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Genome Génome / Conseil National de Recherches Canada

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https://www.readbyqxmd.com/read/30001499/intraspecific-mitogenomics-of-three-marine-species-at-risk-atlantic-spotted-and-northern-wolffish-anarhichas-spp
#1
Linda A Lait, Steven M Carr
High-resolution mitogenomics of within-species relationships can answer such phylogeographic questions as how species survived the most recent glaciation, as well as identify contemporary factors such as physical barriers, isolation, and gene flow. We examined the mitogenomic population structure of three at-risk species of wolffish: Atlantic (Anarhichas lupus), spotted (A. minor), and northern (A. denticulatus). These species are extensively sympatric across the North Atlantic but exhibit very different life history strategies, a combination that results in concordant and discordant patterns of genetic variation and structure...
July 12, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30001497/whole-genome-resequencing-of-ujumqin-sheep-to-investigate-the-determinants-of-the-multi-vertebral-trait
#2
Shuo Li, Rongsong Luo, Defang Lai, Min Ma, Fei Hao, Xuan Qi, Xu Liu, Dongjun Liu
The Ujumqin sheep is one of the most profitable breeds in China, with unique multi-vertebral characteristics. We performed high-throughput genome resequencing of five multi-vertebral and three non-multi-vertebral sheep in an Ujumqin population. We identified the genomic regions that correlated with the germplasm characteristics to establish the cause of the "multi-vertebral" phenotype in this breed. Sequencing generated a total of 314.952 G of raw data. The alignment rate of all the samples was between 98...
July 12, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29962237/variation-and-diversity-of-the-breakpoint-sequences-on-4al-for-4al-5al-translocation-in-triticum
#3
Wei Luo, Na-Na Qin, Yang Mu, Huaping Tang, Mei Deng, Yaxi Liu, Guangdeng Chen, Qian-Tao Jiang, Guo-Yue Chen, Yuming Wei, Youliang Zheng, Xiu-Jin Lan, Jian Ma
The translocation of 4AL/5AL in Triticum, occurred before the differentiation of T. urartu and einkorn, is an important chromosomal rearrangement incident. Recently the first identification of breakpoint sequence on 4AL for this translocation provides the chance to analyze the variation and diversity of this breakpoint in Triticum. In this study, the breakpoint regions of 52 accessions from 21 species were isolated and further characterized. The sequences were divided into 12 types based on length differences ranging from 2009 to 2552 bp...
July 1, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29958096/genome-wide-identification-of-the-ap2-erf-transcription-factor-family-in-pepper-capsicum-annuum-l
#4
Jing-Hao Jin, Min Wang, Huai-Xia Zhang, Abid Khan, Ai-Min Wei, De-Xu Luo, Zhen-Hui Gong
AP2/ERF family is one of the largest transcription factors family in plant. The AP2/ERF genes have been elucidated participating in various processes including plant growth, development and their responses to various stresses. In this study, 175 putative AP2/ERF genes were identified from the latest pepper genome database, and classified into AP2, RAV, ERF and Soloist subfamilies. Then their chromosomal localization, gene structure, conserved motif, cis-acting elements in the promoter region and subcellular locations were analyzed...
June 29, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29958094/comparative-transcript-profiling-reveals-the-mechanism-of-female-sterility-associated-with-seedless-ponkan-mandarin-citrus-reticulata-blanco
#5
Jinping Xiao, Lanlan Zhang, Fangjuan Fan, Xubo Liu
Seedlessness is a highly desirable trait in citrus varieties. Sterility is the key determination for seedlessness formation. However, the molecular basis for female sterility in seedless mandarin remains unclear. Thus, a seedless Ponkan (Citrus reticulata Blanco cv. Lipeng No. 2) considered the bud mutation of normal seedy Ponkan, was collected to identify candidate genes involved in seedless variation. Suppression subtractive hybridization (SSH) screened 1091 uniESTs related to seedy/seedless Ponkan (727 singlets and 364 contigs), which mainly governed catalytic activity, transferase activity, and oxygen binding...
June 29, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29958091/horizontal-transfers-of-ltr-retrotransposons-in-seven-rosales-species
#6
Fei Hou, Bi Ma, Youchao Xin, Lulu Kuang, Ningjia He
Horizontal transposable element transfer (HTT) events have occurred among a large number of species and play important roles in the composition and evolution of eukaryotic genomes. HTTs are also regarded as effective forces in promoting genomic variation and biological innovation. In the present study, HTT events were identified and analyzed in seven sequenced Rosales species using bioinformatics methods by comparing sequence conservation and Ka/Ks value of reverse transcriptase (RT) with 20 conserved genes, estimating the dating of HTTs, and analyzing the phylogenetic relationships...
June 29, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29957088/genome-of-serratia-nematodiphila-mb307-offers-unique-insights-into-its-diverse-traits
#7
Zarrin Basharat, Faouzia Tanveer, Azra Yasmin, Zabta Khan Shinwari, Tongtong He, Yigang Tong
A pigment-producing species of Serratia was isolated from the rhizosphere of a heavy metal resistant Cannabis sativa plant growing in effluent-affected soil of Hattar Industrial Estate, Haripur, Pakistan. Here, we report the genome sequence of this bacterium, which has been identified as Serratia nematodiphila on the basis of whole genome comparison using the OrthoANI classification scheme. The bacterium exhibited diverse traits, including plant growth promotion, antimicrobial, bioremediation, and pollutant tolerance capabilities including metal tolerance, azo dye degradation, ibuprofen degradation, etc...
June 29, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29920212/genome-scale-metabolic-reconstruction-and-analysis-for-clostridium-kluyveri
#8
Wei Zou, Guangbin Ye, Jing Zhang, Changqing Zhao, Xingxiu Zhao, Kaizheng Zhang
Clostridium kluyveri is an anaerobic microorganism that is well-known for producing butyrate and hexanoate using ethanol and acetate. It is also an important bacterium in the production of Chinese strong flavour baijiu (SFB). To obtain a comprehensive understanding of its metabolism, a curated genome-scale metabolic model (GSMM) of C. kluyveri, including 708 genes, 994 reactions and 804 metabolites, was constructed and named iCKL708. This model was used to simulate the growth of C. kluyveri on different carbon substrates and the results agreed well with the experimental data...
June 19, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29916730/dna-barcoding-reveals-cites-listed-species-among-taiwanese-government-seized-chelonian-specimens
#9
Chia-Hao Chang, Wei-Yu Dai, Ting-Yu Chen, An-Hsin Lee, Hsuan-Yi Hou, Shih-Hui Liu, Nian-Hong Jang-Liaw
Compared to traditional morphological identification, DNA barcoding-molecular identification based on sequencing of a segment of mitochondrial cytochrome c oxidase subunit I (COI)-provides a shortcut to authenticating chelonian identifications. Here, we selected 63 government-seized chelonian specimens deposited at Taipei Zoo for DNA barcoding analysis. DNA barcoding and subsequent phylogenetic analysis successfully authenticated 36 chelonian species, including five that are listed in CITES Appendix I. Approximately 90% (57/63) of the specimens were successfully authenticated by our molecular approach, but lack or error of BOLD reference sequences, biological processes such as hybridization, and uncertain species delimitation all reduced the accuracy of DNA barcoding...
June 19, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29913080/post-glacial-recolonization-of-insular-newfoundland-across-the-strait-of-belle-isle-gave-rise-to-an-endemic-subspecies-of-woodland-caribou-rangifer-tarandus-terranovae-bangs-1896-evidence-from-mtdna-haplotypes
#10
Corinne D Wilkerson, Shane P Mahoney, Steven M Carr
Post-glacial origins of Woodland caribou (Rangifer tarandus ssp) on the island of Newfoundland and their relationship to mainland populations have been uncertain. Sequence analysis of 2,223 bp of the mitochondrial DNA Control Region and Cytochrome b gene from 233 Newfoundland caribou identified 32 haplotypes in four major clades. Comparison with other Nearctic caribou confirms a closer affinity of the basal Clade A with animals from the mainland, and as an outgroup to Clades B, C, & D that are endemic to the island...
June 18, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29883552/longissimus-dorsi-muscle-transcriptomic-analysis-of-yunling-and-chinese-simmental-cattle-differing-in-intramuscular-fat-content-and-fatty-acid-composition
#11
Hui-Min Zhang, H L Xia, H R Jiang, Y J Mao, K X Qu, B Z Huang, Y C Gong, Z P Yang
Intramuscular fat (IMF) content and fatty acid (FA) composition vary significantly across beef cattle breeds, which play important roles in taste and nutritional value. However, the molecular mechanisms underlying these phenotypic differences remain unknown. The present study compared meat quality traits between Yunling cattle and Chinese Simmental cattle. Yunling cattle showed a lower IMF content and proportion of monounsaturated fatty acids (MUFA), as well as higher proportions of saturated fatty acids (SFA), polyunsaturated fatty acids (PUFA) and short chain fatty acids (sc-FA) in the longissimus dorsi (LD) muscle than Chinese Simmental cattle...
June 8, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29883551/genome-survey-sequencing-of-dioscorea-zingiberensis
#12
Wen Zhou, Bin Li, Lin Li, Wen Ma, Yuanchu Liu, Shuchao Feng, Zhezhi Wang
Dioscorea zingiberensis (Dioscoreceae) is the main plant source of diosgenin (steroidal sapogenins), the precursor for the production of steroid hormones in the pharmaceutical industry. Despite its large economic value, genomic information of this Dioscorea genus is currently unavailable. Here, we present an initial survey of the D. zingiberensis genome performed by next-generation sequencing technology together with a genome size investigation inferred by flow cytometry. The whole genome survey of D. zingiberensis generated 31...
June 8, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29883550/analysis-of-brachypodium-genomes-with-genome-wide-optical-maps
#13
Tingting Zhu, Zhaorong Hu, Juan C Rodriguez, Karin R Deal, Jan Dvorak, John P Vogel, Zhiyong Liu, Ming-Cheng Luo
<i>Brachypodium distachyon</i> (n=5) is a diploid and has been widely used as a genetic model. <i>Brachypodium stacei</i> (n=10) and <i>B. hybridum</i> (n=15) are species that are related to <i>B. distachyon</i>, leading to a theory that they are part of a polyploid series based on x = 5. Several lines of evidence suggest that this hypothesis is incorrect and that the genomes of the three taxa may have evolved by a more complex process. We constructed an optical whole-genome BioNano genome (BNG) map for each species and pairwise aligned the maps together...
June 8, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29800531/combined-analysis-of-genome-wide-expression-profiling-of-maize-zea-mays-l-leaves-infected-with-ustilago-maydis
#14
Jinglu Wang, Ying Zhang, Jianjun Du, Xiaodi Pan, Liming Ma, Meng Shao, Xinyu Guo
Although many gene expression profiling studies of maize leaves infected with Ustilago maydis have been published, heterogeneity of the results, caused by various data processing methods and pathogenic strains in different data sets, remains strong. Hence, we conducted a combined analysis of six genome-wide expression data sets of maize leaves infected with five different U. maydis strains by using the same pre-processing and quality control procedures. Six data sets were regrouped into five groups according to pathogenic strain used...
May 25, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29792822/genetic-identity-in-genebanks-application-of-the-solcap-12k-snp-array-in-fingerprinting-and-diversity-analysis-in-the-global-in-trust-potato-collection
#15
David Ellis, Oswaldo Chavez, Joseph Coombs, Julian Soto, Rene Gomez, David Douches, Ana Panta, Rocio Silvestre, Noelle L Anglin
Breeders rely on genetic integrity of material from genebanks; however, admixture, mislabeling, and errors in original data can occur and be detrimental. Two hundred and fifty accessions, representing paired samples consisting of original mother plants and their in vitro counterparts from the cultivated potato collection at the International Potato Center (CIP) were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity of the accessions and evaluate genetic diversity of the potato collection...
May 24, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29787681/higher-anthocyanin-accumulation-associated-with-higher-transcription-levels-of-anthocyanin-biosynthesis-genes-in-spinach
#16
Xiaofeng Cai, Lihao Lin, Xiaoli Wang, Chenxi Xu, Quanhua Wang
Spinach (Spinacia oleracea L.) is widely cultivated as an economically important green leafy vegetable crop for fresh and processing consumption. The red-purple spinach shows abundant anthocyanin accumulation in the leaf and leaf petiole. However, the molecular mechanisms of anthocyanin synthesis in this species are still undetermined. In the present study, we investigated pigment formation and identified anthocyanin biosynthetic genes in spinach. We also analyzed the expression of these genes in purple and green cultivars by quantitative PCR...
May 22, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29738283/identification-of-chromosomes-in-thinopyrum-intermedium-and-wheat-th-intermedium-amphiploids-based-on-multiplex-oligonucleotide-probes
#17
Yu Cui, Yanping Zhang, Juan Qi, Honggang Wang, Richard R-C Wang, Yinguang Bao, Xingfeng Li
Synthesized oligonucleotides (oligos) can be used as effective probes similar to plasmid clones for chromosome identification in fluorescence in situ hybridization (FISH) analysis, making oligo FISH a simpler and more efficient molecular cytogenetic technique for studying plants. In this study, multiplex oligonucleotide probes, including pSc119.2-1, pAs1-4, (GAA)10 , (AAC)6 , and pTa71, were combined and used in FISH to identify chromosomes in common wheat, Thinopyrum intermedium, and a wheat - Th. intermedium amphiploid TE256-1...
May 8, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29733232/genetic-mapping-and-a-new-pcr-based-marker-linked-to-a-dwarfing-gene-in-oat-avena-sativa-l
#18
Jun Zhao, Xueqin Tang, Charlene P Wight, Nicholas A Tinker, Yunfeng Jiang, Honghai Yan, Jian Ma, Xiujin Lan, Yuming Wei, Changzhong Ren, Guoyue Chen, Yuanying Peng
Short straw is a desired trait in cultivated hexaploid oat (Avena sativa L.) for some production environments. Marker-assisted selection, a key tool for achieving this objective, is limited by a lack of mapping data and available markers. Here, bulked-segregant analysis was used to identify PCR-based markers associated with a dwarfing gene. Genetic analysis identified a monogenic dominant inheritance of one dwarfing gene from WAOAT2132, temporarily designated DwWA. A simple sequence repeat (SSR) marker (AME117) that was already available and a new codominant PCR-based marker (bi17) developed by homologous cloning in the present study were both associated with the dwarfing gene...
May 7, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29718690/transcriptome-analysis-reveals-hybridization-induced-genome-shock-in-an-interspecific-f-1-hybrid-from-camellia
#19
Min Zhang, Xin-Kai Liu, Wen Fan, Dan-Feng Yan, Nai-Sheng Zhong, Ji-Yin Gao, Wen-Ju Zhang
The combination of two divergent genomes during hybridization can result in "genome shock". Although genome shock has been reported in the hybrids of some herbaceous plants, the pattern and the principle it follows are far from understood, especially in woody plants. Here, the gene expression patterns were remodeled in the F1 hybrid from the crossing of Camellia azalea × Camellia amplexicaulis compared with the parents as revealed by RNA-seq. About 54.5% of all unigenes were differentially expressed between the F1 hybrid and at least one of the parents, including 6404 unigenes with the highest expression level in the F1 hybrid...
May 2, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29701068/corrigendum-molecular-identification-of-species-of-physalis-solanaceae-using-a-candidate-dna-barcode-the-chloroplast-psba-trnh-intergenic-region
#20
Shangguo Feng, Kaili Jiao, Yujia Zhu, Hongfen Wang, Mengying Jiang, Huizhong Wang
No abstract text is available yet for this article.
April 27, 2018: Genome Génome / Conseil National de Recherches Canada
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