1,991 Works

Supporting materials from “Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication”

CW Nossa, P Havlak, JX Yue, J Lv, KY Vincent, HJ Brockmann & NH Putnam
Atlantic horseshoe crabs (Limulus polyphemus) are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per...

Genomic data of the Chinese tree shrew (Tupaia chinensis)

Y Fan, Z Huang, C Cao, C Chen, Y Chen, D Fan, J He, H Hou, L Hu, X Hu, X Jiang, R Lai, Y Lang, B Liang, S Liao, D Mu, Y Ma, Y Niu, X Sun, J Xia, J Xiao, Z Xiong, L Xu, L Yang, Y Zhang … & G Zhang
Chinese tree shrews (Tupaia belangeri chinensis) possess many features valuable in animals used as experimental models in biomedical research. Currently, there are numerous attempts to employ tree shrews as models for a variety of human disorders: depression, myopia, hepatitis B and C virus infections, and hepatocellular carcinoma, to name a few. Here we present a publicly available annotated genome sequence for the Chinese tree shrew. Phylogenomic analysis of the tree shrew and other mammalians highly...

Genomic data of the Bald Eagle (Haliaeetus leucocephalus)

W Warren, ED Jarvis, RK Wilson, JT Howard, MTP Gilbert, G Zhang & The Avian Genome Consortium
The Bald Eagle (Haliaeetus leucocephalus(Linnaeus, 1766)) is the official emblem of the United States and it belongs to a group of birds known as fish eagles. They are a large bird with adults weighing upto 4kg.These data have been produced as part of the Avian Phylogenomic Project . DNA was collected from a male bird bred at the NC Raptor Center, Huntersville, North Carolina, USA. The sequencing was conducted at WUSTL. We sequenced the 1.4Gb...

Genomic data of the Great black cormorant (Phalacrocorax carbo)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Great Cormorant (Phalacrocorax carbo) is a widespread member of the cormorant family and is known by several different names around the world - the Black Shag in New Zealand, the Black Cormorant in Australia and the Large Cormorant in India. It is a large black bird that can be distinguished from the Common Shag by its larger size, heavier build and thicker bill. They are mostly silent birds but can produce various guttural noises...

Genomic data of the Great-crested grebe (Podiceps cristatus)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Great Crested Grebe (Podiceps cristatus) is known for its elaborate mating display and is the largest member of the Grebe family in the Old World. In the 19th century, the species was almost hunted to extinction in the UK for its head plumes, which were used to decorate hats and other female attire.These data have been produced as part of the avian phylogenomic project. DNA from the Podiceps cristatus was collected in Denmark. We...

Genomic data of the Bar-tailed trogon (Apaloderma vittatum)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Bar-tailed Trogon (Apaloderma vittatum) belongs to the Trogonidae family of birds and lives in forests at a preferred altitude of around 1600 metres, and who's vocalisations are described "a yelping crescendo". It is found in several African countries - Angola, Burundi, Cameroon, Democratic Republic of the Congo, Equatorial Guinea, and Kenya, to name a few. These data have been produced as part of the avian phylogenomic project. DNA from the Apaloderma vittatum was collected...

Genomic data of the Javan rhinoceros hornbill (Buceros rhinoceros silvestris)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Javan rhinoceros hornbill (Buceros rhinoceros silvestris ) is a sub species of the Rhinoceros Hornbill (Buceros rhinoceros), one of the world's largest hornbills that has lived in captivity for over 90 years. It is found it lowland and tropical and sub-tropical mountain rainforests in Borneo, Sumatra, Java, the Malay Peninsula, Singapore and southern Thailand. It is also the state bird of the Malaysian state, Sarawak. These data have been produced as part of the...

Genomic data of the Red-legged seriema (Cariama cristata)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Red-legged Seriema (Cariama cristata) is a predatory terrestial bird in the Cariamidae family. It is also known as the Crested Cariama. It is found in the grasslands of Brasil, south of the Amazon to Uruguay and northern Argentina. The Red-legged Seriema has a song described to sound like a cross between a bark of a young dog and a clucking of turkeys. These data have been produced as part of the avian phylogenomic project....

Genomic data of the Northern Fulmar (Fulmarus glacialis)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Northern Fulmar (Fulmarus glacialis), also known as Fulmar or Arctic Fulmar, is a highly abundant sea bird and commonly found in north Pacific and north Atlantic subarctic regions. It is a member of the Procellariidae family, which include petrels and shearwaters, and like other petrels, the Northern Fulmar's walking ability is limited but is a very a strong flier. These data have been produced as part of the avian phylogenomic project. DNA from the...

Genomic data of the Chimney swift (Chaetura pelagica)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Chimney Swift (Chaetura pelagica) is a bird belonging to the swift family Apodidae. It is closely related to both the Vaux's Swift and the Chapman's Swift. The Chimney swift is often described as a sociable species, seldom seen alone and only rarely seen at rest. These data have been produced as part of the avian phylogenomic project. DNA from the Chaetura pelagica was collected in USA, Louisiana. We sequenced the genome to a depth...

Genomic data of the Rifleman (Acanthisitta chloris)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Rifleman (Acanthisitta chloris) is an endemic bird to New Zealand and is also known as Tītipounamu in Maori. It belongs to the Acanthisittidae family, also known as New Zealand wrens, and is one of two surviving species. The Rifleman is named after a colonial New Zealand regiment because its plumage is similar to the military uniform of a rifleman.These data have been produced as part of the avian phylogenomic project. DNA from the Acanthisitta...

Supporting material for \"Galaxy-M: A galaxy workflow for processing and analysing direct infusion and liquid chromatography mass spectrometry-based metabolomics data\"

Robert L Davidson, Ralf JM Weber, Archana Sharma-Oates, & Mark R Viant
Metabolomics is increasingly recognised as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other ‘omics fields, specifically genomics and transcriptomics. To achieve its full potential, including the integration of multiple ‘omics modalities, the accessibility, standardisation and reproducibility of computational metabolomics tools must to be improved significantly. Here we present an end-to-end metabolomics analysis pipeline that has been developed for both direct infusion mass spectrometry (DIMS) and...

Supporting data and materials for \"Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat\"

Nicholas C Wong, Bernard J Pope, Ida Candiloro, Darren Korbie, Matt Trau, Stephen Q Wong, Thomas Mikeska, Bryce J Van Denderen, Erik W Thompson, Stefanie Eggers, Stephen Doyle & Alexander Dobrovic
DNA methylation is a complex epigenetic marker that can be analysed using a wide variety of methods. Interpretation and visualisation of DNA methylation data can mask complexity in terms of methylation status at each CpG site, cellular heterogeneity of samples and allelic DNA methylation patterns within a given DNA strand. Bisulfite sequencing is considered the gold standard, however visualisation of massively parallel sequencing results remains a significant challenge. We created a program called Methpat that...

The genome of the Australian dragon lizard Pogona vitticeps

Arthur Georges, , , Denis OMeally, Janine Deakin, , Pei Zhang, Matthew Fujita, Hardip R Patel, Clare E Holleley, Yang Zhou, , Kazumi Matsubara, Paul Waters, Jennifer AM Graves, Stephen D Sarre &
We present a genomic resource for a wild-caught male ZZ Central Bearded Dragon Pogona vitticeps, from Australia. The genomic sequence, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (185x raw read depth) from 13 insert libraries ranging from 250 bp to 40 Kbp. After filtering for low quality and duplicated reads, a total of 146 Gbp of data (86x) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % SNP plus indels)...

Supporting data for \"Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment\"

Alexei J Drummond, Richard D Newcomb, Thomas R Buckley, Dong Xie, Andrew Dopheide, Benjamin CM Potter, Joseph Heled, Howard A Ross, Leah Tooman, Stefanie Grosser, , Nicholas J Demetras, Mark I Stevens, James C Russell, Sandra H Anderson, Anna Carter & Nicola Nelson
There is increasing demand for rapid biodiversity assessment tools that have broad taxonomic coverage. Traditional approaches typically rely on specialists for identification and only evaluate small subsets of biodiversity. Environmental DNA (eDNA) approaches are being promoted as a solution to these limitations, but questions remain unresolved. Here we evaluate a suite of DNA markers coupled with next generation sequencing (NGS) that span the tree of life. We compare these data to traditional biodiversity monitoring tools,...

Supporting data for the \"Draft genome of the Chinese mitten crab, Eriocheir sinensis\"

, Chao Bian, , , , Jia Li, Ying Qiu, , , Liang Ma, , Ying Lei, Jun Qiang, , , Alex Wong, , Qiong Shi &
Chinese mitten crab, Eriocheir sinensis, has been one of the most famous representatives of crustacean in China. Its transition from swimming type to crawling during the early development process, anadromous migration for growth, and catadromous migration for breeding have been attractive for research. However, the knowledge about the underlying molecular mechanisms to regulate these processes is still very limited. A total of 258.8-Gb raw reads for crab whole-genome sequencing were generated by the Illumina HiSeq2000...

Annotation and analysis of three crocodilian genomes

RE Green, EL Braun, J Armstrong, D Earl, N Nguyen, G Hickey, MW Vandewege, JA St John, S Capella-Gutiérrez, TA Castoe, C Kern, MK Fujita, JC Opazo, J Jurka, KK Kojima, J Caballero, RM Hubley, AF Smit, RN Platt, CA Lavoie, MP Ramakodi, , A Suh, Isberg, L Miles … & DA Ray
Crocodilians are important model organisms in fields as diverse as developmental biology, osmoregulation, cardiophysiology, paleoclimatology, sex determination, population genetics, paleobiogeography, and functional morphology. Crocodilians, birds, dinosaurs, and pterosaurs comprise a monophyletic group known as the archosaurs. Crocodilians and birds are the only extant members and thus crocodilians (alligators, caimans, crocodiles, and gharials) are the closest living relatives of all birds. To provide context for the diversifications of archosaurs, we generated draft genomes of three crocodilians,...

Supporting material for: \"Rapid detection of structural variation in a Human genome using nanochannel-based genome mapping technology\"

HZ Cao, AR Hastie, D Cao, ET Lam, Y Sun, H Huang, X Liu, L Lin, W Andrews, S Chan, S Huang, X Tong, M Requa, T Anantharaman, A Krogh, H Yang, H Cao & X Xu
The nanochannel-based Genome Mapping technology, commercialized as the Irys Platform, automatically images fluorescently labeled DNA molecules in a massively parallel nanochannel array. This technology has previously been used to map the 4.7-Mb highly variable human MHC region, as well as for de novo assembly of a 2.1-Mb region in the highly complex Aegilops tauschii genome, lending great promise for use in complete genome sequence analysis. Here, we apply this rapid and high-throughput genome mapping method...

Gene-set of brown planthopper genome

Wang Zhuo, Yu Li-Li, Zhou Xin & Zhang Chuan-Xi
The brown planthopper, Nilaparvata lugens, the most destructive pest of rice, is a typical monophagous herbivore that feeds exclusively on rice sap, which migrates over long distances. Outbreaks of it have re-occurred approximately every three years in Asia. It has also been used as a model system for ecological studies and for developing effective pest management. The N. lugens population sequenced in the present study was originally collected in Hangzhou, China, in 2008 and had...

Supporting materials for: \"VirAmp: A Galaxy-based viral genome assembly pipeline\".

Y Wan, DW Renner, I Albert & ML Szpara
We have developed a multi-step viral genome assembly pipeline named VirAmp, that combines existing tools and techniques and presents them to end users via a web-enabled Galaxy interface. Our pipeline allows users to assemble, analyze and interpret high coverage viral sequencing data with an ease and efficiency that was not possible previously. Our software makes a large number of genome assembly and related tools available to life scientists and automates the currently recommended best practices...

Supporting materials for \"BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ\"

Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai & Olivier Collin
Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. The Galaxy web-based platform for data intensive biomedical research (http://usegalaxy.org/) offers multiple ways to give access to this data through its web interface. However, the process of adding new reference data was customarily manual and time consuming, even more so when this data needed to be indexed in a variety of formats (e.g. Blast, Bowtie, BWA, or 2bit). BioMAJ is a widely...

The colorectal adenoma-carcinoma microbiome

Qiang Feng, , , Andreas Stadlmayr, , Zhou Lan, , , , , Lili Su, , Xin Li, , Liang Xiao, Ursula Huber-Schonauer, David Niederseer, Xun Xu, Jumana Yousuf Al-Aama, , Jian Wang, Karsten Kristiansen, , Herbert Tilg, Christian Datz … & Jun Wang
Colorectal cancer, a commonly diagnosed cancer in the elderly, often develops slowly from benign polyps called adenoma. The gut microbiota is believed to be directly involved in colorectal carcinogenesis. The identity and functional capacity of the adenoma- or carcinoma-related gutmicrobe(s), however, have not been surveyed in a comprehensive manner. Here we perform a metagenome-wide association study (MGWAS) on stools from advanced adenoma and carcinoma patients and from healthy subjects, revealing microbial genes, strains and functions...

RNA-Seq analysis and annotation of a draft blueberry genome assembly.

V Gupta, AD Estrada, I Blakley, R Reid, K Patel, , SU Andersen, AF Brown, MA Lila & AE Loraine
Blueberries are a popular and commercially important fruit, rich in antioxidants and other beneficial compounds that can protect against disease. To understand and identify genes involved in synthesis of bioactive compounds that could enable breeding berry varieties with enhanced health benefits, a draft blueberry genome assembly was produced using RNA-Seq data from five stages of berry fruit development and ripening. Libraries were prepared from samples of green and ripe fruit from plants of the O’Neal...

Software for \"Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies\"

Darling E Aaron &
Chromosome conformation capture (3C) and HiC DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols.
We describe a computational simulator that, given reference genome sequences and some basic parameters, will simulate HiC sequencing on those sequences. The simulator models...

Supporting material for \"High throughput identification of novel conotoxins from the Chinese tubular cone snail (Conus betulinus) by multi-transcriptome sequencing\"

Chao Peng, Ge Yao, , , Chao Bian, , Ying Cao, Bo Wen, , , , , Jie Bai, Jia Li, , , , Ying Qiu, , Steven L Coon, , Ji-Sheng Chen & Qiong Shi
The venom of predatory marine cone snails mainly contains a diverse array of unique bioactive peptides commonly referred to as conopeptides or conotoxins. These peptides have proven to be valuable pharmacological probes and potential drugs because of their high specificity and affinity to important ion channels, receptors and transporters of the nervous system. Most of previous studies have specifically focused on the conopeptides from piscivorous and molluscivorous cone snails, but little attention has been devoted...

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