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Pengju Zhao, Ying Yu, Wen Feng, Heng Du, Jian Yu, Huimin Kang, Xianrui Zheng, Zhiquan Wang, George E Liu, Catherine W Ernst, Xueqin Ran, Jiafu Wang, Jian-Feng Liu
Background: Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with the unique features are still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to phenotypic traits of Meishan by large-scale sequencing. Results: We found the unique domestication of Meishan pigs happened at the Taihu Basin area between the Majiabang and the Liangzhu culture, during which 300 protein-coding genes have undergone positive selection...
May 22, 2018: GigaScience
Thomas Nind, James Galloway, Gordon McAllister, Donald Scobbie, Wilfred Bonney, Christopher Hall, Leandro Tramma, Parminder Reel, Martin Groves, Philip Appleby, Alex Doney, Bruce Guthrie, Emily Jefferson
Background: The Health Informatics Centre (HIC) at the University of Dundee provides a service to securely host clinical datasets and extract relevant data for anonymised cohorts to researchers to enable them to answer key research questions. As is common in research using routine healthcare data, the service was historically delivered using ad-hoc processes resulting in the slow provision of data whose provenance was often hidden to the researchers using it. This paper describes the development and evaluation of the Research Data Management Platform (RDMP): an open source tool to load, manage, clean, and curate longitudinal healthcare data for research and provide reproducible and updateable datasets for defined cohorts to researchers...
May 22, 2018: GigaScience
Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret
Background: New generations of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses...
May 22, 2018: GigaScience
Ines Herlitze, Benjamin Marie, Frédéric Marin, Daniel J Jackson
Background: Conchiferan molluscs construct a biocalcified shell that likely supported much of their evolutionary success. However beyond broad proteomic and transcriptomic surveys of molluscan shells and the shell-forming mantle tissue, little is known of the spatial and ontogenetic regulation of shell fabrication. In addition, most efforts have been focused on species that deposit nacre, which is at odds with the majority of conchiferan species that fabricate shells using a crossed lamellar microstructure, sensu lato...
May 17, 2018: GigaScience
Xiaobo Sun, Jingjing Gao, Peng Jin, Celeste Eng, Esteban G Burchard, Terri H Beaty, Ingo Ruczinski, Rasika A Mathias, Kathleen C Barnes, Fusheng Wang, Zhaohui Qin
Background: Sorted merging of genomic data is a common data operation necessary in many sequencing-based studies. It involves sorting and merging genomic data from different subjects by their genomic locations. In particular, merging a large number of Variant Call Format (VCF) files is frequently required in large scale whole genome sequencing or whole exome sequencing projects. Traditional single machine based methods become increasingly inefficient when processing large numbers of VCF files due to the excessive computation time and I/O bottleneck...
May 11, 2018: GigaScience
Hudan Pan, Ruijin Guo, Jie Zhu, Qi Wang, Yanmei Ju, Ying Xie, Yanfang Zheng, Zhifeng Wang, Ting Li, Zhongqiu Liu, Linlin Lu, Fei Li, Bin Tong, Liang Xiao, Xun Xu, Runze Li, Zhongwen Yuan, Huanming Yang, Jian Wang, Karsten Kristiansen, Huijue Jia, Liang Liu
Background: Laboratory rats such as the Sprague-Dawley (SD) rats are an important model for biomedical studies in relation to human physiological or pathogenic processes. Here we report the first catalog of microbial genes in fecal samples from Sprague-Dawley rats. Findings: The catalog was established using 98 fecal samples from 49 SD rats, divided in 7 experimental groups, and collected at different time points 30 days apart. The established gene catalog comprises 5,130,167 non-redundant genes with an average length of 750 base pairs (BP), among which 64...
May 11, 2018: GigaScience
Alexandre Almeida, Alex L Mitchell, Aleksandra Tarkowska, Robert D Finn
Background: Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring the composition of complex microbial ecosystems. QIIME and mothur have been the most widely used taxonomic analysis tools for this purpose, with MAPseq and QIIME 2 being two recently released alternatives. However, no independent and direct comparison between these four main tools has been performed. Here, we compared the default classifiers of MAPseq, mothur, QIIME, and QIIME 2 using synthetic simulated datasets comprised of some of the most abundant genera found in the human gut, ocean and soil environments...
May 11, 2018: GigaScience
Yan Wu, Yaolei Zhang, Zhuocheng Hou, Guangyi Fan, Jinsong Pi, Shuai Sun, Jiang Chen, Huaqiao Liu, Xiao Du, Jie Shen, Gang Hu, Wenbin Chen, Ailuan Pan, Pingping Yin, Xiaoli Chen, Yuejin Pu, He Zhang, Zhenhua Liang, Jianbo Jian, Hao Zhang, Bin Wu, Jing Sun, Jianwei Chen, Hu Tao, Ting Yang, Hongwei Xiao, Huan Yang, Chuanwei Zheng, Mingzhou Bai, Xiaodong Fang, David W Burt, Wen Wang, Qingyi Li, Xun Xu, Chengfeng Li, Huanming Yang, Jian Wang, Ning Yang, Xin Liu, Jinping Du
Background: Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution and functional studies. Results: Here, we present a quail genome assembly spanning 1...
May 11, 2018: GigaScience
Fu-Hao Lu, Neil McKenzie, George Kettleborough, Darren Heavens, Matthew D Clark, Michael W Bevan
Background: The accurate sequencing and assembly of very large, often polyploid, genomes remain a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15 Gb hexaploid bread wheat genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors is important for optimising future sequencing and assembly approaches and for comparative genomics...
May 11, 2018: GigaScience
Yong Gao, Haibo Wang, Chao Liu, Honglong Chu, Dongqin Dai, Shengnan Song, Long Yu, Lihong Han, Yi Fu, Bin Tian, Lizhou Tang
Background: Bombax ceiba L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia, and northern Australia. It has great economic and ecological importance, with several applications in industry and traditional medicine in many Asian countries. To facilitate the further utilization of this plant resource, we present here the draft genome sequence for B. ceiba. Findings: We assembled a relatively intact genome of B...
May 10, 2018: GigaScience
Varune Rohan Ramnarine, Mohammed Alshalalfa, Fan Mo, Noushin Nabavi, Nicholas Erho, Mandeep Takhar, Robert Shukin, Sonal Brahmbhatt, Alexander Gawronski, Maxim Kobelev, Mannan Nouri, Dong Lin, Harrison Tsai, Tamara L Lotan, R Jefferey Karnes, Mark A Rubin, Amina Zoubeidi, Martin E Gleave, Cenk Sahinalp, Alexander W Wyatt, Stanislav V Volik, Himisha Beltran, Elai Davicioni, Yuzhuo Wang, Colin C Collins
Background: Treatment induced neuroendocrine prostate cancer (tNEPC) is an aggressive variant of late-stage metastatic castrate resistant (mCRPC) prostate cancer that commonly arises through neuroendocrine transdifferentiation (NEtD). Treatment options are limited, ineffective, and for most patients, results in death in less than a year. We previously developed a first-in-field patient-derived xenograft (PDX) model of NEtD. Longitudinal deep transcriptome profiling of this model enabled monitoring of dynamic transcriptional changes during NEtD and in the context of androgen deprivation...
May 10, 2018: GigaScience
Alex Di Genova, Gonzalo A Ruz, Marie-France Sagot, Alejandro Maass
Background: Long read sequencing technologies are the ultimate solution for genome repeats, allowing near reference level reconstructions of large genomes. However, long read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods which combine short and long read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes...
May 5, 2018: GigaScience
Nadia M Davidson, Alicia Oshlack
Background: RNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating assembled transcriptome with reference annotation are lacking. Findings: Necklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data...
May 2, 2018: GigaScience
Xueya Zhao, Majing Luo, Zhigang Li, Pei Zhong, Yibin Cheng, Fengling Lai, Xin Wang, Jiumeng Min, Mingzhou Bai, Yulan Yang, Hanhua Cheng, Rongjia Zhou
Background: The teleost fish Monopterus albus is emerging as a new model for biological studies due to its natural sex transition and small genome, in addition to its enormous economic and potential medical value. However, no genomic information for the Monopterus is currently available. Findings: Here, we sequenced and de novo assembled the genome of Monopterus albus and report the de novochromosome assembly by FISH walking assisted by conserved synteny (Cafs)...
April 24, 2018: GigaScience
Barbara Baro, Soraya Játiva, Inés Calabria, Judith Vinaixa, Joan-Josep Bech-Serra, Carolina de LaTorre, João Rodrigues, María Luisa Hernáez, Concha Gil, Silvia Barceló-Batllori, Martin R Larsen, Ethel Queralt
Background: Protein phosphatase 2A (PP2A) is a family of conserved serine/threonine phosphatases involved in several essential aspects of cell growth and proliferation. PP2ACdc55 phosphatase has been extensively related to cell cycle events in budding yeast, however few PP2ACdc55 substrates have been identified. Here, we performed a quantitative mass spectrometry approach to reveal new substrates of PP2ACdc55 phosphatase and new PP2A-related processes in mitotic arrested cells. Results: We identified 62 statistically significant PP2ACdc55 substrates involved mainly in actin-cytoskeleton organization...
April 24, 2018: GigaScience
José Horacio Grau, Thomas Hackl, Klaus-Peter Koepfli, Michael Hofreiter
Background: Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. Findings: In order to improve genome contiguity, we have developed Cross-Species Scaffolding-a new pipeline which imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico...
April 21, 2018: GigaScience
Haotian Teng, Minh Duc Cao, Michael B Hall, Tania Duarte, Sheng Wang, Lachlan J M Coin
Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology which offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling: directly translating the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4000 reads, we show that our model provides state-of-the-art basecalling accuracy even on previously unseen species...
April 10, 2018: GigaScience
Zebin Zhang, Yaxiong Jia, Pedro Almeida, Judith E Mank, Marcel van Tuinen, Qiong Wang, Zhihua Jiang, Yu Chen, Kai Zhan, Shuisheng Hou, Zhengkui Zhou, Huifang Li, Fangxi Yang, Yong He, Zhonghua Ning, Ning Yang, Lujiang Qu
Background: The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual. Results: Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages...
April 9, 2018: GigaScience
Brendan Lawlor, Richard Lynch, Micheál Mac Aogáin, Paul Walsh
Background: Bioinformatic research is increasingly dependent on large-scale data sets, accessed either from private or public repositories. An example of a public repository is NCBI's RefSeq. These repositories must decide in what form to make their data available. Unstructured data can be put to almost any use, but are limited in how access to them can be scaled. Highly structured data offer improved performance for specific algorithms but limit the wider usefulness of the data. We present an alternative: lightly-structured data stored in Apache Kafka in a way that is amenable to parallel access and streamed processing, including subsequent transformations into more highly-structured representations...
April 9, 2018: GigaScience
Yang Zhou, Erin E Connor, Derek M Bickhart, Congjun Li, Ransom L Baldwin, Steven G Schroeder, Benjamin D Rosen, Liguo Yang, Curtis P Van Tassell, George E Liu
Background: Although sperm DNA methylation has been studied in humans and other species, its status in cattle is largely unknown. Results: Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with three somatic tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats...
April 9, 2018: GigaScience
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