College of Agriculture and Life Sciences (CALS)

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Browsing College of Agriculture and Life Sciences (CALS) by Department "Advanced Research Computing"

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    The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere
    Compton, Austin; Liang, Jiangtao; Chen, Chujia; Lukyanchikova, Varvara; Qi, Yumin; Potters, Mark B.; Settlage, Robert; Miller, Dustin; Deschamps, Stephane; Mao, Chunhong; Llaca, Victor; Sharakhov, Igor V.; Tu, Zhijian Jake (Genetics Society of America, 2020-10-01)
    Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce a de novo assembly of the New World malaria mosquito, Anopheles albimanus by integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50 = 13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is the first in mosquito assemblies and represents a significant step toward the completion of a genome assembly. These telomeres consist of tandem repeats of a novel 30-32 bp Telomeric Repeat Unit (TRU) and are confirmed by analyzing the termini of long reads and through both chromosomal in situ hybridization and a Bal31 sensitivity assay. The AalbS3 assembly included previously uncharacterized centromeric and rDNA clusters and more than doubled the content of transposable elements and other repetitive sequences. This telomere-to-telomere assembly, although still containing gaps, represents a significant step toward resolving biologically important but previously hidden genomic components. The comparison of different scaffolding methods will also inform future efforts to obtain reference-quality genomes for other mosquito species.
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    Public Access: A Driver for Preservation and Discovery of Datasets at a US Land-Grant Institution
    Ogier, Andrea; Petters, Jonathan L.; Pannabecker, Virginia; Settledge, Robert; Grant, Elizabeth J.; Harden, Samantha M.; Griffin, Julie; Walters, Tyler (2019-08-24)
    Public access to federally funded research data ensures preservation and discovery of datasets to promote translation of research evidence into meaningful outcomes. However, historical policy and concerns regarding making data publicly accessible impede realization of implementing public access to data. These concerns include worry over the treatment of intellectual property, the cost (in time and money) of making research publicly accessible, and the danger of accidentally releasing human subjects data. To overcome these issues, a Public Access to Data Committee was established at a public university in rural southwest Virginia. In this paper we review the history of federal public access provisions, share goals, and describe the committee’s process to ultimately engage faculty and administrators in this critical link from research to practice.