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GigaScience

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https://read.qxmd.com/read/30715332/genome-sequence-of-the-barred-knifejaw-oplegnathus-fasciatus-temminck-schlegel-1844-the-first-chromosome-level-draft-genome-in-the-family-oplegnathidae
#1
Yongshuang Xiao, Zhizhong Xiao, Daoyuan Ma, Jing Liu, Jun Li
Background: The barred knifejaw (Oplegnathus fasciatus), a member of the Oplegnathidae family of the Centrarchiformes, is a commercially important rocky reef fish native to East Asia. O. fasciatus has become an important fishery resource for offshore cage aquaculture and fish stocking of marine ranching in China, Japan and Korea. Recently, sexual dimorphism in growth with neo-sex chromosome and widespread biotic diseases in O. fasciatus has been received increasing concern. However, adequate genome resources for gaining insight into sex-determining mechanisms and establishing genetically resistant breeding systems for O...
February 1, 2019: GigaScience
https://read.qxmd.com/read/30715329/cropsight-a-scalable-and-open-source-information-management-system-for-distributed-plant-phenotyping-and-iot-based-crop-management
#2
Daniel Reynolds, Joshua Ball, Alan Bauer, Robert Davey, Simon Griffiths, Ji Zhou
Background: High-quality plant phenotyping and climate data lay the foundation of phenotypic analysis and genotype-environment interaction, providing important evidence not only for plant scientists to understand the dynamics between crop performance, genotypes, and environmental factors, but also for agronomists and farmers to closely monitor crops in fluctuating agricultural conditions. With the rise of Internet of Things technologies (IoT) in recent years, many IoT-based remote sensing devices have been applied to plant phenotyping and crop monitoring, which are generating terabytes of biological datasets every day...
January 31, 2019: GigaScience
https://read.qxmd.com/read/30715320/modelling-genotypes-in-their-microenvironment-to-predict-single-and-multi-cellular-behaviour
#3
Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa
A cell's phenotype is the set of observable characteristics resulting from the interaction of the genotype with the surrounding environment, determining cell behaviour. Deciphering genotype-phenotype relationships has been crucial to understand normal and disease biology. Analysis of molecular pathways has provided an invaluable tool to such understanding; however, it does typically not consider the physical microenvironment, which is a key determinant of phenotype.In this study, we present a novel modelling framework that enables to study the link between genotype, signalling networks and cell behaviour in a 3D microenvironment...
January 31, 2019: GigaScience
https://read.qxmd.com/read/30715311/integrating-genomic-resources-to-present-full-gene-and-putative-promoter-capture-probe-sets-for-bread-wheat
#4
Laura-Jayne Gardiner, Thomas Brabbs, Alina Akhunov, Katherine Jordan, Hikmet Budak, Todd Richmond, Sukhwinder Singh, Leah Catchpole, Eduard Akhunov, Anthony Hall
Background: Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented cDNA/exon or gene-based probe sets where promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences...
January 31, 2019: GigaScience
https://read.qxmd.com/read/30715294/haplotype-phased-genome-and-evolution-of-phytonutrient-pathways-of-tetraploid-blueberry
#5
Marivi Colle, Courtney P Leisner, Ching Man Wai, Shujun Ou, Kevin A Bird, Jie Wang, Jennifer H Wisecaver, Alan E Yocca, Elizabeth I Alger, Haibao Tang, Zhiyong Xiong, Pete Callow, Gil Ben-Zvi, Avital Brodt, Kobi Baruch, Thomas Swale, Lily Shiue, Guo-Qing Song, Kevin L Childs, Anthony Schilmiller, Nicholi Vorsa, C Robin Buell, Robert VanBuren, Ning Jiang, Patrick P Edger
Background: Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble in large part to its polyploid nature and genome size...
January 31, 2019: GigaScience
https://read.qxmd.com/read/30715293/linking-genetic-metabolic-and-phenotypic-diversity-among-s-cerevisiae-strains-using-multi-omics-associations
#6
Kang Kang, Basti Bergdahl, Daniel Machado, Laura Dato, Ting-Li Han, Jun Li, Silas Villas-Boas, Markus J Herrgård, Jochen Förster, Gianni Panagiotou
The selection of bioengineering platform strains and engineering strategies to improve the stress resistance of Saccharomyces cerevisiae remains a pressing need in bio-based chemical production. Thus, a systematic effort to exploit the genotypic and phenotypic diversity to boost yeast's industrial value is still urgently needed. Here, we analyzed 5400 growth curves obtained from 36 S. cerevisiae strains and comprehensively profiled their resistances against 13 industrially relevant stresses. We observed that bioethanol and brewing strains exhibit higher resistance against acidic conditions, however, plant isolates tend to have wider range of resistance, which may be associated with their metabolome and fluxome signatures in TCA cycle and fatty acid metabolism...
January 31, 2019: GigaScience
https://read.qxmd.com/read/30715292/the-genomic-basis-for-colonizing-the-freezing-southern-ocean-revealed-by-antarctic-toothfish-and-patagonia-robalo-genomes
#7
Liangbiao Chen, Ying Lu, Wenhao Li, Yandong Ren, Mengchao Yu, Shouwen Jiang, Yanxia Fu, Jian Wang, Sihua Peng, Kevin T Bilyk, Katherine R Murphy, Xuan Zhuang, Mathias Hune, Wanying Zhai, Wen Wang, Qianghua Xu, Chi-Hing Christina Cheng
The Southern Ocean is the coldest ocean on Earth but a hotspot of evolution. The bottom-dwelling Eocene ancestor of Antarctic notothenioid fishes survived polar marine glaciation and underwent adaptive radiation forming >120 species that fill all water column niches today. Genome-wide changes enabling physiological adaptations and rapid expansion of the Antarctic Notothenioids remain poorly understood. To advance our understanding, we sequenced and compared two notothenioid genomes-the cold-adapted and neutrally buoyant Antarctic toothfish Dissostichus mawsoni, and the basal Patagonian robalo (also known as the Patagonian blenny) Eleginops maclovinus representing the temperate ancestor...
January 31, 2019: GigaScience
https://read.qxmd.com/read/30715291/understanding-of-researcher-behaviour-is-required-to-improve-data-reliability
#8
Mark N Wass, Larry Ray, Martin Michaelis
Background: A lack of data reproducibility ("reproducibility crisis") has been extensively debated across many academic disciplines. Main body: Although a reproducibility crisis is widely perceived, conclusive data on the scale of the problem and the underlying reasons are largely lacking. The debate is primarily focused on methodological issues. However, examples such as the use of misidentified cell lines illustrate that the availability of reliable methods does not guarantee good practice...
January 31, 2019: GigaScience
https://read.qxmd.com/read/30698704/eeg-dataset-and-openbmi-toolbox-for-three-bci-paradigms-an-investigation-into-bci-illiteracy
#9
Min-Ho Lee, O-Yeon Kwon, Yong-Jeong Kim, Hong-Kyung Kim, Young-Eun Lee, John Williamson, Siamac Fazli, Seong-Whan Lee
Background: Electroencephalography (EEG)-based brain-computer interface (BCI) systems are mainly divided into three major paradigms: motor-imagery (MI), event-related potential (ERP), and steady-state visually evoked potential (SSVEP). In this paper, we present a BCI dataset that includes the three major BCI paradigms with a large number of subjects over multiple sessions. In addition, information about the psychological and physiological conditions of BCI users was obtained using a questionnaire, and task-unrelated parameters such as resting state, artifacts, and electromyography of both arms were also recorded...
January 30, 2019: GigaScience
https://read.qxmd.com/read/30698701/a-chromosomal-scale-genome-assembly-of-tectona-grandis-reveals-the-importance-of-tandem-gene-duplication-and-enables-discovery-of-genes-in-natural-product-biosynthetic-pathways
#10
Dongyan Zhao, John P Hamilton, Wajid Waheed Bhat, Sean R Johnson, Grant T Godden, Taliesin J Kinser, Benoît Boachon, Natalia Dudareva, Douglas E Soltis, Pamela S Soltis, Bjoern Hamberger, C Robin Buell
Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits...
January 30, 2019: GigaScience
https://read.qxmd.com/read/30698687/the-unique-composition-of-indian-gut-microbiome-gene-catalogue-and-associated-faecal-metabolome-deciphered-using-multi-omics-approaches
#11
D B Dhakan, A Maji, A K Sharma, R Saxena, J Pulikkan, T Grace, A Gomez, J Scaria, K R Amato, V K Sharma
Background: Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health, however, the Indian gut microbiome is not well explored yet. We analysed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole genome shotgun metagenomic sequencing, and metabolomic profiling of faecal and serum samples...
January 30, 2019: GigaScience
https://read.qxmd.com/read/30698692/new-de-novo-assembly-of-the-atlantic-bottlenose-dolphin-tursiops-truncatus-improves-genome-completeness-and-provides-haplotype-phasing
#12
Karine A Martinez-Viaud, Cindy Taylor Lawley, Milmer Martinez Vergara, Gil Ben-Zvi, Tammy Biniashvili, Kobi Baruch, Judy St Leger, Jennie Le, Aparna Natarajan, Marlem Rivera, Marbie Guillergan, Erich Jaeger, Brian Steffy, Aleksey Zimin
High quality genomes are essential to resolve challenges in breeding, comparative biology, medicine and conservation planning. New library preparation techniques along with better assembly algorithms result in continued improvements in assemblies for non-model organisms, moving them toward reference quality genomes. We report on the latest genome assembly of the Atlantic bottlenose dolphin leveraging Illumina sequencing data coupled with a combination of several library preparation techniques. These include Linked-Reads (Chromium, 10x Genomics), mate pairs, long insert paired ends and standard paired ends...
January 29, 2019: GigaScience
https://read.qxmd.com/read/30698691/smagexp-a-galaxy-tool-suite-for-transcriptomics-data-meta-analysis
#13
Samuel Blanck, Guillemette Marot
With the proliferation of available microarray and high throughput sequencing experiments in the public domain, the use of meta-analysis methods increases. In these experiments, where the sample size is often limited, meta-analysis offers the possibility to considerably enhance the statistical power and give more accurate results. For those purposes, it combines either effect sizes or results of single studies in a appropriate manner. R packages metaMA and metaRNASeq perform meta-analysis on microarray and NGS data, respectively...
January 29, 2019: GigaScience
https://read.qxmd.com/read/30689836/molecular-digitization-of-a-botanical-garden-high-depth-whole-genome-sequencing-of-689-vascular-plant-species-from-the-ruili-botanical-garden
#14
Huan Liu, Jinpu Wei, Ting Yang, Weixue Mu, Bo Song, Tuo Yang, Yuan Fu, Xuebing Wang, Guohai Hu, Wangsheng Li, Hongcheng Zhou, Yue Chang, Xiaoli Chen, Hongyun Chen, Le Cheng, Xuefei He, Hechen Cai, Xianchu Cai, Mei Wang, Yang Li, Sunil Kumar Sahu, Jinlong Yang, Yu Wang, Ranchang Mu, Jie Liu, Jianming Zhao, Ziheng Huang, Xun Xu, Xin Liu
Background: Genome sequencing has been widely used in plant research to construct reference genomes and provide evolutionary insights. However, few plant species have had their whole genome sequenced, thus restraining the utility of these data. We collected 1,093 samples of vascular plant species growing in the Ruili Botanical Garden, located in South West China. Of these, we sequenced 761 samples, and collected voucher specimens stored in the Herbarium of China National GeneBank. Results: The 761 sequenced samples represented 689 vascular plant species from 137 families belonging to 49 orders...
January 25, 2019: GigaScience
https://read.qxmd.com/read/30689855/nanopipe-a-web-server-for-nanopore-minion-sequencing-data-analysis
#15
Victoria Shabardina, Tabea Kischka, Felix Manske, Norbert Grundmann, Martin C Frith, Yutaka Suzuki, Wojciech Makalowski
Background: The fast-moving progress of the third generation long read sequencing technologies will soon bring the biological and medical sciences to a new era of research. Altogether the technique and experimental procedures are becoming more straightforward and available to biologists from diverse fields, even without any profound experience in DNA sequencing. Thus, the introduction of the MinIONTM device by Oxford Nanopore Technologies promises to "bring sequencing technology to the masses" and also allows quick and operative analysis in field studies...
January 24, 2019: GigaScience
https://read.qxmd.com/read/30689848/genome-sequence-of-malania-oleifera-a-tree-with-great-value-for-nervonic-acid-production
#16
Chao-Qun Xu, Hui Liu, Shan-Shan Zhou, Dong-Xu Zhang, Wei Zhao, Sihai Wang, Fu Chen, Yan-Qiang Sun, Shuai Nie, Kai-Hua Jia, Si-Qian Jiao, Ren-Gang Zhang, Quan-Zheng Yun, Wenbin Guan, Xuewen Wang, Qiong Gao, Jeffrey L Bennetzen, Fatemeh Maghuly, Ilga Porth, Yves Van de Peer, Xiao-Ru Wang, Yongpeng Ma, Jian-Feng Mao
Background: Malania oleifera, a member of the Olacaceae family, is an IUCN Red Listed tree, endemic and restricted to the Karst region of South West China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic make-up, and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings: We generated 51 Gigabases (Gb) and 135 Gb of raw DNA sequences, using PacBio Single-Molecule Real-Time (SMRT) and 10x Genomics sequencing, respectively...
January 24, 2019: GigaScience
https://read.qxmd.com/read/30689847/comparative-analyses-identify-genomic-features-potentially-involved-in-the-evolution-of-birds-of-paradise
#17
Stefan Prost, Ellie E Armstrong, Johan Nylander, Gregg W C Thomas, Alexander Suh, Bent Petersen, Love Dalen, Brett W Benz, Mozes P K Blom, Eleftheria Palkopoulou, Per G P Ericson, Martin Irestedt
The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and laymen alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity...
January 24, 2019: GigaScience
https://read.qxmd.com/read/30649288/a-near-chromosome-scale-genome-assembly-of-the-gemsbok-oryx-gazella-an-iconic-antelope-of-the-kalahari-desert
#18
Marta Farré, Qiye Li, Yang Zhou, Joana Damas, Leona G Chemnick, Jaebum Kim, Oliver A Ryder, Jian Ma, Guojie Zhang, Denis M Larkin, Harris A Lewin
Background: The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts. Findings: Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2...
January 16, 2019: GigaScience
https://read.qxmd.com/read/30624602/a-critical-comparison-of-technologies-for-a-plant-genome-sequencing-project
#19
Pirita Paajanen, George Kettleborough, Elena López-Girona, Michael Giolai, Darren Heavens, David Baker, Ashleigh Lister, Fiorella Cugliandolo, Gail Wilde, Ingo Hein, Iain Macaulay, Glenn J Bryan, Matthew D Clark
Background: A high quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone based methods are slow and expensive, whereas faster, cheaper short read only assemblies can be incomplete and highly fragmented, which minimises their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and associated new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, on larger (e...
January 9, 2019: GigaScience
https://read.qxmd.com/read/30597007/galaxy-mothur-toolset-gmt-a-user-friendly-application-for-16s-rrna-gene-sequencing-analysis-using-mothur
#20
Saskia D Hiltemann, Stefan A Boers, Peter J van der Spek, Ruud Jansen, John P Hays, Andrew P Stubbs
Background: The determination of microbial communities using the mothur tool suite (https://www.mothur.org) is well established. However, mothur requires bioinformatics-based proficiency in order to perform calculations via the command-line. Galaxy is a project dedicated to providing a user-friendly web interface for such command-line tools (https://galaxyproject.org/). Results: We have integrated the full set of 125+ mothur tools into Galaxy as the Galaxy mothur Toolset (GmT) and provided a set of workflows to perform end-to-end 16S rRNA gene analyses and integrate with third-party visualization and reporting tools...
December 28, 2018: GigaScience
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