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Yuan-Ming Wu, Jiang Li, Xiang-Sheng Chen
Background: Commonly known as blister beetles or Spanish fly, there are more than 1,500 species in the Meloidae family (Hexapoda: Coleoptera: Tenebrionoidea) that produce the potent defensive blistering agent cantharidin. Cantharidin and its derivatives have been used to treat cancers, such as liver, stomach, lung and esophageal cancers. Hycleus cichorii and Hycleus phaleratus are the most commercially important blister beetles in China due to their ability to biosynthesize this potent vesicant...
February 10, 2018: GigaScience
C Foulon, L Cerliani, S Kinkingnéhun, R Levy, C Rosso, M Urbanski, E Volle, M Thiebaut de Schotten
Background: Patients with brain lesions provide a unique opportunity to understand the functioning of the human mind. However, even when focal, brain lesions have local and remote effects that impact functionally and structurally connected circuits. Similarly, function emerges from the interaction between brain areas rather than their sole activity. For instance, category fluency requires the association between executive, semantic and language production functions. Findings: Here we provide, for the first time, a set of complementary solutions to measure the impact of a given lesion upon the neuronal circuits...
February 8, 2018: GigaScience
Anil S Thanki, Nicola Soranzo, Wilfried Haerty, Robert P Davey
Background: Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level...
February 7, 2018: GigaScience
Audrey Dubourg, Dong Xia, John P Winpenny, Suha Al Naimi, Maha Bouzid, Darren W Sexton, Jonathan M Wastling, Paul R Hunter, Kevin M Tyler
Background: Giardia is a protozoan parasite of public health relevance that causes gastroenteritis in a wide range of hosts. Two genetically distinct lineages (assemblages A and B) are responsible for the human disease. Although it is clear that differences in virulence occur, pathogenesis and virulence of Giardia remains poorly understood. Findings: The genome of Giardia is believed to contain ORFs that could encode as many as 6,000 proteins. By successfully applying quantitative proteomic analyses to the whole parasite and to the supernatants derived from parasite culture of assemblages A and B, we confirm expression of ∼1,600 proteins from each assemblage, the vast majority of which being common to both lineages...
January 29, 2018: GigaScience
Tomáš Lukeš, Jakub Pospíšil, Karel Fliegel, Theo Lasser, Guy M Hagen
Background: Super-resolution single molecule localization microscopy (SMLM) is a method for achieving resolution beyond the classical limit in optical microscopes (approx. 200 nm laterally). Yellow fluorescent protein (YFP) has been used for super-resolution single molecule localization microscopy, but less frequently than other fluorescent probes. Working with YFP in SMLM is a challenge because a lower number of photons are emitted per molecule compared to organic dyes which are more commonly used...
January 19, 2018: GigaScience
Dijun Chen, Rongli Shi, Jean-Michel Pape, Kerstin Neumann, Daniel Arend, Andreas Graner, Ming Chen, Christian Klukas
Background: Image-based high-throughput phenotyping technologies have been rapidly developed in plant science recently and they provide a great potential to gain more valuable information than traditionally destructive methods. Predicting plant biomass is regarded as a key purpose for plant breeders and ecologist. However, it is a great challenge to find a predictive biomass model across experiments. Results: In the present study, we constructed four predictive models to examine the quantitative relationship between image-based features and plant biomass accumulation...
January 16, 2018: GigaScience
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
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
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
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
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
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
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
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
Qiang Qiu
No abstract text is available yet for this article.
December 18, 2017: GigaScience
Hui Shen, Dongmei Jin, Jiang-Ping Shu, Xi-Le Zhou, Ming Lei, Ran Wei, Hui Shang, Hong-Jin Wei, Rui Zhang, Li Liu, Yu-Feng Gu, Xian-Chun Zhang, Yue-Hong Yan
Background: Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results: With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders...
February 1, 2018: GigaScience
Zhikai Liang, Piyush Pandey, Vincent Stoerger, Yuhang Xu, Yumou Qiu, Yufeng Ge, James C Schnable
Background: Maize (Zea mays ssp. mays) is 1 of 3 crops, along with rice and wheat, responsible for more than one-half of all calories consumed around the world. Increasing the yield and stress tolerance of these crops is essential to meet the growing need for food. The cost and speed of plant phenotyping are currently the largest constraints on plant breeding efforts. Datasets linking new types of high-throughput phenotyping data collected from plants to the performance of the same genotypes under agronomic conditions across a wide range of environments are essential for developing new statistical approaches and computer vision-based tools...
February 1, 2018: GigaScience
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...
January 1, 2018: GigaScience
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, Digital Gene Expression, and metagenomic experiments, respectively...
January 1, 2018: GigaScience
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 ∼2800 functionally characterized rice genes and ∼5000 members of different gene families by integrating data from available databases and reviewing every publication on rice functional genomic studies...
January 1, 2018: GigaScience
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