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Víctor Resco de Dios, Arthur Gessler, Juan Pedro Ferrio, Josu G Alday, Michael Bahn, Jorge Del Castillo, Sébastien Devidal, Sonia García-Muñoz, Zachary Kayler, Damien Landais, Paula Martín-Gómez, Alexandru Milcu, Clément Piel, Karin Pirhofer-Walzl, Olivier Ravel, Serajis Salekin, David T Tissue, Mark G Tjoelker, Jordi Voltas, Jacques Roy
BACKGROUND: Molecular clocks drive oscillations in leaf photosynthesis, stomatal conductance, and other cell and leaf-level processes over ~24 h under controlled laboratory conditions. The influence of such circadian regulation over whole-canopy fluxes remains uncertain; diurnal CO2 and H2O vapor flux dynamics in the field are currently interpreted as resulting almost exclusively from direct physiological responses to variations in light, temperature and other environmental factors. We tested whether circadian regulation would affect plant and canopy gas exchange at the Montpellier European Ecotron...
October 20, 2016: GigaScience
Qing Mao, Serban Ciotlos, Rebecca Yu Zhang, Madeleine P Ball, Robert Chin, Paolo Carnevali, Nina Barua, Staci Nguyen, Misha R Agarwal, Tom Clegg, Abram Connelly, Ward Vandewege, Alexander Wait Zaranek, Preston W Estep, George M Church, Radoje Drmanac, Brock A Peters
BACKGROUND: Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. FINDINGS: As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology...
October 11, 2016: GigaScience
Ángel G Muñoz, Madeleine C Thomson, Lisa Goddard, Sylvain Aldighieri
BACKGROUND: The emergence of Zika virus (ZIKV) in Latin America and the Caribbean in 2014-2016 occurred during a period of severe drought and unusually high temperatures, conditions that have been associated with the 2015-2016 El Niño event, and/or climate change; however, no quantitative assessment has been made to date. Analysis of related flaviviruses transmitted by the same vectors suggests that ZIKV dynamics are sensitive to climate seasonality and longer-term variability and trends...
October 6, 2016: GigaScience
Taylor J Noble, Christopher J Lortie, Michael Westphal, H Scott Butterfield
BACKGROUND: Carrizo Plain National Monument (San Joaquin Desert, California, USA) is home to many threatened and endangered species including the blunt-nosed leopard lizard (Gambelia sila). Vegetation is dominated by annual grasses, and shrubs such as Mormon tea (Ephedra californica), which is of relevance to our target species, the federally listed blunt-nosed leopard lizard, and likely also provides key ecosystem services. We used relatively nonintrusive camera traps, or trail cameras, to capture interactions between animals and these shrubs using a paired shrub-open deployment...
September 27, 2016: GigaScience
Hailin Pan, Hao Yu, Vydianathan Ravi, Cai Li, Alison P Lee, Michelle M Lian, Boon-Hui Tay, Sydney Brenner, Jian Wang, Huanming Yang, Guojie Zhang, Byrappa Venkatesh
BACKGROUND: The ocean sunfish (Mola mola), which can grow up to a length of 2.7 m and weigh 2.3 tons, is the world's largest bony fish. It has an extremely fast growth rate and its endoskeleton is mainly composed of cartilage. Another unique feature of the sunfish is its lack of a caudal fin, which is replaced by a broad and stiff lobe that results in the characteristic truncated appearance of the fish. RESULTS: To gain insights into the genomic basis of these phenotypic traits, we sequenced the sunfish genome and performed a comparative analysis with other teleost genomes...
2016: GigaScience
Xiaohui Chen, Liqiang Zhong, Chao Bian, Pao Xu, Ying Qiu, Xinxin You, Shiyong Zhang, Yu Huang, Jia Li, Minghua Wang, Qin Qin, Xiaohua Zhu, Chao Peng, Alex Wong, Zhifei Zhu, Min Wang, Ruobo Gu, Junmin Xu, Qiong Shi, Wenji Bian
BACKGROUND: The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world, especially in the United States' aquaculture industry. Since its introduction into China in 1984, both cultivation area and yield of this species have been dramatically increased such that China is now the leading producer of channel catfish. To aid genomic research in this species, data sets such as genetic linkage groups, long-insert libraries, physical maps, bacterial artificial clones (BAC) end sequences (BES), transcriptome assemblies, and reference genome sequences have been generated...
2016: GigaScience
Gaik Tamazian, Pavel Dobrynin, Ksenia Krasheninnikova, Aleksey Komissarov, Klaus-Peter Koepfli, Stephen J O'Brien
BACKGROUND: As the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts, reference-assisted assemblies that use comparative inference have become widely used, prompting the development of several reference-assisted assembly programs for prokaryotic and eukaryotic genomes. FINDINGS: We developed Chromosomer - a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a closely related species...
2016: GigaScience
Zongji Wang, Jinmin Lian, Qiye Li, Pei Zhang, Yang Zhou, Xiaoyu Zhan, Guojie Zhang
BACKGROUND: High-throughput sequencing (HTS) provides a powerful solution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to distinguish RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors. RESULTS: Here we present RES-Scanner, a flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data from the same individuals or samples...
2016: GigaScience
Xuewei Li, Ling Kui, Jing Zhang, Yinpeng Xie, Liping Wang, Yan Yan, Na Wang, Jidi Xu, Cuiying Li, Wen Wang, Steve van Nocker, Yang Dong, Fengwang Ma, Qingmei Guan
BACKGROUND: Domesticated apple (Malus × domestica Borkh) is a popular temperate fruit with high nutrient levels and diverse flavors. In 2012, global apple production accounted for at least one tenth of all harvested fruits. A high-quality apple genome assembly is crucial for the selection and breeding of new cultivars. Currently, a single reference genome is available for apple, assembled from 16.9 × genome coverage short reads via Sanger and 454 sequencing technologies. Although a useful resource, this assembly covers only ~89 % of the non-repetitive portion of the genome, and has a relatively short (16...
2016: GigaScience
Chenhao Li, Kern Rei Chng, Esther Jia Hui Boey, Amanda Hui Qi Ng, Andreas Wilm, Niranjan Nagarajan
BACKGROUND: Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relatively high single-read error rates (>10 %), including RNA-seq, haplotype sequencing and 16S sequencing. RESULTS: We developed the Intramolecular-ligated Nanopore Consensus Sequencing (INC-Seq) as a strategy for obtaining long and accurate nanopore reads, starting with low input DNA...
2016: GigaScience
Tamer A Mansour, Joshua J C Rosenthal, C Titus Brown, Loretta M Roberson
BACKGROUND: Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (>10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host-symbiont interactions...
2016: GigaScience
Minh Duc Cao, Devika Ganesamoorthy, Alysha G Elliott, Huihui Zhang, Matthew A Cooper, Lachlan J M Coin
The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid diagnosis of bacterial infection and identification of drug resistance. However, there are few tools available for streaming analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, strain typing and antibiotic resistance profile identification...
2016: GigaScience
Simo V Zhang, Luting Zhuo, Matthew W Hahn
BACKGROUND: Genomes sequenced using short-read, next-generation sequencing technologies can have many errors and may be fragmented into thousands of small contigs. These incomplete and fragmented assemblies lead to errors in gene identification, such that single genes spread across multiple contigs are annotated as separate gene models. Such biases can confound inferences about the number and identity of genes within species, as well as gene gain and loss between species. RESULTS: We present AGOUTI (Annotated Genome Optimization Using Transcriptome Information), a tool that uses RNA sequencing data to simultaneously combine contigs into scaffolds and fragmented gene models into single models...
2016: GigaScience
Stephen R Piccolo, Michael B Frampton
When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others...
2016: GigaScience
Fernando Cruz, Irene Julca, Jèssica Gómez-Garrido, Damian Loska, Marina Marcet-Houben, Emilio Cano, Beatriz Galán, Leonor Frias, Paolo Ribeca, Sophia Derdak, Marta Gut, Manuel Sánchez-Fernández, Jose Luis García, Ivo G Gut, Pablo Vargas, Tyler S Alioto, Toni Gabaldón
BACKGROUND: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). FINDINGS: A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv...
2016: GigaScience
Erica E Tassone, Gina Zastrow-Hayes, John Mathis, Mark E Nelson, Gusui Wu, J Lindsey Flexner, Yves Carrière, Bruce E Tabashnik, Jeffrey A Fabrick
BACKGROUND: The pink bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is one of the world's most important pests of cotton. Insecticide sprays and transgenic cotton producing toxins of the bacterium Bacillus thuringiensis (Bt) are currently used to manage this pest. Bt toxins kill susceptible insects by specifically binding to and destroying midgut cells, but they are not toxic to most other organisms. Pink bollworm is useful as a model for understanding insect responses to Bt toxins, yet advances in understanding at the molecular level have been limited because basic genomic information is lacking for this cosmopolitan pest...
2016: GigaScience
Jai Ram Rideout, John H Chase, Evan Bolyen, Gail Ackermann, Antonio González, Rob Knight, J Gregory Caporaso
BACKGROUND: Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians...
2016: GigaScience
Ola Spjuth, Erik Bongcam-Rudloff, Johan Dahlberg, Martin Dahlö, Aleksi Kallio, Luca Pireddu, Francesco Vezzi, Eija Korpelainen
With ever-increasing amounts of data being produced by next-generation sequencing (NGS) experiments, the requirements placed on supporting e-infrastructures have grown. In this work, we provide recommendations based on the collective experiences from participants in the EU COST Action SeqAhead for the tasks of data preprocessing, upstream processing, data delivery, and downstream analysis, as well as long-term storage and archiving. We cover demands on computational and storage resources, networks, software stacks, automation of analysis, education, and also discuss emerging trends in the field...
2016: GigaScience
Guilhem Sempéré, Florian Philippe, Alexis Dereeper, Manuel Ruiz, Gautier Sarah, Pierre Larmande
BACKGROUND: Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. DESCRIPTION: Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns...
2016: GigaScience
François Olivier Hébert, Stephan Grambauer, Iain Barber, Christian R Landry, Nadia Aubin-Horth
BACKGROUND: Schistocephalus solidus is a well-established model organism for studying the complex life cycle of cestodes and the mechanisms underlying host-parasite interactions. However, very few large-scale genetic resources for this species are available. We have sequenced and de novo-assembled the transcriptome of S. solidus using tissues from whole worms at three key developmental states - non-infective plerocercoid, infective plerocercoid and adult plerocercoid - to provide a resource for studying the evolution of complex life cycles and, more specifically, how parasites modulate their interactions with their hosts during development...
2016: GigaScience
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