotgun sequences together with high-confidence gene models, we detected 433 genes on a SSG. Greater gene loss was observed in A and D subgenomes compared with B subgenome. More than 79% of the orthologs for these SSG genes were detected in diploid and tetraploid relatives of hexaploid wheat...
March 2017: Genome Génome / Conseil National de Recherches Canada
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