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https://www.readbyqxmd.com/read/28431028/hybrid-de-novo-genome-assembly-of-the-chinese-herbal-fleabane-erigeron-breviscapus
#1
Jing Yang, Guanghui Zhang, Jing Zhang, Hui Liu, Wei Chen, Xiao Wang, Yahe Li, Yang Dong, Shengchao Yang
Background: The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus , which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant...
April 18, 2017: GigaScience
https://www.readbyqxmd.com/read/28430827/dual-role-of-the-toxoplasma-gondii-clathrin-adaptor-ap1-in-the-sorting-of-rhoptry-and-microneme-proteins-and-in-parasite-division
#2
Kannan Venugopal, Elisabeth Werkmeister, Nicolas Barois, Jean-Michel Saliou, Anais Poncet, Ludovic Huot, Fabien Sindikubwabo, Mohamed Ali Hakimi, Gordon Langsley, Frank Lafont, Sabrina Marion
Toxoplasma gondii possesses a highly polarized secretory system, which efficiently assembles de novo micronemes and rhoptries during parasite replication. These apical secretory organelles release their contents into host cells promoting parasite invasion and survival. Using a CreLox-based inducible knock-out strategy and the ddFKBP over-expression system, we unraveled novel functions of the clathrin adaptor complex TgAP1. First, our data indicate that AP1 in T. gondii likely functions as a conserved heterotetrameric complex composed of the four subunits γ, β, μ1, σ1 and interacts with known regulators of clathrin-mediated vesicular budding such as the unique ENTH-domain containing protein, which we named Epsin-like protein (TgEpsL)...
April 21, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28429320/euglena-gracilis-genome-and-transcriptome-organelles-nuclear-genome-assembly-strategies-and-initial-features
#3
ThankGod Echezona Ebenezer, Mark Carrington, Michael Lebert, Steven Kelly, Mark C Field
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28428989/generation-and-characterization-of-the-blood-transcriptome-of-macaca-thibetana-and-comparative-analysis-with-m-mulatta
#4
Peng Li, Lianming Du, Wujiao Li, Zhenxin Fan, Daiwen Zeng, Hui Chen, Liang Zhou, Yong Yi, Na Yang, Kefeng Dou, Bisong Yue, Jing Li
Transcriptome profiles provide a large transcript sequence data set for genomic study, particularly in organisms that have no accurate genome data published. The Tibetan macaque (Macaca thibetana) is commonly considered to be an endemic species to China and an important animal in biomedical research in the present day. In the present study, we report the de novo assembly and characterization of the blood transcriptome of the Tibetan macaque from three individuals, and we also sequenced the blood transcriptome of the rhesus macaque (Macaca mulatta) for comparison...
April 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28428870/gene-expression-profiling-during-the-embryo-to-larva-transition-in-the-giant-red-sea-urchin-mesocentrotus-franciscanus
#5
Juan Diego Gaitán-Espitia, Gretchen E Hofmann
In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo-to-larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28425468/transcriptome-analysis-of-mango-mangifera-indica-l-fruit-epidermal-peel-to-identify-putative-cuticle-associated-genes
#6
Julio C Tafolla-Arellano, Yi Zheng, Honghe Sun, Chen Jiao, Eliel Ruiz-May, Miguel A Hernández-Oñate, Alberto González-León, Reginaldo Báez-Sañudo, Zhangjun Fei, David Domozych, Jocelyn K C Rose, Martín E Tiznado-Hernández
Mango fruit (Mangifera indica L.) are highly perishable and have a limited shelf life, due to postharvest desiccation and senescence, which limits their global distribution. Recent studies of tomato fruit suggest that these traits are influenced by the expression of genes that are associated with cuticle metabolism. However, studies of these phenomena in mango fruit are limited by the lack of genome-scale data. In order to gain insight into the mango cuticle biogenesis and identify putative cuticle-associated genes, we analyzed the transcriptomes of peels from ripe and overripe mango fruit using RNA-Seq...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424528/elucidation-of-quantitative-structural-diversity-of-remarkable-rearrangement-regions-shufflons-in-inci2-plasmids
#7
Tsuyoshi Sekizuka, Michiko Kawanishi, Mamoru Ohnishi, Ayaka Shima, Kengo Kato, Akifumi Yamashita, Mari Matsui, Satowa Suzuki, Makoto Kuroda
A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424352/chromatin-module-inference-on-cellular-trajectories-identifies-key-transition-points-and-poised-epigenetic-states-in-diverse-developmental-processes
#8
Sushmita Roy, Rupa Sridharan
Changes in chromatin state play important roles in cell fate transitions. Current computational approaches to analyze chromatin modifications across multiple cell types do not model how the cell types are related on a lineage or over time. To overcome this limitation, we have developed a method called CMINT (Chromatin Module INference on Trees), a probabilistic clustering approach to systematically capture chromatin state dynamics across multiple cell types. Compared to existing approaches, CMINT can handle complex lineage topologies, capture higher quality clusters, and reliably detect chromatin transitions between cell types...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28423598/next-generation-mapping-reveals-novel-large-genomic-rearrangements-in-prostate-cancer
#9
Weerachai Jaratlerdsiri, Eva K F Chan, Desiree C Petersen, Claire Yang, Peter I Croucher, M S Riana Bornman, Palak Sheth, Vanessa M Hayes
Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28421378/transcriptome-based-identification-of-the-desiccation-response-genes-in-marine-red-algae-pyropia-tenera-rhodophyta-and-enhancement-of-abiotic-stress-tolerance-by-ptdrg2-in-chlamydomonas
#10
Sungoh Im, Ha-Nul Lee, Hyun Shin Jung, Sunghwan Yang, Eun-Jeong Park, Mi Sook Hwang, Won-Joong Jeong, Dong-Woog Choi
Pyropia tenera (Kjellman) are marine red algae that grow in the intertidal zone and lose more than 90% of water during hibernal low tides every day. In order to identify the desiccation response gene (DRG) in P. tenera, we generated 1,444,210 transcriptome sequences using the 454-FLX platform from the gametophyte under control and desiccation conditions. De novo assembly of the transcriptome reads generated 13,170 contigs, covering about 12 Mbp. We selected 1160 differentially expressed genes (DEGs) in response to desiccation stress based on reads per kilobase per million reads (RPKM) expression values...
April 18, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28420173/transcriptome-sequencing-of-dianthus-spiculifolius-and-analysis-of-the-genes-involved-in-responses-to-combined-cold-and-drought-stress
#11
Aimin Zhou, Hongping Ma, Enhui Liu, Tongtong Jiang, Shuang Feng, Shufang Gong, Jingang Wang
Dianthus spiculifolius, a perennial herbaceous flower and a member of the Caryophyllaceae family, has strong resistance to cold and drought stresses. To explore the transcriptional responses of D. spiculifolius to individual and combined stresses, we performed transcriptome sequencing of seedlings under normal conditions or subjected to cold treatment (CT), simulated drought treatment (DT), or their combination (CTDT). After de novo assembly of the obtained reads, 112,015 unigenes were generated. Analysis of differentially expressed genes (DEGs) showed that 2026, 940, and 2346 genes were up-regulated and 1468, 707, and 1759 were down-regulated in CT, DT, and CTDT samples, respectively...
April 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28419381/enhancing-faba-bean-vicia-faba-l-genome-resources
#12
James W Cooper, Michael H Wilson, Martijn F L Derks, Sandra Smit, Karl J Kunert, Christopher Cullis, Christine H Foyer
Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed on faba bean (cv. Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16 300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly...
April 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28418726/u50-a-new-metric-for-measuring-assembly-output-based-on-non-overlapping-target-specific-contigs
#13
Christina J Castro, Terry Fei Fan Ng
Advances in next-generation sequencing technologies enable routine genome sequencing, generating millions of short reads. A crucial step for full genome analysis is the de novo assembly, and currently, performance of different assembly methods is measured by a metric called N50. However, the N50 value can produce skewed, inaccurate results when complex data are analyzed, especially for viral and microbial datasets. To provide a better assessment of assembly output, we developed a new metric called U50. The U50 identifies unique, target-specific contigs by using a reference genome as baseline, aiming at circumventing some limitations that are inherent to the N50 metric...
April 18, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28418049/systems-chemistry
#14
REVIEW
Gonen Ashkenasy, Thomas M Hermans, Sijbren Otto, Annette F Taylor
Building on our ability to design and synthesise molecules and our understanding of the noncovalent interactions between these molecules, the chemical sciences are currently entering the new territory of Systems Chemistry. This young field aims to develop complex molecular systems showing emergent properties; i.e. properties that go beyond the sum of the characteristics of the individual consituents of the system. This review gives an impression of the state of the art of the field by showing a diverse number of recent highlights, including out-of-equilibrium self-assembly, chemically fuelled molecular motion, compartmentalised chemical networks and designed oscillators...
April 18, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28417189/draft-genome-sequence-of-a-biosurfactant-producing-bacillus-subtilis-umx-103-isolated-from-hydrocarbon-contaminated-soil-in-terengganu-malaysia
#15
Yousri Abdelmutalab Abdelhafiz, Thamilvaani Manaharan, Saharuddin BinMohamad, Amir Feisal Merican
The draft genome here presents the sequence of Bacillus subtilis UMX-103. The bacterial strain was isolated from hydrocarbon-contaminated soil from Terengganu, Malaysia. The whole genome of the bacterium was sequenced using Illumina HiSeq 2000 sequencing platform. The genome was assembled using de novo approach. The genome size of UMX-103 is 4,234,627 bp with 4399 genes comprising 4301 protein-coding genes and 98 RNA genes. The analysis of assembled genes revealed the presence of 25 genes involved in biosurfactant production, where 14 of the genes are related to biosynthesis and 11 of the genes are in the regulation of biosurfactant productions...
April 17, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28414526/assessing-the-impact-of-assemblers-on-virus-detection-in-a-de-novo-metagenomic-analysis-pipeline
#16
Daniel J White, Jing Wang, Richard J Hall
Applying high-throughput sequencing to pathogen discovery is a relatively new field, the objective of which is to find disease-causing agents when little or no background information on disease is available. Key steps in the process are the generation of millions of sequence reads from an infected tissue sample, followed by assembly of these reads into longer, contiguous stretches of nucleotide sequences, and then identification of the contigs by matching them to known databases, such as those stored at GenBank or Ensembl...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28414515/zseq-an-approach-for-preprocessing-next-generation-sequencing-data
#17
Abedalrhman Alkhateeb, Luis Rueda
Next-generation sequencing technology generates a huge number of reads (short sequences), which contain a vast amount of genomic data. The sequencing process, however, comes with artifacts. Preprocessing of sequences is mandatory for further downstream analysis. We present Zseq, a linear method that identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. Zseq finds the complexity of the sequences by counting the number of unique k-mers in each sequence as its corresponding score and also takes into the account other factors such as ambiguous nucleotides or high GC-content percentage in k-mers...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28413781/sequencing-and-de-novo-transcriptome-assembly-of-the-chinese-giant-salamander-andrias-davidianus
#18
Yong Huang, Xiao Chan Gao, Jian Li Xiong, Hong Tao Ren, Xi Hong Sun
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of A. davidianus tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600 bp were obtained, corresponding to 102,659,984 raw reads...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28413758/de-novo-modular-development-of-a-foldameric-protein-protein-interaction-inhibitor-for-separate-hot-spots-a-dynamic-covalent-assembly-approach
#19
Éva Bartus, Zsófia Hegedüs, Edit Wéber, Brigitta Csipak, Gerda Szakonyi, Tamás A Martinek
Protein-protein interactions stabilized by multiple separate hot spots are highly challenging targets for synthetic scaffolds. Surface-mimetic foldamers bearing multiple recognition segments are promising candidate inhibitors. In this work, a modular bottom-up approach is implemented by identifying short foldameric recognition segments that interact with the independent hot spots, and connecting them through dynamic covalent library (DCL) optimization. The independent hot spots of a model target (calmodulin) are mapped with hexameric β-peptide helices using a pull-down assay...
April 2017: ChemistryOpen
https://www.readbyqxmd.com/read/28413162/whole-genome-sequence-of-the-metastatic-pc3-and-lncap-human-prostate-cancer-cell-lines
#20
Inge Seim, Penny L Jeffery, Patrick B Thomas, Colleen C Nelson, Lisa K Chopin
The bone metastasis-derived PC3 and the lymph node metastasis-derived LNCaP prostate cancer cell lines are widely studied, having been described in thousands of publications over the last four decades. Here, we report short-read whole-genome sequencing and de novo assembly of PC3 (ATCC CRL-1435) and LNCaP (clone FGC; ATCC CRL-1740) at ~70X coverage. A known homozygous mutation in TP53 and homozygous loss of PTEN were robustly identified in the PC3 cell line, whereas the LNCaP cell line exhibited a larger number of putative inactivating somatic point and indel mutations (and in particular loss of stop codon events)...
April 16, 2017: G3: Genes—Genomes—Genetics
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