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Genome Génome / Conseil National de Recherches Canada

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https://www.readbyqxmd.com/read/30227080/detection-of-large-sequence-insertions-by-a-hybrid-approach-that-combine-i-de-novo-i-assembly-and-resequencing-of-medium-coverage-genome-sequences
#1
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 (<i>Glycine soja</i>) genotypes, we designed a hybrid approach combining <i>de novo </i>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-i-saguinus-midas-i-compared-to-other-callitrichinae-monkeys
#2
Roscoe Stanyon, Dorotea Giusti, Naiara Pereira de Araújo, Francesca Bigoni, Marta Svartman
Here we present, for the first time, the complete chromosome painting map of <i>Saguinus midas</i>, 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: <i>Leontopithecus rosalia</i>, <i>Callithrix geoffroyi</i>, <i>C</i>. <i>penicillata</i> and <i>Mico argentatus</i>...
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
#3
Carlos Lopez-Vaamonde, Lucas Sire, Bruno Rasmussen, Rodolphe Rougerie, Christian Wieser, Allaoui Ahamadi, 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...
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
#4
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
#5
Ilze Skujina, Clare Winton, Matthew Hegarty, Robert McMahon, Deborah Nash, Mina C G Davies Morel, Neil 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 4 pony breeds native to the British Isles, including 2 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
#6
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
#7
Yingzhen Wang, Jiahong Lv, Dan Chen, Jun Zhang, Kaijie Qi, Rui Cheng, Huping Zhang, Shao-Ling Zhang
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. The results of phylogenetic analysis showed that PbrKT/HAK/KUP genes were clustered into three major groups (Groups I-III). Among the 20 PbrKT/HAK/KUP genes, 18 were mapped to nine chromosomes and two to scaffolds. Four WGD/segmental gene pairs have been identified, indicating that WGD/segmental duplicationmay have contributed to the expansion of KT/HAK/KUP family in pear...
August 21, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30092656/characterization-of-gata-gene-family-in-vitis-vinifera-genome-wide-analysis-expression-profiles-and-involvement-in-light-and-phytohormone-response
#8
Zhan Zhang, Chong Ren, Luming Zou, Yi Wang, Shaohua Li, Zhenchang Liang
The plant GATA family is one of the most important transcription factors involved in light-responsive development, nitrogen metabolism, phytohormone signaling, and source/sink balance. However, the function of the GATA gene is less known in grape (Vitis vinifera L.). In this study, we comprehensively analyzed the GATA family in grape (V. vinifera L.), particularly the phylogenetic evolution, duplication patterns, conserved motifs, gene structures, cis-elements, tissue expression patterns, and predicted function of VvGATA genes in response to abiotic stress...
August 9, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30092654/genome-wide-characterization-and-expression-profiling-of-diacylglycerol-acyltransferase-genes-from-maize
#9
Bowei Yan, Xiaoxuan Xu, Yingnan Gu, Ying Zhao, Xunchao Zhao, Lin He, Changjiang Zhao, Jingyu Xu, Zuotong Li
Diacylglycerol acyltransferase (DGAT) catalyzes the only rate-limiting step in the pathway of plant oil (TAG) biosynthesis and involves in plant development. In this study, five <i>DGAT</i> family members were identified from maize genome database. Phylogenetic analysis classified the ZmDGATs into type-I, II and III clusters, respectively. The conserved functional domain analysis revealed that the proteins encoded by ZmDGAT1s contained the conserved MBOAT domains, while two ZmDGAT2s encoding proteins harbored the LPLAT domains...
August 9, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30075091/decoding-ice-plants-challenges-associated-with-barcoding-and-phylogenetics-in-the-diverse-succulent-family-aizoaceae
#10
Robyn Faye Powell, Anthony Richard Magee, James Stephen Boatwright
Aizoaceae is the largest succulent plant family in the world, including in excess of 1800 species. Despite its richness, a large proportion of its taxa are listed as data deficient and it has been identified as the top priority for taxonomic research in South Africa. Limitations to accurate identification of taxa in the family may be partly attributed to the degree of technical knowledge required to identify taxa in the Aizoaceae. DNA barcoding may provide an alternative method of identification; however, the suitability of commonly-used gene regions has not been tested in the family...
August 3, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30075086/genome-wide-survey-characterization-and-expression-analysis-of-ring-finger-protein-genes-in-brassica-oleracea-and-their-syntenic-comparison-to-brassica-rapa-and-arabidopsis-thaliana
#11
Yan-Qing Yang, Yun-Hai Lu
The ubiquitin-mediated post-translational regulatory pathway regulates a broad range of cell functions in all eukaryotes. It requires the involvement of a large number of E3 ligases, of which more than one third belongs to the RING protein family as in Arabidopsis thaliana. In this study, a total of 756 RING domains in 734 predicted proteins were identified in Brassica oleracea. Their encoding genes were characterized by RING domain type, additional domain, and expression pattern, and mapped on the nine chromosomes of B...
September 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30067086/fish-analysis-of-zanthoxylum-armatum-based-on-oligonucleotides-for-5s-rdna-and-gaa-6
#12
Xiaomei Luo, Juncheng Liu, Jingyan Wang, Wei Gong, Liang Chen, Wenlin Wan
Fluorescence in situ hybridization (FISH) using oligonucleotide probes for (GAA)6 (18 bp) and ribosomal DNA (rDNA) (5S rDNA, 41 bp) was applied to analyse Zanthoxylum armatum. (GAA)6 loci were detected on the pericentromeric regions of five chromosome pairs, and 5S rDNA loci were also detected on the pericentromeric regions of another two chromosome pairs. The densities and locations of (GAA)6 and 5S rDNA signals varied between individual chromosomes. High-intensity (GAA)6 signals were detected at the centromeres of two large and two smaller metacentric chromosomes...
September 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30067084/organization-and-evolution-of-two-repetitive-sequences-18-24j-and-12-13p-in-the-genome-of-chenopodium-amaranthaceae
#13
Maja Orzechowska, Maciej Majka, Hanna Weiss-Schneeweiss, Ales Kovařík, Natalia Borowska-Zuchowska, Bozena Kolano
The abundance and chromosomal organization of two repetitive sequences named 12-13P and 18-24J were analyzed in 24 diploid and nine polyploid species of Chenopodium s.l., with special attention to Chenopodium s.s. Both sequences were predominantly present in species of Chenopodium s.s.; however, differences in the amplification levels were observed among the species. The 12-13P repeat was highly amplified in all of the analyzed Eurasian species, whereas the American diploids showed a marked variation in the amplification levels...
September 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30067072/genome-wide-identification-and-expression-analysis-of-the-spl-gene-family-in-woodland-strawberry-fragaria-vesca
#14
Jin-Song Xiong, Dan Zheng, Hong-Yu Zhu, Jian-Qiu Chen, Ran Na, Zong-Ming Cheng
SQUAMOSA promoter-binding protein-like (SPL) is a class of plant-specific transcription factors that play critical roles in regulating plant growth and development. However, little systematic research on SPL genes has been conducted in strawberry. In this study, 14 SPL genes were identified in the genome of woodland strawberry (Fragaria vesca), one of the model plants of the family Rosaceae. Chromosome localization analysis indicated that the 14 FvSPL genes were unevenly distributed on six chromosomes. Phylogenetic analysis indicated that the FvSPL proteins could be clustered into six groups (G1 to G6)...
September 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30001499/intraspecific-mitogenomics-of-three-marine-species-at-risk-atlantic-spotted-and-northern-wolffish-anarhichas-spp
#15
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...
September 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
#16
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 314 952 000 000 bp of raw data. The alignment rate of all the samples was between 98...
September 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29962237/variation-and-diversity-of-the-breakpoint-sequences-on-4al-for-the-4al-5al-translocation-in-triticum
#17
Wei Luo, Nana Qin, Yang Mu, Huaping Tang, Mei Deng, Yaxi Liu, Guangdeng Chen, Qiantao Jiang, Guoyue Chen, Yuming Wei, Youliang Zheng, Xiujin Lan, Jian Ma
The translocation of 4AL/5AL in Triticum, which occurred before the differentiation of T. urartu and einkorn, is an important chromosomal rearrangement. Recently, the first identification of breakpoint sequence on 4AL for this translocation provides the opportunity to analyze the variation and diversity of breakpoints 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 their lengths, which ranged from 2009 to 2552 bp...
September 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
#18
Jing-Hao Jin, Min Wang, Huai-Xia Zhang, Abid Khan, Ai-Min Wei, De-Xu Luo, Zhen-Hui Gong
The AP2/ERF family is one of the largest transcription factor families in the plant kingdom. AP2/ERF genes contributing to various processes including plant growth, development, and response to various stresses have been identified. In this study, 175 putative AP2/ERF genes were identified in the latest pepper genome database and classified into AP2, RAV, ERF, and Soloist subfamilies. Their chromosomal localization, gene structure, conserved motif, cis-acting elements within the promoter region, and subcellular locations were analyzed...
September 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
#19
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 mandarin (Citrus reticulata Blanco '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 and seedless Ponkan (727 singlets and 364 contigs), which mainly governed catalytic activity, transferase activity, and oxygen binding...
August 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29958091/horizontal-transfers-of-ltr-retrotransposons-in-seven-species-of-rosales
#20
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 species of Rosales 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...
August 2018: Genome Génome / Conseil National de Recherches Canada
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