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https://www.readbyqxmd.com/read/29346625/complete-genomic-and-transcriptional-landscape-analysis-using-third-generation-sequencing-a-case-study-of-saccharomyces-cerevisiae-cen-pk113-7d
#1
Piroon Jenjaroenpun, Thidathip Wongsurawat, Rui Pereira, Preecha Patumcharoenpol, David W Ussery, Jens Nielsen, Intawat Nookaew
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29344683/the-root-transcriptome-of-achyranthes-bidentata-and-the-identification-of-the-genes-involved-in-the-replanting-benefit
#2
Yan Hui Yang, Ming Jie Li, Yan Jie Yi, Rui Fang Li, Cheng Dong, Zhong Yi Zhang
The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit...
January 17, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29343235/comparison-of-three-assembly-strategies-for-a-heterozygous-seedless-grapevine-genome-assembly
#3
Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y Fennell
BACKGROUND: De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC)...
January 17, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29341480/cutis-laxa-and-excessive-bone-growth-due-to-de-novo-mutations-in-ptdss1
#4
Juliette Piard, James Lespinasse, Marketa Vlckova, Martin A Mensah, Sorin Iurian, Martina Simandlova, Marcela Malikova, Oliver Bartsch, Massimiliano Rossi, Marion Lenoir, Frédérique Nugues, Stefan Mundlos, Uwe Kornak, Philip Stanier, Sérgio B Sousa, Lionel Van Maldergem
The cutis laxa syndromes are multisystem disorders that share loose redundant inelastic and wrinkled skin as a common hallmark clinical feature. The underlying molecular defects are heterogeneous and 13 different genes have been involved until now, all of them being implicated in elastic fiber assembly. We provide here molecular and clinical characterization of three unrelated patients with a very rare phenotype associating cutis laxa, facial dysmorphism, severe growth retardation, hyperostotic skeletal dysplasia, and intellectual disability...
January 17, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29338812/comprehensive-assessment-of-the-quality-of-salmonella-whole-genome-sequence-data-available-in-public-sequence-databases-using-the-salmonella-in-silico-typing-resource-sistr
#5
James Robertson, Catherine Yoshida, Peter Kruczkiewicz, Celine Nadon, Anil Nichani, Eduardo N Taboada, John Howard Eagles Nash
Public health and food safety institutions around the world are adopting whole genome sequencing (WGS) to replace conventional methods for characterizing Salmonella for use in surveillance and outbreak response. Falling costs and increased throughput of WGS have resulted in an explosion of data, but questions remain as to the reliability and robustness of the data. Due to the critical importance of serovar information to public health, it is essential to have reliable serovar assignments available for all of the Salmonella records...
January 17, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29338057/rna-sequencing-analysis-of-fungi-induced-transcripts-from-the-bamboo-wireworm-melanotus-cribricollis-coleoptera-elateridae-larvae
#6
Bi-Huan Ye, Ya-Bo Zhang, Jin-Ping Shu, Hong Wu, Hao-Jie Wang
Larvae of Melanotus cribricollis, feed on bamboo shoots and roots, causing serious damage to bamboo in Southern China. However, there is currently no effective control measure to limit the population of this underground pest. Previously, a new entomopathogenic fungal strain isolated from M. cribricollis larvae cadavers named Metarhizium pingshaense WP08 showed high pathogenic efficacy indoors, indicated that the fungus could be used as a bio-control measure. So far, the genetic backgrounds of both M. cribricollis and M...
2018: PloS One
https://www.readbyqxmd.com/read/29337410/transcriptomic-insight-into-pathogenicity-associated-factors-of-conidiobolus-obscurus-an-obligate-aphid-pathogenic-fungus-from-entomopthoromycota
#7
Jianghong Wang, Xiang Zhou, Kai Guo, Xinqi Zhang, Haipin Lin, Cristian Montalva
BACKGROUND: Conidiobolus obscurus is a wide spread fungal entomopathogen holding aphid biocontrol potential. This study focuses on a de novo transcriptomic analysis of C. obscurus. RESULTS: A number of pathogenicity-associated factors were annotated for the first time from the assembled 17,231 fungal unigenes, including those encoding subtilisin-like proteolytic enzymes (Pr1s), trypsin-like proteases, metalloproteases, carboxypeptidases and endochitinases. Many of these genes were transcriptionally up-regulated by at least twofold in mycotized cadavers compared to the in vitro fungal cultures...
January 16, 2018: Pest Management Science
https://www.readbyqxmd.com/read/29337313/complete-genome-sequencing-of-the-luminescent-bacterium-vibrio-qinghaiensis-sp-q67-using-pacbio-technology
#8
Liang Gong, Yu Wu, Qijie Jian, Chunxiao Yin, Taotao Li, Vijai Kumar Gupta, Xuewu Duan, Yueming Jiang
Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands...
January 16, 2018: Scientific Data
https://www.readbyqxmd.com/read/29336997/modulation-of-nonessential-amino-acid-biosynthetic-pathways-in-virulent-hessian-fly-larvae-mayetiola-destructor-feeding-on-susceptible-host-wheat-triticum-aestivum
#9
Subhashree Subramanyam, Jacob T Shreve, Jill A Nemacheck, Alisha J Johnson, Brandi Schemerhorn, Richard H Shukle, Christie E Williams
Compatible interactions between wheat (Triticum aestivum), and its dipteran pest Hessian fly (Hf, Mayetiola destructor) result in successful establishment of larval feeding sites rendering the host plant susceptible. Virulent larvae employ an effector-based feeding strategy to reprogram the host physiology resulting in formation of a protein- and sugar-rich nutritive tissue beneficial to developing larvae. Previous studies documented increased levels of nonessential amino acids (NAA; that need not be received through insect diet) in the susceptible wheat in response to larval feeding, suggesting importance of plant-derived NAA in larval nutrition...
January 11, 2018: Journal of Insect Physiology
https://www.readbyqxmd.com/read/29335547/pan-genome-analysis-highlights-the-extent-of-genomic-variation-in-cultivated-and-wild-rice
#10
Qiang Zhao, Qi Feng, Hengyun Lu, Yan Li, Ahong Wang, Qilin Tian, Qilin Zhan, Yiqi Lu, Lei Zhang, Tao Huang, Yongchun Wang, Danlin Fan, Yan Zhao, Ziqun Wang, Congcong Zhou, Jiaying Chen, Chuanrang Zhu, Wenjun Li, Qijun Weng, Qun Xu, Zi-Xuan Wang, Xinghua Wei, Bin Han, Xuehui Huang
The rich genetic diversity in Oryza sativa and Oryza rufipogon serves as the main sources in rice breeding. Large-scale resequencing has been undertaken to discover allelic variants in rice, but much of the information for genetic variation is often lost by direct mapping of short sequence reads onto the O. sativa japonica Nipponbare reference genome. Here we constructed a pan-genome dataset of the O. sativa-O. rufipogon species complex through deep sequencing and de novo assembly of 66 divergent accessions...
January 15, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29335419/a-global-view-of-transcriptome-dynamics-during-male-floral-bud-development-in-populus-tomentosa
#11
Zhong Chen, Pian Rao, Xiaoyu Yang, Xiaoxing Su, Tianyun Zhao, Kai Gao, Xiong Yang, Xinmin An
To obtain a comprehensive overview of the dynamic transcriptome during male floral bud development in Populus tomentosa, high-throughput RNA-seq was conducted during eight flowering-related stages. Among the 109,212 de novo assembled unigenes, 6,959 were differentially expressed during the eight stages. The overrepresented classed of genes identified by Gene Ontology (GO) enrichment included 'response to environmental stimuli' and 'plant-type spore development'. One-third of the differentially expressed genes were transcription factors (TFs)...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29332190/transcriptomic-profiling-of-developing-fiber-in-levant-cotton-gossypium-herbaceum-l
#12
Mithil J Parekh, Sushil Kumar, Ranbir S Fougat, Harshvardhan N Zala, Ramesh J Pandit
Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but produce coarse lint. This undesirable characteristic strongly needs the knowledge of fiber development at molecular basis. The present study reported the transcriptome sequence of the developing fiber of G...
January 13, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29330441/pathway-design-using-de-novo-steps-through-uncharted-biochemical-spaces
#13
Akhil Kumar, Lin Wang, Chiam Yu Ng, Costas D Maranas
Existing retrosynthesis tools generally traverse production routes from a source to a sink metabolite using known enzymes or de novo steps. Generally, important considerations such as blending known transformations with putative steps, complexity of pathway topology, mass conservation, cofactor balance, thermodynamic feasibility, microbial chassis selection, and cost are largely dealt with in a posteriori fashion. The computational procedure we present here designs bioconversion routes while simultaneously considering any combination of the aforementioned design criteria...
January 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29329601/nicotiana-glauca-whole-genome-investigation-for-ct-dna-study
#14
Galina Khafizova, Pavel Dobrynin, Dmitrii Polev, Tatiana Matveeva
OBJECTIVE: Nicotiana glauca (tree tobacco) is a naturally transgenic plant, containing sequences acquired from Agrobacterium rhizogenes by horizontal gene transfer. Besides, N. glauca contains a wide profile of alkaloids of medical interest. DATA DESCRIPTION: We report a high-depth sequencing and de novo assembly of N. glauca full genome and analysis of genome elements with bacterial origin. The draft genome assembly is 3.2 Gb, with N50 size of 31.1 kbp. Comparative analysis confirmed the presence of single, previously described gT insertion...
January 12, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29329292/transcriptome-profiling-with-focus-on-potential-key-genes-for-wing-development-and-evolution-in-megaloprepus-caerulatus-the-damselfly-species-with-the-world-s-largest-wings
#15
Wiebke Feindt, Sara J Oppenheim, Robert DeSalle, Paul Z Goldstein, Heike Hadrys
The evolution, development and coloration of insect wings remains a puzzling subject in evolutionary research. In basal flying insects such as Odonata, genomic research regarding bauplan evolution is still rare. Here we focus on the world's largest odonate species-the "forest giant" Megaloprepus caerulatus, to explore its potential for looking deeper into the development and evolution of wings. A recently discovered cryptic species complex in this genus previously considered monotypic is characterized by morphological differences in wing shape and color patterns...
2018: PloS One
https://www.readbyqxmd.com/read/29326217/draft-genome-sequences-of-bifidobacterium-strains-n4g05-and-n5g01-isolated-from-the-human-vaginal-microbiome
#16
Aline C Freitas, Janet E Hill
We report here the draft genome sequences of Bifidobacterium strains N4G05 and N5G01, isolated from the human vaginal microbiome. Genome sequences were obtained by de novo assembly from high-quality reads. Both strains were closely related to Bifidobacterium kashiwanohense based on barcode marker sequences and average nucleotide identity analysis.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29325570/de-novo-assembly-of-the-complex-genome-of-nippostrongylus-brasiliensis-using-minion-long-reads
#17
David Eccles, Jodie Chandler, Mali Camberis, Bernard Henrissat, Sergey Koren, Graham Le Gros, Jonathan J Ewbank
BACKGROUND: Eukaryotic genome assembly remains a challenge in part due to the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing methods. At the same time, many nematodes are parasites and some represent a serious threat to human health. There is a pressing need for better molecular characterization of animal and plant parasitic nematodes...
January 11, 2018: BMC Biology
https://www.readbyqxmd.com/read/29325009/efficient-generation-of-complete-sequences-of-mdr-encoding-plasmids-by-rapid-assembly-of-minion-barcoding-sequencing-data
#18
Ruichao Li, Miaomiao Xie, Ning Dong, Dachuan Lin, Xuemei Yang, Marcus Ho Yin Wong, Edward Wai-Chi Chan, Sheng Chen
Background: Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive and time-consuming...
January 9, 2018: GigaScience
https://www.readbyqxmd.com/read/29323185/biogenesis-of-podosome-rosettes-through-fission
#19
Szu-Lin Kuo, Chien-Lin Chen, Yi-Ru Pan, Wen-Tai Chiu, Hong-Chen Chen
Podosomes are dynamic actin-based membrane protrusions that are important for extracellular matrix degradation and invasive cell motility. Individual podosomes are often found to organize into large rosette-like structures in some types of cells, such as osteoclasts, endothelial cells, Src-transformed fibroblasts, and certain highly invasive cancer cells. In this study, we show that new podosome rosettes arise through one of two mechanisms; de novo assembly or fission of a pre-existing podosome rosette in Src-transformed fibroblasts...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321980/transcriptome-sequencing-and-de-novo-assembly-in-arecanut-areca-catechu-l-elucidates-the-secondary-metabolite-pathway-genes
#20
Ramaswamy Manimekalai, Smita Nair, A Naganeeswaran, Anitha Karun, Suresh Malhotra, V Hubbali
Areca catechu L. belongs to the Arecaceae family which comprises many economically important palms. The palm is a source of alkaloids and carotenoids. The lack of ample genetic information in public databases has been a constraint for the genetic improvement of arecanut. To gain molecular insight into the palm, high throughput RNA sequencing and de novo assembly of arecanut leaf transcriptome was undertaken in the present study. A total 56,321,907 paired end reads of 101 bp length consisting of 11.343 Gb nucleotides were generated...
March 2018: Biotechnology Reports
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