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GigaScience

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https://www.readbyqxmd.com/read/28637310/the-metagenomic-data-life-cycle-standards-and-best-practices
#1
Petra Ten Hoopen, Robert D Finn, Lars Ailo Bongo, Erwan Corre, Bruno Fosso, Folker Meyer, Alex Mitchell, Eric Pelletier, Graziano Pesole, Monica Santamaria, Nils Peder Willassen, Guy Cochrane
Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing.Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28637269/announcing-the-genome-atlas-of-bamboo-and-rattan-gabr-project-promoting-research-in-evolution-and-in-economically-and-ecologically-beneficial-plants
#2
Hansheng Zhao, Shancen Zhao, Benhua Fei, Huan Liu, Huanming Yang, Honghai Dai, Dan Wang, Wei Jin, Feng Tang, Qiang Gao, Hang Xun, Yuwei Wang, Lianghua Qi, Xianghua Yue, Shuyan Lin, Lianfeng Gu, Lubin Li, Tiansheng Zhu, Qiang Wei, Zhen Su, Tarmeze Bin Wan Ariffin Wan, Daniel A Ofori, George Mbeva Muthike, Yigardu Mulatu Mengesha, Roberto Magno de Castro E Silva, Antonio Ludovico Beraldo, Zhimin Gao, Xin Liu, Zehui Jiang
Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking. We launched the Genome Atlas of Bamboo and Rattan (GABR) project, a comprehensive, coordinated international effort to accelerate understanding of BR genetics through genome analysis...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28637275/16gt-a-fast-and-sensitive-variant-caller-using-a-16-genotype-probabilistic-model
#3
Ruibang Luo, Michael C Schatz, Steven L Salzberg
16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy for calling indels as compared to the GATK HaplotypeCaller. 16GT is available at https://github.com/aquaskyline/16GT...
June 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28609785/comprehensive-analysis-of-microorganisms-accompanying-human-archaeological-remains
#4
Anna Philips, Ireneusz Stolarek, Bogna Kuczkowska, Anna Juras, Luiza Handschuh, Janusz Piontek, Piotr Kozlowski, Marek Figlerowicz
Background.: Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. Findings.: We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains...
June 13, 2017: GigaScience
https://www.readbyqxmd.com/read/28605506/multi-locus-and-long-amplicon-sequencing-approach-to-study-microbial-diversity-at-species-level-using-the-miniontm-portable-nanopore-sequencer
#5
Alfonso Benítez-Páez, Yolanda Sanz
Background: The miniaturised and portable DNA sequencer MinION TM has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION TM platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. Results: After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67,000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION TM device using R9 and R9...
June 12, 2017: GigaScience
https://www.readbyqxmd.com/read/28595343/sequencing-de-novo-assembling-and-annotating-the-genome-of-the-endangered-chinese-crocodile-lizard-shinisaurus-crocodilurus
#6
Jian Gao, Qiye Li, Zongji Wang, Yang Zhou, Paolo Martelli, Fang Li, Zijun Xiong, Jian Wang, Huanming Yang, Guojie Zhang
The Chinese crocodile lizard, Shinisaurus crocodilurus, is the only living representative of the monotypic family Shinisauridae under the order Squamata. It is an obligate semi-aquatic, viviparous, diurnal species restricted to specific portions of mountainous locations in southwestern China and northeastern Vietnam. However, in the past several decades, this species has undergone a rapid decrease in population size due to illegal poaching and habitat disruption, making this unique reptile species endangered and listed in CITES Appendix II since 1990...
June 8, 2017: GigaScience
https://www.readbyqxmd.com/read/28595314/a-combined-meta-barcoding-and-shotgun-metagenomic-analysis-of-spontaneous-wine-fermentation
#7
Peter R Sternes, Danna Lee, Dariusz R Kutyna, Anthony R Borneman
Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. Commercially, there is now a growing trend away from using wine yeast ( Saccharomyces ) starter cultures, towards the historic practice of uninoculated or "wild" fermentation, where the yeasts and bacteria associated with the grapes and/or winery perform the fermentation. It is the varied metabolic contributions of these numerous non- Saccharomyces species that are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts...
June 8, 2017: GigaScience
https://www.readbyqxmd.com/read/28535200/the-draft-genome-of-blunt-snout-bream-megalobrama-amblycephala-reveals-the-development-of-intermuscular-bone-and-adaptation-to-herbivorous-diet
#8
Han Liu, Chunhai Chen, Zexia Gao, Jiumeng Min, Yongming Gu, Jianbo Jian, Xiewu Jiang, Huimin Cai, Ingo Ebersberger, Meng Xu, Xinhui Zhang, Jianwei Chen, Wei Luo, Boxiang Chen, Junhui Chen, Hong Liu, Jiang Li, Ruifang Lai, Mingzhou Bai, Jin Wei, Shaokui Yi, Huanling Wang, Xiaojuan Cao, Xiaoyun Zhou, Yuhua Zhao, Kaijian Wei, Ruibin Yang, Bingnan Liu, Shancen Zhao, Xiaodong Fang, Manfred Schartl, Xueqiao Qian, Weimin Wang
Background: The blunt snout bream, Megalobrama amblycephala , is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption. Results: As a first towards optimizing this aquatic livestock, we present a 1.116-Gb draft genome of M. amblycephala , with 779.54 Mb anchored on 24 linkage groups...
May 23, 2017: GigaScience
https://www.readbyqxmd.com/read/28531267/alignment-of-1000-genomes-project-reads-to-reference-assembly-grch38
#9
Xiangqun Zheng-Bradley, Ian Streeter, Susan Fairley, David Richardson, Laura Clarke, Paul Flicek
BACKGROUND: The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes project variants to the new assembly, this is a potentially error prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies...
May 20, 2017: GigaScience
https://www.readbyqxmd.com/read/28520864/from-chromatogram-to-analyte-to-metabolite-how-to-pick-horses-for-courses-from-the-massive-web-resources-for-mass-spectral-plant-metabolomics
#10
Leonardo Perez de Souza, Thomas Naake, Takayuki Tohge, Alisdair R Fernie
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell towards the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome with the number of metabolites in the plant kingdom generally being considered to be in excess of 200 000. In this review we focus on web-resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification...
May 17, 2017: GigaScience
https://www.readbyqxmd.com/read/28505362/lipidomic-profiling-reveals-distinct-differences-in-plasma-lipid-composition-in-healthy-prediabetic-and-type-2-diabetic-individuals
#11
Huanzi Zhong, Chao Fang, Yanqun Fan, Yan Lu, Bo Wen, Huahui Ren, Guixue Hou, Fangming Yang, Hailiang Xie, Zhuye Jie, Ye Peng, Zhiqiang Ye, Jiegen Wu, Jin Zi, Guoqing Zhao, Jiayu Chen, Xiao Bao, Yihe Hu, Yan Gao, Jun Zhang, Huanming Yang, Jian Wang, Lise Madsen, Karsten Kristiansen, Chuanming Ni, Junhua Li, Siqi Liu
Background: The relationship between dyslipidemia and type 2 diabetes mellitus (T2D) has been extensively reported, but the global lipid profiles, especially in the East Asia population, associated with the development of T2D remain to be characterized. Results: Liquid chromatography coupled to tandem mass spectrometry was applied to detect the global lipidome in the fasting plasma of 293 Chinese individuals, including 114 T2D patients, 81 prediabetic subjects and 98 individuals with normal glucose tolerance (NGT)...
May 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28486658/a-high-coverage-draft-genome-of-the-mycalesine-butterfly-bicyclus-anynana
#12
Reuben W Nowell, Ben Elsworth, Vicencio Oostra, Bas J Zwaan, Christopher W Wheat, Marjo Saastamoinen, Ilik J Saccheri, Arjen E Van't Hof, Bethany R Wasik, Heidi Connahs, Muhammad L Aslam, Sujai Kumar, Richard J Challis, Antónia Monteiro, Paul M Brakefield, Mark Blaxter
Background: The mycalesine butterfly Bicyclus anynana , the 'Squinting bush brown', is a model organism in the study of lepidopteran ecology, development and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Findings: Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology...
May 9, 2017: GigaScience
https://www.readbyqxmd.com/read/28472337/eeg-datasets-for-motor-imagery-brain-computer-interface
#13
Hohyun Cho, Minkyu Ahn, Sangtae Ahn, Moonyoung Kwon, Sung Chan Jun
BACKGROUND: Most investigators of brain computer interface (BCI) research believe that BCI can be achieved through induced neuronal activity from the cortex, but not by evoked neuronal activity. Motor imagery (MI) based BCI is one of the standard concepts of BCI, in that the user can generate induced activity by imagining motor movements. However, variations in performance over sessions and subjects are too severe to overcome easily; therefore, a basic understanding and investigation of BCI performance variation is necessary to find critical evidence of performance variation...
May 4, 2017: GigaScience
https://www.readbyqxmd.com/read/28459977/gsuite-hyperbrowser-integrative-analysis-of-dataset-collections-across-the-genome-and-epigenome
#14
Boris Simovski, Daniel Vodák, Sveinung Gundersen, Diana Domanska, Abdulrahman Azab, Lars Holden, Marit Holden, Ivar Grytten, Knut Rand, Finn Drabløs, Morten Johansen, Antonio Mora, Christin Lund-Andersen, Bastian Fromm, Ragnhild Eskeland, Odd Stokke Gabrielsen, Egil Ferkingstad, Sigve Nakken, Mads Bengtsen, Alexander Johan Nederbragt, Hildur Sif Thorarensen, Johannes Andreas Akse, Ingrid Glad, Eivind Hovig, Geir Kjetil Sandve
Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation. We here present a first principled treatment of the analysis of collections of genomic tracks...
April 27, 2017: GigaScience
https://www.readbyqxmd.com/read/28475810/draft-genome-sequence-of-the-tibetan-medicinal-herb-rhodiola-crenulata
#15
Yuanyuan Fu, Liangwei Li, Shijie Hao, Rui Guan, Guangyi Fan, Chengcheng Shi, Haibo Wan, Wenbin Chen, He Zhang, Guocheng Liu, Jihua Wang, Lulin Ma, Jianling You, Xuemei Ni, Zhen Yue, Xun Xu, Xiao Sun, Xin Liu, Simon Ming-Yuen Lee
Rhodiola crenulata, a well-known medicinal Tibetan herb, is mainly grown in high-altitude regions of the Tibet, Yunnan, and Sichuan provinces in China. In the past few years, increasing numbers of studies have been published on the potential pharmacological activities of R. crenulata, strengthening our understanding into its putitive active ingredient composition, pharmacological activity, and mechanism of action. These findings also provide strong evidence supporting the important medicinal and economical value of R...
June 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28449062/calculating-the-quality-of-public-high-throughput-sequencing-data-to-obtain-a-suitable-subset-for-reanalysis-from-the-sequence-read-archive
#16
Tazro Ohta, Takeru Nakazato, Hidemasa Bono
It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC...
June 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28444351/comparative-genomic-analysis-of-set-domain-family-reveals-the-origin-expansion-and-putative-function-of-the-arthropod-specific-smyda-genes-as-histone-modifiers-in-insects
#17
Feng Jiang, Qing Liu, Yanli Wang, Jie Zhang, Huimin Wang, Tianqi Song, Meiling Yang, Xianhui Wang, Le Kang
The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain-containing genes (SET genes) in all of the 147 arthropod genomes sequenced at the time of carrying out this experiment to understand the evolutionary history by which SET domains have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, that is ancestral to arthropod animals and specifically diversified during insect evolution...
June 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28444302/draft-genome-of-the-lined-seahorse-hippocampus-erectus
#18
Qiang Lin, Ying Qiu, Ruobo Gu, Meng Xu, Jia Li, Chao Bian, Huixian Zhang, Geng Qin, Yanhong Zhang, Wei Luo, Jieming Chen, Xinxin You, Mingjun Fan, Min Sun, Pao Xu, Byrappa Venkatesh, Junming Xu, Hongtuo Fu, Qiong Shi
The lined seahorse, Hippocampus erectus , is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding...
June 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28431039/genomic-data-for-78-chickens-from-14-populations
#19
Diyan Li, Tiandong Che, Binlong Chen, Shilin Tian, Xuming Zhou, Guolong Zhang, Miao Li, Uma Gaur, Yan Li, Majing Luo, Long Zhang, Zhongxian Xu, Xiaoling Zhao, Huadong Yin, Yan Wang, Long Jin, Qianzi Tang, Huailiang Xu, Mingyao Yang, Rongjia Zhou, Ruiqiang Li, Qing Zhu, Mingzhou Li
Since the domestication of the red jungle fowls ( Gallus gallus ; dating back to ∼10 000 B.P.) in Asia, domestic chickens ( Gallus gallus domesticus ) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production, and skin color. Population genomic variations through diversifying selection have not been fully investigated. The whole genomes of 78 domestic chickens were sequenced to an average of 18-fold coverage for each bird...
June 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28431028/hybrid-de-novo-genome-assembly-of-the-chinese-herbal-fleabane-erigeron-breviscapus
#20
Jing Yang, Guanghui Zhang, Jing Zhang, Hui Liu, Wei Chen, Xiao Wang, Yahe Li, Yang Dong, Shengchao Yang
The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus , which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant. With the purpose of finding novel medicinal compounds and understanding their biosynthetic pathways, we propose to sequence the genome of E...
June 1, 2017: GigaScience
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