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Genome Génome / Conseil National de Recherches Canada

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https://www.readbyqxmd.com/read/30398899/dna-barcoding-reveals-insect-diversity-in-the-mangrove-ecosystems-of-the-hainan-island-china
#1
Lu Liu, Zixiao Guo, Cairong Zhong, Suhua Shi
Insect diversity is an indicator of environmental conditions. Frequent outbreaks of mangrove pests have threatened the fragile mangrove ecosystem in China and the sustainable utilization of mangrove resources. The understanding of mangrove pests as well as a fundamental knowledge of insect diversity in mangrove forests in China has been hindered by the difficulty of morphological species delimitation because captured insect specimens are either larvae or incompletely-preserved adults. DNA barcoding technology uses only a small amount of DNA to conduct species identification...
November 6, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30395487/transcriptomic-characterization-elucidates-a-signaling-network-that-controls-antler-growth
#2
Baojin Yao, Mei Zhang, Meixin Liu, Yuxin Liu, Yaozhong Hu, Yu Zhao
Deer antlers are amazing appendages with the fastest growth rate among mammalian organs. Antler growth is driven by the growth center through a modified endochondral ossification process. Thus, identification of signaling pathways functioning in antler growth center would help us to uncover the underlying molecular mechanism of rapid antler growth. Furthermore, exploring and dissecting the molecular mechanism that regulates antler growth is extremely important and helpful for identifying methods to enhance long bone growth and treat cartilage- and bone-related diseases...
November 5, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30388379/dna-barcoding-of-i-bacopa-i-species-coupled-with-high-resolution-melting-analysis
#3
Chayapol Tungphatthong, Jutharat Somnuek, Thatree Phadungcharoen, Kornkanok Ingkaninan, Jessada Denduangboripant, Suchada Sukrong
In Thailand, there are three species of<i> Bacopa</i>, namely, <i>B. monnieri</i>, <i>B. caroliniana</i> and <i>B. floribunda</i>. Among these <i>Bacopa</i> species, <i>B. monnieri</i> is the only medicinal species used for the treatment of cognitive impairment and improvement of cognitive abilities because of its bioactive constituents, bacoside A and B. However, due to the similar characteristics of plants, it is difficult to differentiate among related species, resulting in confusion during identification...
November 2, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30365918/barcoding-of-parasitoid-wasps-braconidae-and-chalcidoidea-associated-with-wild-and-cultivated-olives-in-the-western-cape-of-south-africa
#4
Chanté Powell, Virgilio Caleca, Martina Sinno, Michaela van Staden, Simon van Noort, Clint Rhode, Elleunorah Allsopp, Barbara van Asch
Wild and cultivated olives harbor and share a diversity of insects, some of which are considered agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the Western Cape Province of South Africa, no comprehensive study has been performed in the region in the molecular era...
October 26, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30365909/dna-barcode-data-reveal-biogeographic-trends-in-arctic-non-biting-midges
#5
Torbjørn Ekrem, Elisabeth Stur, Matthew G Orton, Sarah J Adamowicz
Chironomid flies (non-biting midges) are among the most abundant and diverse animals in Arctic regions, but detailed analyses of species distributions and biogeographical patterns are hampered by challenging taxonomy and reliance on morphology for species-level identification. Here we take advantage of available DNA barcode data of Arctic Chironomidae in BOLD to analyse similarities in species distributions across a northern Nearctic - West Palearctic gradient. Using more than 260 thousand barcodes representing 4,666 BINs (Barcode Index Numbers) and 826 named species (some with interim names) from a combination of public and novel data, we show that the Greenland chironomid fauna shows affinities to both the Nearctic and the West Palearctic regions...
October 26, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30365901/comparative-analysis-of-swallowtail-transcriptomes-suggests-molecular-determinants-for-speciation-and-adaptation
#6
Qian Cong, Nick Grishin
Genetic determinants of speciation in closely related species are poorly understood. We sequenced and analyzed transcriptomes of swallowtail butterflies Heraclides cresphontes (northeastern species) and Heraclides rumiko (southwestern species), a pair of mostly allopatric sister species whose distribution ranges overlap narrowly in central Texas. We found that the two swallowtails confidently differ (Fst > 0.5 for both species) in about 5% of genes, similarly to the divergence in another pair of swallowtail species Pterourus glaucus (southern species) and Pterourus canadensis (northern species)...
October 26, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30354691/functional-characterization-of-a-reproductive-tissue-specific-promoter-from-eucalyptus-camaldulensis
#7
Boby Unnikrishnan, Gurumurthy Demalapura Shankaranarayana
SWEET proteins are essential for the maintenance of nectar production, seed and pollen development in plants. Sequence similarity search in Eucalyptus genome resulted in 52 putative genes from SWEET gene family. Expression of two selected SWEET family genes namely EcSWEET2 and EcSWEET5 were analyzed in vegetative and reproductive tissues of Eucalyptus camaldulensis. Expression of EcSWEET5 was specific to male reproductive tissues and transcripts were detected only at certain stages of flower development. Tobacco Rattle Virus-mediated suppression of EcSWEET5 resulted in significant reduction in pollen germination percentage in Nicotiana benthamiana with no adverse effect on vegetative growth...
October 24, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30347172/phylogenetically-diverse-native-systems-are-more-resistant-to-invasive-plant-species-on-robben-island-south-africa
#8
Kowiyou Yessoufou, Simeon Bezeng Bezeng, Orou Gaoue, Thato Silindile Bengu, Michelle VAN DER Bank
Alien invasive species are problematic both economically and ecologically, particularly on islands. As such, understanding how they interact with their environment is necessary to inform invasive species management. Here, we ask the following questions: What are the main functional traits that correlate with invasion success of alien plants on Robben Island? How does phylogenetic structure shape biotic interactions on the island? Using multiple approaches to explore these questions, we found that alien invasive species flower later during the year and for longer period, although flowering phenology was sensitive to alternative starting date...
October 22, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30312548/challenges-for-assessing-vertebrate-diversity-in-turbid-saharan-water-bodies-using-environmental-dna
#9
Bastian Egeter, Sara Peixoto, José Carlos Brito, Simon Jarman, Pamela Puppo, Guillermo Velo-Antón
The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful tool for species detection and is being increasingly used to conduct biodiversity assessments. However, there are a number of difficulties with sampling eDNA from such turbid water-bodies and it is often not feasible to rely on electrical tools in remote desert environments. We trialled a manually-powered filtering method in Mauritania, using pre-filtration to circumvent problems posed by turbid water in remote arid areas...
October 12, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30278148/considerations-for-incorporating-real-time-pcr-assays-into-routine-marine-biosecurity-surveillance-programmes-a-case-study-targeting-the-mediterranean-fanworm-sabella-spallanzanii-and-club-tunicate-styela-clava
#10
Susanna Amy Wood, Xavier Pochon, Witold Ming, Ulla von Ammon, Chris Woods, Megan Carter, Matt Smith, Graeme J Inglis, Anastasija Zaiko
Molecular techniques may provide effective tools to enhance marine biosecurity surveillance. Prior to routine implementation, evidence-based consideration of their benefits and limitations is needed. In this study, we assessed the efficiency and practicality of visual diver surveys and real-time PCR assays (targeting DNA and RNA) for detecting two marine invasive species whose infestation levels varied between species and location; Sabella spallanzanii and Styela clava. Filtered water samples (n=171) were collected in parallel with dive surveys at two locations as part of the New Zealand Marine High Risk Site Surveillance programme: Nelson Harbour (27 sites) and Waitemata Harbour (30 sites)...
October 2, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30278147/characterization-and-comparison-of-poorly-known-moth-communities-through-dna-barcoding-in-two-afrotropical-environments-in-gabon
#11
Sylvain Delabye, Rodolphe Rougerie, Sandrine M Bayendi Loudit, Myrianne Andeime-Eyene, Evgeny V Zakharov, Jeremy R deWaard, Paul D N Hebert, Roger Kamgang, Philippe Le-Gall, Carlos Lopez-Vaamonde, Jacques-François Mavoungou, Ghislain Moussavou, Nicolas Moulin, Richard Oslisly, Nil Rahola, David Sebag, Thibaud Decaëns
Biodiversity research in tropical ecosystems - popularized as the most biodiverse habitats on Earth - often neglects invertebrates, yet representing the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon...
October 2, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30278145/dna-barcoding-of-forensically-important-flies-in-the-western-cape-south-africa
#12
Tenielle Cooke, Kyle Sieghard Kulenkampff, Marise Heyns, Laura Jane Heathfield
Forensic entomology aids the determination of post mortem interval based on arthropods associated with a deceased body. This relies on the accurate identification of insects that visit the body, particularly first colonisers such as Calliphoridae (Diptera). Traditional species identification though morphological keys can be challenging as immature or closely related specimens can look similar. Some of these challenges have been overcome through 'DNA barcoding', which involves the sequencing of informative regions within a species' DNA and comparison to a database of reference sequences...
October 2, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30257096/expedited-assessment-of-terrestrial-arthropod-diversity-by-coupling-malaise-traps-with-dna-barcoding
#13
Jeremy R deWaard, Valerie Levesque-Beaudin, Stephanie L deWaard, Natalia V Ivanova, Jaclyn T A McKeown, Renee Miskie, Suresh Naik, Kate H J Perez, Sujeevan Ratnasingham, Crystal N Sobel, Jayme E Sones, Claudia Steinke, Angela C Telfer, Andrew D Young, Monica R Young, Evgeny V Zakharov, Paul D N Hebert
Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species...
September 26, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30227080/detection-of-large-sequence-insertions-by-a-hybrid-approach-that-combine-de-novo-assembly-and-resequencing-of-medium-coverage-genome-sequences
#14
Taeyoung Lee, Moon Young Kim, Jungmin Ha, Suk-Ha Lee
Large sequence insertion (LSI) is one of the structural variations (SVs) that may cause phenotypic differences in plants. To identify the LSIs using medium-coverage sequencing data of four wild soybean (Glycine soja) genotypes, we designed a hybrid approach combining de novo assembly and read mapping. Total reads and reads with both ends unmapped were independently assembled into "ordinary contigs" and "orphan contigs", respectively, and subjected to pairwise alignment and stringent filtering...
September 18, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30222938/chromosome-painting-of-the-red-handed-tamarin-saguinus-midas-compared-to-other-callitrichinae-monkeys
#15
Roscoe Stanyon, Dorotea Giusti, Naiara Pereira Araújo, Francesca Bigoni, Marta Svartman
Here we present, for the first time, the complete chromosome painting map of Saguinus midas, the red-handed tamarin. Chromosome banding and painting with human chromosome-specific probes were used to compare the karyotype of this species with those of four other Neotropical primates of the subfamily Callitrichinae: Leontopithecus rosalia, Callithrix geoffroyi, C. penicillata, and Mico argentatus. The chromosome painting map of S. midas was identical to that of L. rosalia and other previously studied tamarin species (genera Saguinus and Leontopithecus)...
September 17, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30184444/dna-barcodes-reveal-deeply-neglected-diversity-and-numerous-invasions-of-micromoths-in-madagascar
#16
Carlos Lopez-Vaamonde, Lucas Sire, Bruno Rasmussen, Rodolphe Rougerie, Christian Wieser, Allaoui Ahamadi Allaoui, Joël Minet, Jeremy R deWaard, Thibaud Decaëns, David C Lees
Madagascar is a prime evolutionary hotspot globally, but its unique biodiversity is under threat, essentially from anthropogenic disturbance. There is a race against time to describe and protect the Madagascan endangered biota. Here we present a first molecular characterization of the micromoth fauna of Madagascar. We collected 1572 micromoths mainly using light traps in both natural and anthropogenically disturbed habitats in 24 localities across eastern and northwest Madagascar. We also collected 1384 specimens using a Malaise trap in a primary rain forest at Andasibe, eastern Madagascar...
September 5, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30184440/draft-genome-sequence-disease-resistance-genes-and-phenotype-of-a-paenibacillus-terrae-strain-nk3-4-with-the-potential-to-control-plant-diseases
#17
Wen Qing Yu, Gui Ping Zheng, De Wen Qiu, Feng Chao Yan, Wen Zhi Liu, Wan Xue Liu
Paenibacillus terrae NK3-4 is a plant growth-promoting rhizobacterium that may be useful for controlling plant diseases. We conducted a genomic analysis and identified the genes mediating antimicrobial functions. Additionally, an extracellular antifungal protein component was isolated and identified. The draft genome sequence was assembled into 54 contigs, with 5,458,568 bp and a G+C content of 47%. Moreover, 4,690,015 bp encoded 5,090 proteins, 7 rRNAs, and 54 tRNAs. Forty-four genes involved in antimicrobial functions were detected...
September 5, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30184439/detecting-genetic-regions-associated-with-height-in-the-native-ponies-of-the-british-isles-by-using-high-density-snp-genotyping
#18
Ilze Skujina, Clare L Winton, Matthew J Hegarty, Robert McMahon, Deborah M Nash, Mina C G Davies Morel, Neil R McEwan
Height is an important characteristic in the equine industry although little is known about its genetic control in native British breeds of ponies. This study aimed to map QTL data with the withers height in four pony breeds native to the British Isles, including two different sections within Welsh Cobs. In this study, a genome-wide analysis approach using the Illumina EquineSNP50 Infinium BeadChip was applied to 105 ponies and cobs. Analysis identified 222 highly significant height-associated SNPs (P ≤ 10-5 ), among which three SNPs on ECA9 have also been previously reported elsewhere...
September 5, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30134125/development-of-dna-markers-for-slmlo1-1-a-new-mutant-allele-of-the-powdery-mildew-resistance-gene-slmlo1-in-tomato-solanum-lycopersicum
#19
Daeun Kim, Bingkui Jin, Byoung Il Je, Youngmi Choi, Byung Sup Kim, Hee-Jeong Jung, Ill-Sup Nou, Younghoon Park
Reductions in growth and quality due to powdery mildew (PM) disease cause significant economic losses in tomato production. Oidium neolycopersici was identified as the fungal species responsible for tomato PM disease in South Korea in the present study, based on morphological and internal transcribed spacer DNA sequence analyses of PM samples collected from two remote regions (Muju and Miryang). The genes involved in resistance to this pathogen in the tomato accession 'KNU-12' (Solanum lycopersicum var. cerasiforme) were evaluated, and the inheritance of PM resistance in 'KNU-12' was found to be conferred via simple Mendelian inheritance of a mutant allele of the PM susceptibility locus Ol-2 (SlMlo1)...
August 22, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30130425/genome-wide-identification-evolution-and-expression-analysis-of-the-kt-hak-kup-family-in-pear
#20
Yingzhen Wang, Jiahong Lü, Dan Chen, Jun Zhang, Kaijie Qi, Rui Cheng, Huping Zhang, Shaoling Zhang
The K+ transporter/high-affinity K+ /K+ uptake (KT/HAK/KUP) family, as one of the largest K+ transporter families in higher plants, plays an essential role in plant growth, mineral element absorption, salt stress tolerance, and other physiological processes. However, little is known about this family in pear (Pyrus). Here, we identified 20 K+ transporter genes in pear (P. bretschneideri) using genome-wide analysis. Their gene structure, chromosomal distribution, conserved motifs, phylogenetics, duplication events, and expression patterns were also examined...
August 21, 2018: Genome Génome / Conseil National de Recherches Canada
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