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GigaScience

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https://www.readbyqxmd.com/read/29342277/finding-nemo-hybrid-assembly-with-oxford-nanopore-and-illumina-reads-greatly-improves-the-clownfish-amphiprion-ocellaris-genome-assembly
#1
Mun Hua Tan, Christopher M Austin, Michael P Hammer, Yin Peng Lee, Laurence J Croft, Han Ming Gan
Background: Some of the most widely recognised coral-reef fishes are clownfish or anemonefishes, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes which warrant investigation...
January 12, 2018: GigaScience
https://www.readbyqxmd.com/read/29329394/analysis-of-the%C3%A2-aedes-albopictus%C3%A2-c6-36-genome-provides-insight-into-cell-line-utility-for-viral-propagation
#2
Jason R Miller, Sergey Koren, Kari A Dilley, Vinita Puri, David M Brown, Derek M Harkins, Françoise Thibaud-Nissen, Benjamin Rosen, Xiao-Guang Chen, Zhijian Tu, Igor V Sharakhov, Maria V Sharakhova, Robert Sebra, Timothy B Stockwell, Nicholas H Bergman, Granger G Sutton, Adam M Phillippy, Peter M Piermarini, Reed S Shabman
Background: The 50-year old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome. Results: The C6/36 genome assembly has the largest contig N50 (3...
January 10, 2018: GigaScience
https://www.readbyqxmd.com/read/29325009/efficient-generation-of-complete-sequences-of-mdr-encoding-plasmids-by-rapid-assembly-of-minion-barcoding-sequencing-data
#3
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/29300887/construction-of-the-third-generation-zea-mays-haplotype-map
#4
Robert Bukowski, Xiaosen Guo, Yanli Lu, Cheng Zou, Bing He, Zhengqin Rong, Bo Wang, Dawen Xu, Bicheng Yang, Chuanxiao Xie, Longjiang Fan, Shibin Gao, Xun Xu, Gengyun Zhang, Yingrui Li, Yinping Jiao, John F Doebley, Jeffrey Ross-Ibarra, Anne Lorant, Vince Buffalo, M Cinta Romay, Edward S Buckler, Doreen Ware, Jinsheng Lai, Qi Sun, Yunbi Xu
Background: Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole genome sequencing data from 1,218 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world. Results: A new computational pipeline was set up to process over 12 trillion bp of sequencing data and a set of population genetics filters were applied to identify over 83 million variant sites...
December 30, 2017: GigaScience
https://www.readbyqxmd.com/read/29293960/assessment-of-the-cpas-based-bgiseq-500-platform-for-metagenomic-sequencing
#5
Chao Fang, Huanzi Zhong, Yuxiang Lin, Bin Chen, Mo Han, Huahui Ren, Haorong Lu, Jacob Mayne Luber, Min Xia, Wangsheng Li, Shayna Stein, Xun Xu, Wenwei Zhang, Radoje Drmanac, Jian Wang, Huanming Yang, Lennart Hammarström, Aleksandar David Kostic, Karsten Kristiansen, Junhua Li
Background: More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of two Illumina platforms. Findings: Using fecal samples from 20 healthy individuals we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates...
December 23, 2017: GigaScience
https://www.readbyqxmd.com/read/29272399/ehistology-image-and-annotation-data-from-the-kaufman-atlas-of-mouse-development
#6
Richard A Baldock, Chris Armit
"The Atlas of Mouse Development" by Kaufman is a classic paper atlas that is the de facto standard for the definition of mouse embryo anatomy in the context of standard histological images. We have re-digitised the original H&E stained tissue sections used for the book at high resolution and transferred the hand-drawn annotations to digital form. We have augmented the annotations with standard ontological assignments (EMAPA anatomy) and made the data freely available via an online viewer (eHistology) and from the University of Edinburgh DataShare archive...
December 20, 2017: GigaScience
https://www.readbyqxmd.com/read/29267927/vadir-an-integrated-approach-to-variant-detection-in-rna
#7
Lisa Neums, Seiji Suenaga, Peter Beyerlein, Sara Anders, Devin Koestler, Andrea Mariani, Jeremy Chien
Background: Advances in next-generation DNA sequencing technologies are now enabling detailed characterization of sequence variations in cancer genomes. With whole genome sequencing, variations in coding and non-coding sequences can be discovered. But the cost associated with it is currently limiting its general use in research. Whole exome sequencing is used to characterize sequence variations in coding regions, but the cost associated with capture reagents and biases in capture rate limit its full use in research...
December 18, 2017: GigaScience
https://www.readbyqxmd.com/read/29267855/bs-virus-finder-virus-integration-calling-using-bisulfite-sequencing-data
#8
Shengjie Gao, Xuesong Hu, Fengping Xu, Changduo Gao, Kai Xiong, Xiao Zhao, Haixiao Chen, Shancen Zhao, Mengyao Wang, Dongke Fu, Xiaohui Zhao, Jie Bai, Likai Mao, Bo Li, Song Wu, Jian Wang, Shengbin Li, Huangming Yang, Lars Bolund, Christian N S Pedersen
Background: DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling SNP, DMR, and ASM. Until now, only a few software tools focus on virus integration using bisulfite sequencing data. Findings: We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github...
December 18, 2017: GigaScience
https://www.readbyqxmd.com/read/29267854/draft-genome-of-the-milu-elaphurus-davidianus
#9
Qiang Qiu
No abstract text is available yet for this article.
December 18, 2017: GigaScience
https://www.readbyqxmd.com/read/29267887/snake-fangs-3d-morphological-and-mechanical-analysis-by-microct-simulation-and-physical-compression-testing
#10
Anton du Plessis, Chris Broeckhoven, Stephan G le Roux
This data note provides data from an experimental campaign to analyse the detailed internal and external morphology and mechanical properties of venomous snake fangs. The aim of the experimental campaign was to investigate the evolutionary development of three fang phenotypes and investigate their mechanical behaviour. The study involved the use of load simulations to compare maximum Von Mises stress values, when a load is applied to the tip of the fang. The conclusions of this study have been published elsewhere, but in this data note we extend the analysis, providing morphological comparisons including details such as curvature comparisons, thickness, etc...
December 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29267859/accurate-prediction-of-personalized-olfactory-perception-from-large-scale-chemoinformatic-features
#11
Hongyang Li, Bharat Panwar, Gilbert S Omenn, Yuanfang Guan
Background: The olfactory stimulus-percept problem has been studied for more than a century, yet it is still hard to precisely predict the odor given the large-scale chemoinformatic features of an odorant molecule. A major challenge is that the perceived qualities vary greatly among individuals due to different genetic and cultural backgrounds. Moreover, the combinatorial interactions between multiple odorant receptors and diverse molecules significantly complicate the olfaction prediction...
December 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29267858/hybrid-denovo-a-de-novo-otu-picking-pipeline-integrating-single-end-and-paired-end-16s-sequence-tags
#12
Xianfeng Chen, Stephen Johnson, Patricio Jeraldo, Junwen Wang, Nicholas Chia, Jean-Pierre A Kocher, Jun Chen
Background: Illumina paired-end sequencing has been increasingly popular for 16S rRNA gene-based microbiota profiling. It provides higher phylogenetic resolution than single-end reads due to a longer read length. However, the reverse read (R2) often has significant low base quality and a large proportion of R2s will be discarded after quality control, resulting in a mixture of paired-end and single-end reads. A typical 16S analysis pipeline usually processes either paired-end or single-end reads but not a mixture...
December 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29267857/a-hybrid-hierarchical-genome-assembly-strategy-to-sequence-the-invasive-golden-mussel-limnoperna-fortunei
#13
Marcela Uliano-Silva, Francesco Dondero, Thomas Dan Otto, Igor Costa, Nicholas Costa Barroso Lima, Juliana Alves Americo, Camila Junqueira Mazzoni, Francisco Prosdocimi, Mauro de Freitas Rebelo
Background: For more than 25 years, the golden mussel Limnoperna fortunei has aggressively invaded South American freshwaters, having travelled more than 5,000 km upstream across five countries. Along the way, the golden mussel has outcompeted native species and economically harmed aquaculture, hydroelectric powers, and ship transit. We have sequenced the complete genome of the golden mussel to understand the molecular basis of its invasiveness and search for ways to control it. Findings: We assembled the 1...
December 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29253216/genome-assembly-of-the-pink-ip%C3%A3%C2%AA-handroanthus-impetiginosus-bignoniaceae-a-highly-valued-ecologically-keystone-neotropical-timber-forest-tree
#14
Orzenil Bonfim da Silva-Junior, Dario Grattapaglia, Evandro Novaes, Rosane G Collevatti
Background: Handroanthus impetiginosus (Mart. ex DC.) Mattos is a keystone Neotropical hardwood tree widely distributed in seasonally dry tropical forests of South and Mesoamerica. Regarded as the "new mahogany," it is the second most expensive timber, the most logged species in Brazil, and currently under significant illegal trading pressure. The plant produces large amounts of quinoids, specialized metabolites with documented antitumorous and antibiotic effects. The development of genomic resources is needed to better understand and conserve the diversity of the species, to empower forensic identification of the origin of timber and to identify genes for important metabolic compounds...
December 13, 2017: GigaScience
https://www.readbyqxmd.com/read/29253147/single-molecule-sequencing-and-optical-mapping-yields-an-improved-genome-of-woodland-strawberry-fragaria-vesca-with-chromosome-scale-contiguity
#15
Patrick P Edger, Robert VanBuren, Marivi Colle, Thomas J Poorten, Ching Man Wai, Chad E Niederhuth, Elizabeth I Alger, Shujun Ou, Charlotte B Acharya, Jie Wang, Pete Callow, Michael R McKain, Jinghua Shi, Chad Collier, Zhiyong Xiong, Jeffrey P Mower, Janet P Slovin, Timo Hytönen, Ning Jiang, Kevin L Childs, Steven J Knapp
Background: Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings: Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio)...
December 13, 2017: GigaScience
https://www.readbyqxmd.com/read/29228281/the-intriguing-evolution-of-effect-sizes-in-biomedical-research-over-time-smaller-but-more-often-statistically-significant
#16
Paul Monsarrat, Jean-Noel Vergnes
Background: In medicine, effect sizes (ESs) allow the effects of independent variables (including risk/protective factors, or treatment interventions) on dependent variables (e.g., health outcomes) to be quantified. Given that many public health decisions and health care policies are based on ES estimates, it is important to assess how ESs are used in the biomedical literature and to investigate potential trends in their reporting over time. Results: Through a big data approach, the text mining process automatically extracted 814 120 ESs from 13 322 754 PubMed abstracts...
December 6, 2017: GigaScience
https://www.readbyqxmd.com/read/29220494/soapnuke-a-mapreduce-acceleration-supported-software-for-integrated-quality-control-and-preprocessing-of-high-throughput-sequencing-data
#17
Yuxin Chen, Yongsheng Chen, Chunmei Shi, Zhibo Huang, Yong Zhang, Shengkang Li, Yan Li, Jia Ye, Chang Yu, Zhuo Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Lin Fang, Qiang Chen
Quality Control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures and highly-scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a "QC-Preprocess-QC" workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA (sRNA), Digital Gene Expression (DGE) and metagenomic experiments respectively...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29220491/cnvcaller-highly-efficient-and-widely-applicable-software-for-detecting-copy-number-variations-in-large-populations
#18
Xihong Wang, Zhuqing Zheng, Yudong Cai, Ting Chen, Chao Li, Weiwei Fu, Yu Jiang
Background: The increasing amount of sequencing data available for a wide variety of species can be theoretically used for detecting copy number variations (CNVs) at the population level. However, the growing sample sizes and the divergent complexity of non-human genomes challenge the efficiency and robustness of current human-oriented CNV detection methods. Results: Here, we present CNVcaller, a read-depth method for discovering CNVs in population sequencing data...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29220485/funricegenes-dataset-for-comprehensive-understanding-and-application-of-rice-functional-genes
#19
Wen Yao, Guangwei Li, Yiming Yu, Yidan Ouyang
Background: As a main staple food, rice is also a model plant for functional genomic studies of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement. Findings: We built a comprehensive and accurate dataset of ∼2,800 functionally characterized rice genes and ∼5,000 members of different gene families, by integrating data from available databases and reviewing of every publication on rice functional genomic studies...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29194536/circlncrnanet-an-integrated-web-based-resource-for-mapping-functional-networks-of-long-or-circular-forms-of-non-coding-rnas
#20
Shao-Min Wu, Hsuan Liu, Po-Jung Huang, Ian Yi-Feng Chang, Chi-Ching Lee, Chia-Yu Yang, Wen-Sy Tsai, Bertrand Chin-Ming Tan
Background: Despite their lack of protein-coding potential, lncRNAs and circRNAs have emerged as key determinants in gene regulation, acting to fine-tune transcriptional and signaling output. These non-coding RNA transcripts are known to affect expression of messenger RNAs (mRNAs) via epigenetic and post-transcriptional regulation. Given their widespread target spectrum as well as extensive modes of action, a complete understanding of their biological relevance will depend on integrative analyses of systems data at various levels...
November 29, 2017: GigaScience
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