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Genome Génome / Conseil National de Recherches Canada

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https://read.qxmd.com/read/30998854/complete-plastome-sequences-of-picea-asperata-mast-p-crassifolia-kom-and-comparative-analyses-with-p-abies-l-karst-and-p-morrisonicola-hayata
#1
Fangqun Ouyang, Jiwen Hu, Junchen Wang, Juanjuan Ling, Zhi Wang, Nan Wang, Jianwei Ma, Hanguo Zhang, Jianfeng Mao, Junhui Wang
Picea asperata and P. crassifolia have sympatric ranges and are closely related, but the differences between these species at the plastome level are unknown. To better understand the patterns of variation among Picea plastomes, the complete plastomes of P. asperata and P. crassifolia were sequenced. Then, the plastomes were compared with the complete plastomes of P. abies and P. morrisonicola, which are closely and distantly related to the focal species, respectively. We also used these sequences to construct phylogenetic trees to determine the relationships among and between the four species as well as additional taxa from Pinaceae and other gymnosperms...
April 18, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30998112/lsu-rdna-d5-region-the-dna-barcode-for-molecular-classification-and-identification-of-demodex
#2
Li Hu, Yae Zhao, Yuanjun Yang, Dongling Niu, Rui Yang
Whether ribosomal genes can be used as DNA barcodes for molecular identification of Demodex (Acariformes: Demodicidae) is unclear. To examine this, Demodex folliculorum , D. brevis , D. canis , and D. caprae were collected for DNA extraction, rDNA fragments amplification, sequencing, and analysis. The V2 and V4 regions of SSU rDNA; D5, D6, and D8 regions of LSU rDNA; and ITS region were obtained from the four morphospecies. BLAST analysis showed that the obtained sequences matched those of Demodex or Aplonobia (Acariformes: Tetranychidae) in Raphignathae...
April 18, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30933665/physical-organization-of-repetitive-sequences-and-chromosome-diversity-of-barley-revealed-by-fluorescence-in-situ-hybridization-fish
#3
Siyu Zhang, Minqiu Zhu, Yi Shang, Jiaqi Wang, Dawadondup Dawadondup, Lifang Zhuang, Jinlong Zhang, Chenggen Chu, Zengjun Qi
Fluorescence in situ hybridization (FISH) using oligonucleotides is a simple and convenient method for chromosome research. In this study, 34 of 46 previously developed oligonucleotides produced signals in barley. Together with two plasmid clones and one PCR-amplified cereal centromere repeat (CCS1) probe, 37 repetitive sequences were chromosomally located produced three types of signals covering different positions on the chromosomes. The centromeric and pericentric regions had a more complex genomic organization and sequence composition probably indicative of higher contents of heterochromatin...
April 1, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30920312/dna-barcoding-detects-floral-origin-of-indian-honey-samples
#4
Mohanasundaram Saravanan, Gunasekaran Mohanapriya, Ramachandra Laha, Ramalingam Sathishkumar
The unique medicinal and nutritional properties of honey are determined by its chemical composition. To evaluate the quality of honey, it is essential to study the surrounding vegetation where honeybees forage. In this study we used conventional melissopalynological and DNA barcoding techniques to determine the floral source of honey samples collected from different districts of the state of Mizoram, India. Pollen grains were isolated and genomic DNA was extracted from the honey samples. PCR amplification was carried out using universal barcode candidates ITS2 and rbcL to identify the plant species...
March 28, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30913397/an-integrated-analysis-of-mrna-and-mirna-in-skeletal-muscle-from-myostatin-edited-meishan-pigs
#5
Shanshan Xie, Xiang Li, Lili Qian, Chunbo Cai, Gaojun Xiao, Shengwang Jiang, Biao Li, Ting Gao, Wentao Cui
Myostatin (MSTN) was a key muscle factor that negatively regulates skeletal muscle growth and development. Our lab recently produced genetically engineered Meishan pigs containing a ZFN-edited myostatin loss-of-function (MSTN-/-,MKO) mutation that led to the hypertrophy of skeletal muscles. In this study, we performed transcriptome sequencing and miRNA sequencing in skeletal muscle samples from MKO and wild type Meishan pigs (MWT) to investigate the effect of loss-of-function MSTN mutation on expression of mRNA and miRNA...
March 26, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30865850/genome-wide-analysis-of-hak-potassium-transporter-gene-family-reveals-asymmetrical-evolution-in-tobacco-nicotiana-tabacum
#6
Zhongbang Song, Xingfu Wu, Yulong Gao, Xiang Cui, Fangchan Jiao, Xuejun Chen, Yongping Li
Being an essential mineral nutrient, potassium (K+) plays numerous important roles in plant growth and development and determines the yield and quality of crop products. The cellular level of K+ is controlled to a large extent by the potassium transporter which belongs to the KT/HAK/KUP (HAK) family. However, little is known about these genes in tobacco. In this study, we surveyed the tobacco genome and identified forty-one putative NtHAK genes (NtHAKS1-NtHAKS21 and NtHAKT1-NtHAKT20). Investigation of the cis-elements in upstream regions of these NtHAKs suggests that members of this family respond to environmental clues and phytohormones...
March 13, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30865849/preserving-the-tree-of-life-of-the-fish-family-cyprinidae-in-africa-in-the-face-of-the-ongoing-extinction-crisis
#7
Mariam Iyabo Adeoba, Solomon Tesfamichael, Kowiyou Yessoufou
Our understanding of how the phylogenetic tree of fishes might be affected by the ongoing extinction risk is poor. This is due to the unavailability of comprehensive DNA data, especially for many African lineages. In addition, the ongoing taxonomic confusion within some lineages, e.g. Cyprinidae, makes it difficult to contribute to the debate on how the fish tree of life might be shaped by extinction. Here, we combine COI sequences and taxonomic information to assemble a fully sampled phylogeny of the African Cyprinidae and investigate whether we might lose more phylogenetic diversity (PD) than expected if currently-threatened species go extinct...
March 13, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30817213/non-destructive-dna-extraction-methods-for-entomophagous-insects-with-emphasis-in-biological-control
#8
Alba P Suaste-Dzul, José Manuel Rodríguez-Vélez, Beatriz Rodríguez-Vélez, Hugo Cesar Arredondo-Bernal, Adrien Gallou
One of the major challenges in molecular analysis of arthropods, especially for natural enemies of insect pests, is the intact preservation of the specimens to be integrated into entomological collections. However, most of the DNA extraction protocols involve maceration of the tissue, avoiding the preservation of the original specimen. Two general methods were adapted into non-destructive DNA extraction protocols, DNeasy® Blood & Tissue Kit (A) and the CaCl2 lysis buffer method (B), while the potential of the method with the alkaline lysis buffer (HotSHOT; C) was evaluated for the first time on insect specimens...
February 28, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30807237/molecular-analysis-of-anthocyanin-biosynthesis-related-genes-reveal-bott8-associated-with-purple-hypocotyl-of-broccoli-brassica-oleracea-var-italica-l
#9
Md Abdur Rahim, Khandker Shazia Afrin, Hee-Jeong Jung, Hoy-Taek Kim, Jong-In Park, Yoonkang Hur, Ill Sup Nou
Broccoli (Brassica oleracea var. italica L.) is a highly nutritious vegetable that typically forms pure green or purple florets. However, green broccoli florets sometimes accumulate slight purplish pigmentation due to environmental factors which reduces the market value. In the present study, we aimed to develop molecular markers to distinguish broccoli genotypes as pure green or purplish floret color at the early seedling stage. Anthocyanins are known to be involved in the purple pigmentation in plants. The purplish broccoli lines were shown to accumulate purple pigmentation in the hypocotyls of very young seedlings; therefore, the expression profiles of the structural and regulatory genes of anthocyanin biosynthesis were analyzed in the hypocotyls using qRT-PCR...
February 26, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30785785/comparative-karyotype-analysis-among-six-i-ipomoea-i-species-based-on-two-newly-identified-repetitive-sequences
#10
Jianying Sun, Lixuan Yu, Zexi Cai, An Zhang, Weiwei Jin, Yonghua Han, Zongyun Li
Sweet potato is one of the most important crops worldwide; however, basic research in this crop is limited. In this study, we aimed to construct a detailed karyotype of six Ipomoea species (hexaploid Ipomoea batatas and five related species, namely, one tetraploid, I. tabascana and four diploids, I. splendor-sylvae, I. trifida, I. tenuissima, and I. × leucantha) and understand the relationship among these species. Two satellite repeats (viz., Itf_1 and Itf_2) were identified from the diploid I. trifida genome sequence using RepeatExplorer on Galaxy...
February 20, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30779599/comparative-population-genomics-unveils-candidate-genes-for-athletic-performance-in-hanoverians
#11
Hojjat Asadollahpour Nanaei, Ahmad Ayatollahi Mehrgardi, Ali Esmailizadeh
Equine athletes have a genetic heritage that has been evolved for millions of years, which provides an opportunity to study the genetics of locomotion pattern and performance in mammals. The Hanoverian, a breed originating in Germany, is arguably among the most athletic horse breeds, due to its balanced character and beautiful appearance. Here, we compared the whole genomes of Hanoverian with other three horse breeds (Akhal-Teke, Franches-Montagnes and Standardbred), using the fixation index (Fst) and cross-population composite likelihood ratio (XP-CLR) methods for testing the multilocus allele frequency differentiation between populations...
February 19, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30742542/dna-barcoding-of-fish-species-reveals-low-rate-of-package-mislabeling-in-qatar
#12
Kuei-Chiu Chen, Dalia Zakaria, Heba Altarawneh, Gabriala Andrews, Gowrii Saswathy Ganesan, Karen Maria John, Sarah Khan, Heta Ladumor
DNA barcoding technique has made it possible to authenticate various species used for food and medicinal purposes. In the identification of seafood species, studies are concentrated in North America, Europe and Asia. Elsewhere, including countries in the Middle East and North Africa, studies of this sort are scarce. This study focuses on packaged fresh or minimally processed fish fillet available at eight major supermarket chains in Qatar. A cocktail of eight primers attached with M13 tails established for fish species identification was adopted to facilitate PCR and sequencing...
February 11, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30730769/barcoding-the-neotropical-freshwater-fish-fauna-using-a-new-pair-of-universal-coi-primers-with-a-discussion-of-primer-dimers-and-m13-primer-tails
#13
W Bryan Jennings, Piero Angeli Ruschi, Gustavo Andrés Ferraro, Carla Christie Diban Quijada, Ana Cecilia Gomes Silva-Malanski, Francisco Prosdocimi, Paulo Andreas Buckup
Designing primers for DNA barcoding is a significant challenge for the rich Neotropical fish fauna, which is comprised of ~6,000 species. Previously, researchers required multiple pairs of PCR primers or primer cocktails to obtain standard COI (i.e. mitochondrial cytochrome c oxidase subunit I) barcode sequences from assemblages of freshwater fish in this region. To simplify DNA barcoding and metabarcoding studies of Neotropical freshwater fish, we present a new pair of COI primers, which have yielded high quality barcodes across six teleost orders-Characiformes, Cichliformes, Cyprinodontiformes, Gymnotiformes, Siluriformes, and Synbranchiformes-native to South America...
February 7, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30998120/trends-in-dna-barcoding-and-metabarcoding
#14
(no author information available yet)
No abstract text is available yet for this article.
March 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30998119/trends-in-dna-barcoding-and-metabarcoding
#15
Sarah J Adamowicz, James S Boatwright, Frédéric Chain, Brian L Fisher, Ian D Hogg, Florian Leese, Darío A Lijtmaer, Monica Mwale, Amanda M Naaum, Xavier Pochon, Dirk Steinke, John-James Wilson, Susanna Wood, Jianping Xu, Sen Xu, Xin Zhou, Michelle van der Bank
No abstract text is available yet for this article.
March 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30830800/gene-expression-patterns-indicate-that-a-high-fat-high-carbohydrate-diet-causes-mitochondrial-dysfunction-in-fish
#16
Wassana Prisingkorn, Ivan Jakovlić, Shao-Kui Yi, Fang-Yu Deng, Yu-Hua Zhao, Wei-Min Wang
Expensive and unsustainable fishmeal is increasingly being replaced with cheaper lipids and carbohydrates as sources of energy in aquaculture. Although it is known that the excess of lipids and carbohydrates has negative effects on nutrient utilization, growth, metabolic homeostasis, and health of fish, our current understanding of mechanisms behind these effects is limited. To improve the understanding of diet-induced metabolic disorders (both in fish and other vertebrates), we conducted an eight-week high-fat-high-carbohydrate diet feeding trial on blunt snout bream (Megalobrama amblycephala), and studied gene expression changes (transcriptome and qPCR) in the liver...
February 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30673361/biodiversity-assessments-in-the-21st-century-the-potential-of-insect-traps-to-complement-environmental-samples-for-estimating-eukaryotic-and-prokaryotic-diversity-using-high-throughput-dna-metabarcoding
#17
Camila D Ritter, Sibylle Häggqvist, Ilari Sääksjärvi, Dave Karlsson, Muthama Muasya, R Henrik Nilsson, Alexandre Antonelli
The rapid loss of biodiversity, coupled with difficulties in species identification, call for innovative approaches to assess biodiversity. Insects make up a substantial proportion of extant diversity and play fundamental roles in any given ecosystem. To complement morphological species identification, new techniques such as metabarcoding make it possible to quantify insect diversity and insect-ecosystem interactions through DNA sequencing. Here we examine the potential of bulk insect samples (i.e., containing many non-sorted specimens) to assess prokaryote and eukaryote biodiversity and to complement the taxonomic coverage of soil samples...
January 23, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30649978/genome-based-taxonomic-classification
#18
Bobby Paul, Gunjan Dixit, Thokur Sreepathy Murali, K Satyamoorthy
Bacterial populations are routinely characterized based on the microscopic examination, colony formation and biochemical tests. However, in recent past, bacterial identification, classification and nomenclature have been strongly influenced by genome sequence information. Advances in bioinformatics and growth in genome databases has placed genome-based metadata analysis in the hands of researchers who will require taxonomic experience to resolve intricacies. To achieve this, different tools are now available to quantitatively measure genome relatedness within members of the same species and genome-wide average nucleotide identity (gANI) is one such reliable tool to measure genome similarity...
January 16, 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30707055/forensic-botany-and-forensic-chemistry-working-together-application-of-plant-dna-barcoding-as-a-complement-to-forensic-chemistry-a-case-study-in-brazil
#19
Renato T F Paranaiba, Carlos B V Carvalho, Jorge M Freitas, Levy H Fassio, Élvio D Botelho, Diana B J Neves, Ronaldo C Silva, Sérgio M Aguiar
Recently, Brazilian Federal Police used forensic chemistry and forensic botany techniques on a case. Two packets containing fragmented plant matter were seized and sent for forensic analysis. Forensic chemistry, the gold standard for evaluating plant material suspected to contain illicit substances, did not find illicit materials. Gas chromatography coupled mass spectrometry (GC-MS) identified thujone in the botanical material. Thujone is a chemical compound naturally found in many plant species, notably Artemisia absinthium...
January 2019: Genome Génome / Conseil National de Recherches Canada
https://read.qxmd.com/read/30557098/minimalist-barcodes-for-sponges-a-case-study-classifying-african-freshwater-spongillida
#20
Dirk Erpenbeck, Markus Steiner, Astrid Schuster, Martin J Genner, Renata Manconi, Roberto Pronzato, Bernhard Ruthensteiner, Didier Van den Spiegel, Rob Wm van Soest, Gert Wörheide
African sponges, particularly freshwater sponges, are understudied relative to demosponges in most other geographical regions. Freshwater sponges (Spongillida) likely share a common ancestor; however, their evolutionary history, particularly during their radiation into endemic and allegedly cosmopolitan groups, is unclear. Freshwater sponges of at least 58 species of 17 genera and four families are described from Central and Eastern Africa, but the diversity is underestimated due to limited distinguishable morphological features...
December 17, 2018: Genome Génome / Conseil National de Recherches Canada
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