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Shengyong Xu, Shijun Xiao, Shilin Zhu, Xiaofei Zeng, Jing Luo, Jiaqi Liu, Tianxiang Gao, Nansheng Chen
Background: Sillaginidae, also known as smelt-whitings, is a family of benthic coastal marine fishes in the Indo-West Pacific that have high ecological and economic importance. Many Sillaginidae species, including the Chinese sillago (Sillago sinica) have been recently described in China, providing valuable material to analyze genetic diversification of the family Sillaginidae. Here, we constructed a reference genome for the Chinese sillago, with the aim to setup a platform for comparative analysis of all species in this family...
September 10, 2018: GigaScience
Hansheng Zhao, Zhimin Gao, Le Wang, Jiongliang Wang, Songbo Wang, Benhua Fei, Chunhai Chen, Chengcheng Shi, Xiaochuan Liu, Hailin Zhang, Yongfeng Lou, LianFu Chen, Huayu Sun, Xianqiang Zhou, Sining Wang, Chi Zhang, Hao Xu, Lichao Li, Yihong Yang, Yanli Wei, Wei Yang, Qiang Gao, Huanming Yang, Shancen Zhao, Zehui Jiang
Background: Bamboo is one of the most important non-timber forest products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies. Results: Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79...
September 8, 2018: GigaScience
Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer
Background: In addition to mapping quality information, the Genome coverage contains valuable biological information like the presence of repetitive regions, deleted genes or copy number variations. It is essential to take into consideration atypical regions, trends (e.g., origin of replication) or known and unknown biases that influence coverage. It is also important that reported events have robust statistics (e.g. z-score) associated with their detections as well as precise location...
September 6, 2018: GigaScience
Honghao Zhao, Jasmine Chong, Rong Tang, Li Li, Jianguo Xia, Dapeng Li
Background: The ultra-high density intensive farming model of grass carp (Ctenopharyngodon idellus) may elicit growth inhibition, decline flesh quality and increase disease susceptibility of fish. The quality degradation and excessive fat accumulation in cultured C. idellus have long been attributed to possible alterations in the lipid metabolism of fish muscle tissues as a result of over-nutrition from artificial diets. To investigate the effects of different diets on fish muscle quality, a large-scale metabolomics study was performed on 250 tails of C...
September 6, 2018: GigaScience
Simon P Sadedin, Justine A Ellis, Seth L Masters, Alicia Oshlack
Background: While exome and targeted next generation DNA sequencing are primarily used for detecting single nucleotide changes and small indels, detection of copy number variants (CNVs) can provide highly valuable additional information from the data. Although there are dozens of exome CNV detection methods available, these are often difficult to use and accuracy varies unpredictably between and within data sets. Findings: We present Ximmer, a tool which supports an end to end process for evaluating, tuning and running analysis methods for detection of CNVs in germline samples...
September 6, 2018: GigaScience
Guangqi Gao, Meng Xu, Chunling Bai, Yulan Yang, Guangpeng Li, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, Jun Yin, Yongchun Zuo
Background: As one of the most recognizable characteristics in birds, plumage colour has a high impact on understanding the evolution and mechanisms of colouration. Feather and skin are ideal tissues to explore the genomics and complexity of colour patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst's pheasant (Chrysolophus amherstiae), exhibit brilliant colours in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage colouration mechanisms in birds...
September 6, 2018: GigaScience
Chen Chen, Fei Li, Weixia Wei, Zirong Wang, Juanjuan Dai, Lilan Hao, Liju Song, Xiaowei Zhang, Liping Zeng, Hui Du, Huiru Tang, Na Liu, Huanming Yang, Jian Wang, Lise Madsen, Susanne Brix, Karsten Kristiansen, Xun Xu, Junhua Li, Ruifang Wu, Huijue Jia
Background: The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis identifying the overall microorganism communities has been lacking. Results: We performed shotgun-sequencing using the Illumina platform of 52 samples from the cervical canal and peritoneal fluid of Chinese women in reproductive age...
September 6, 2018: GigaScience
Bao Zhang, Liao Chang, Yong Xian Lan, Nadeem Asif, Fang Lin Guan, Ke Dong Fu, Bo Li, Xia Chun Yan, Bo Hong Zhang, Yan Xiao Zhang, Zhen Yong Huang, Hong Chen, Jun Yu, Bin Sheng Li
Background: The domestication of wild goats and subsequent intensive trait-driven crossing, inbreeding, and selection have led to dramatic phenotypic purification and intermediate breeds for the high-quality production of dairy, cashmere, and meat. Genomic re-sequencing provides a powerful means for the direct identification of trait-associated sequence variations that underlie molecular mechanisms of domestication. Results: Here, we report our effort to define such variations based on data from domestic goat breeds (Capra aegagrus hircus; 5 each) selected for dairy, cashmere, and meat production in referencing to their wild ancestors, the Sindh ibex (Capra aegagrus blythi; 2) and the Markhor (Capra falconeri; 2)...
August 27, 2018: GigaScience
Zhijin Liu, Xinxin Tan, Pablo Orozco-terWengel, Xuming Zhou, Liye Zhang, Shilin Tian, Zhongze Yan, Huailiang Xu, Baoping Ren, Peng Zhang, Zuofu Xiang, Binghua Sun, Christian Roos, Michael W Bruford, Ming Li
Background: The rhesus macaque (RM, Macaca mulatta) is the most important nonhuman primate model in biomedical research. We present the first genomic survey of wild RMs, sequencing 81 geo-referenced individuals of five subspecies from 17 locations in China, a large fraction of the species' natural distribution. Results: Populations were structured into five genetic lineages on the mainland and Hainan Island, recapitulating current subspecies designations. These subspecies are estimated to have diverged 125...
August 27, 2018: GigaScience
Sascha Herzinger, Valentin Grouès, Wei Gu, Venkata Satagopam, Peter Banda, Christophe Trefois, Reinhard Schneider
Background: Translational research platforms share the aim to promote a deeper understanding of stored data by providing visualization and analysis tools for data exploration and hypothesis generation. However, such tools are usually platform-bound and are not easily reusable by other systems. Furthermore, they rarely address access restriction issues when direct data transfer is not permitted. In this article we present an analytical service that works in tandem with a visualization library to address these problems...
August 27, 2018: GigaScience
Ove J R Gustafsson, Lyron J Winderbaum, Mark R Condina, Berin A Boughton, Brett R Hamilton, Eivind A B Undheim, Michael Becker, Peter Hoffmann
Reproducibility, or a lack thereof, is an increasingly important topic across many research fields. A key aspect of reproducibility is accurate reporting of both experiments and the resulting data. Herein, we propose a reporting guideline for mass spectrometry imaging (MSI). Previous standards have laid out guidelines sufficient to guarantee a certain quality of reporting, however they set a high bar and as a consequence can be exhaustive and broad, thus limiting uptake.To help address this lack of uptake, we propose a reporting supplement-Minimum Information About a Mass Spectrometry Imaging Experiment (MIAMSIE)-and its abbreviated reporting standard version, MSIcheck...
August 14, 2018: GigaScience
Guangyi Fan, Judy Chan, Kailong Ma, Binrui Yang, He Zhang, Xianwei Yang, Chengcheng Shi, Henry Law, Zhitao Ren, Qiwu Xu, Qun Liu, Jiahao Wang, Wenbin Chen, Libin Shao, David Gonçalves, Andreia Ramos, Sara D Cardoso, Min Guo, Jing Cai, Xun Xu, Jian Wang, Huanming Yang, Xin Liu, Yitao Wang
Background: Siamese fighting fish Betta splendens (NCBI Taxonomy ID: 158456) are notorious for their aggressiveness and accordingly have been widely used to study aggression. However, the lack of a reference genome has so far limited the understanding of the genetic basis of aggression in this species. Here we present the first reference genome assembly of the Siamese fighting fish. Findings: We first sequenced and de novo assembled a 465.24 Mb genome for the B...
July 11, 2018: GigaScience
Sung-Huan Yu, Jörg Vogel, Konrad U Förstner
To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps...
September 1, 2018: GigaScience
Xiaoping Li, Suisha Liang, Zhongkui Xia, Jing Qu, Huan Liu, Chuan Liu, Huanming Yang, Jian Wang, Lise Madsen, Yong Hou, Junhua Li, Huijue Jia, Karsten Kristiansen, Liang Xiao
Macaca fascicularis, the cynomolgus macaque, is a widely used model in biomedical research and drug development as its genetics and physiology are close to those of humans. Detailed information on the cynomolgus macaque gut microbiota, the functional interplay between the gut microbiota and host physiology, and possible similarities to humans and other mammalians is very limited. The aim of this study was to construct the first cynomolgus macaque gut microbial gene catalog and compare this catalog to the human, pig, and mouse gut microbial gene catalogs...
September 1, 2018: GigaScience
Haiping Liu, Qiyong Liu, Zhiqiang Chen, Yanchao Liu, Chaowei Zhou, Qiqi Liang, Caixia Ma, Jianshe Zhou, Yingzi Pan, Meiqun Chen, Wangjiu, Wenkai Jiang, Shijun Xiao, Zhenbo Mou
Background: Mechanisms for high-altitude adaption have attracted widespread interest among evolutionary biologists. Several genome-wide studies have been carried out for endemic vertebrates in Tibet, including mammals, birds, and amphibians. However, little information is available about the adaptive evolution of highland fishes. Glyptosternon maculatum (Regan 1905), also known as Regan or barkley and endemic to the Tibetan Plateau, belongs to the Sisoridae family, order Siluriformes (catfishes)...
September 1, 2018: GigaScience
Conghui Liu, Yan Zhang, Yuwei Ren, Hengchao Wang, Shuqu Li, Fan Jiang, Lijuan Yin, Xi Qiao, Guojie Zhang, Wanqiang Qian, Bo Liu, Wei Fan
Background: The golden apple snail (Pomacea canaliculata) is a freshwater snail listed among the top 100 worst invasive species worldwide and a noted agricultural and quarantine pest that causes great economic losses. It is characterized by fast growth, strong stress tolerance, a high reproduction rate, and adaptation to a broad range of environments. Results: Here, we used long-read sequencing to produce a 440-Mb high-quality, chromosome-level assembly of the P...
September 1, 2018: GigaScience
Hansheng Zhao, Songbo Wang, Jiongliang Wang, Chunhai Chen, Shijie Hao, Lianfu Chen, Benhua Fei, Kai Han, Rongsheng Li, Chengcheng Shi, Huayu Sun, Sining Wang, Hao Xu, Kebin Yang, Xiurong Xu, Xuemeng Shan, Jingjing Shi, Aiqin Feng, Guangyi Fan, Xin Liu, Shancen Zhao, Chi Zhang, Qiang Gao, Zhimin Gao, Zehui Jiang
Background: Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied biology on rattan. Findings: We produced two chromosome-level genome assemblies of C. simplicifolius and D. jenkinsiana using Illumina, Pacific Biosciences, and Hi-C sequencing data. A total of ∼730 Gb and ∼682 Gb of raw data covered the predicted genome lengths (∼1...
September 1, 2018: GigaScience
Richard J Edwards, Daniel Enosi Tuipulotu, Timothy G Amos, Denis O'Meally, Mark F Richardson, Tonia L Russell, Marcelo Vallinoto, Miguel Carneiro, Nuno Ferrand, Marc R Wilkins, Fernando Sequeira, Lee A Rollins, Edward C Holmes, Richard Shine, Peter A White
Background: The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research. Findings: We report a draft genome assembly for R...
September 1, 2018: GigaScience
Jie Zheng, Tom G Richardson, Louise A C Millard, Gibran Hemani, Benjamin L Elsworth, Christopher A Raistrick, Bjarni Vilhjalmsson, Benjamin M Neale, Philip C Haycock, George Davey Smith, Tom R Gaunt
Background: Identifying phenotypic correlations between complex traits and diseases can provide useful etiological insights. Restricted access to much individual-level phenotype data makes it difficult to estimate large-scale phenotypic correlation across the human phenome. Two state-of-the-art methods, metaCCA and LD score regression, provide an alternative approach to estimate phenotypic correlation using only genome-wide association study (GWAS) summary results. Results: Here, we present an integrated R toolkit, PhenoSpD, to use LD score regression to estimate phenotypic correlations using GWAS summary statistics and to utilize the estimated phenotypic correlations to inform correction of multiple testing for complex human traits using the spectral decomposition of matrices (SpD)...
August 1, 2018: GigaScience
Robert VanBuren, Ching Man Wai, Marivi Colle, Jie Wang, Shawn Sullivan, Jill M Bushakra, Ivan Liachko, Kelly J Vining, Michael Dossett, Chad E Finn, Rubina Jibran, David Chagné, Kevin Childs, Patrick P Edger, Todd C Mockler, Nahla V Bassil
Background: The fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies. Findings: Here, we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding...
August 1, 2018: GigaScience
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