The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

Merchant, Nirav; Lyons, Eric; Goff, Stephen A.; Vaughn, Matthew; Ware, Doreen; Micklos, David; Antin, Parker B.

doi:10.1371/journal.pbio.1002342

Cited by 293 publications

(246 citation statements)

References 5 publications

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“…Bacterial genomes include representatives of 4 phyla. A total of 132 prophage sequences were identified including 99 prophages identified by CyVerse 54 implementation of VirSorter 55 in the categories 1, 2, 4, and 5, and 33 prophages identified by manual curation based on the presence of hallmark phage genes and analysis of synteny with closely related strains. Coordinates of 35 prophages predicted by VirSorter had to be manually adjusted to eliminate bacterial genes (including ribosomal RNAs and other housekeeping genes) and to separate 2 prophage sequences called as one prophage over an intervening stretch of bacterial genes.…”

Section: Isolate Reference Viruses (Ivgs)mentioning

confidence: 99%

Uncovering Earth’s virome

Páez-Espino

Eloe‐Fadrosh

Pavlopoulos

et al. 2016

Nature

923

977

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Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the number of known viral genes by 16-fold. Half of the predicted partial viral genomes were clustered into genetically distinct groups, most of which included genes unrelated to those in known viruses. Using CRISPR spacers and transfer RNA matches to link viral groups to microbial host(s), we doubled the number of microbial phyla known to be infected by viruses, and identified viruses that can infect organisms from different phyla. Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups. Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host-virus interactions.

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Section: Isolate Reference Viruses (Ivgs)mentioning

confidence: 99%

Uncovering Earth’s virome

Páez-Espino

Eloe‐Fadrosh

Pavlopoulos

et al. 2016

Nature

923

977

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“…Project data, code, and a wiki were maintained using CyVerse (Merchant et al 2016). Jetstream cloud computing cyberinfrastructure (Stewart et al 2015) was used for uncertainty analyses in R and R-Studio (R-Studio Team 2015).…”

Section: Aboveground Biomass and Carbon Contentmentioning

confidence: 99%

Topographically driven differences in energy and water constrain climatic control on forest carbon sequestration

et al. 2017

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. 2017. Topographically driven differences in energy and water constrain climatic control on forest carbon sequestration. Ecosphere 8(4):e01797. 10.1002/ecs2.1797Abstract. Mountains are vital to ecosystems and human society given their influence on global carbon and water cycles. Yet the extent to which topography regulates montane forest carbon uptake and storage remains poorly understood. To address this knowledge gap, we compared forest aboveground carbon loading to topographic metrics describing energy balance and water availability across three headwater catchments of the Boulder Creek Watershed, Colorado, USA. The catchments range from 1800 to 3500 m above mean sea level with 46-102 cm/yr mean annual precipitation and À1.2°to 12.3°C mean annual temperature. In all three catchments, we found mean forest carbon loading consistently increased from ridges (27 AE 19 Mg C ha) to valley bottoms (60 AE 28 Mg C ha). Low topographic positions held up to 185 AE 76 Mg C ha, more than twice the peak value of upper positions. Toe slopes fostered disproportionately high net carbon uptake relative to other topographic positions. Carbon storage was on average 20-40 Mg C ha greater on north to northeast aspects than on south to southwest aspects, a pattern most pronounced in the highest elevation, coldest and wettest catchment. Both the peak and mean aboveground carbon storage of the three catchments, crossing an 11°C range in temperature and doubling of local precipitation, defied the expectation of an optimal elevation-gradient climatic zone for net primary production. These results have important implications for models of forest sensitivity to climate change, as well as to predicted estimates of continental carbon reservoirs.

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“…Processed data files formatted for the IGV, as well as a pregenerated IGV session containing the data files, are available for download from the CyVerse Data Store (previously iPlant Collaborative; Merchant et al, 2016) via the links listed in Supplemental Table 5. Sequence data from this article can be found in the NCBI Sequence Read Archive (SRA) under the umbrella accession number PRJNA335625.…”

Section: Accession Numbersmentioning

confidence: 99%

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear

Song²,

Zynda³

et al. 2017

Plant Cell

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All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ;32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.

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The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

Cited by 293 publications

References 5 publications

Uncovering Earth’s virome

Uncovering Earth’s virome

Topographically driven differences in energy and water constrain climatic control on forest carbon sequestration

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

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