To jump or not to jump - The Bereitschaftspotential required to jump into 192-meter abyss.
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ABSTRACT:
SUBMITTER: Nann M
PROVIDER: S-EPMC6381093 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Abstract We investigated, for the first time, the hitchhiker‐host fidelity of deep‐diving whale sharks and Chilean devil rays. We found that two of the most ubiquitous oceanic hitchhikers, the common remora and the pilot fish, are able to follow their hosts to bathypelagic depths, where they are exposed to extreme gradients of light, dissolved oxygen, temperature, and pressure. We documented a deep dive of a large whale shark hosting remoras and pilot fish. Common remora was observed at the deepest section of the dive, at 1460 m, where the water temperature was 3.6°C. A pilot fish was recorded at 900 m, during the ascent phase, with the water temperature of 7.5°C. Although the adaptations that allow these hitchhikers to mitigate the impacts of such extreme environmental conditions remain unknown, we discuss these findings in the framework of the ecophysiology of deep diving and the hitchhiker‐host fidelity. We found that common remora and the pilot fish are able to follow their hosts to bathypelagic depths, where they are exposed to extreme gradients of light, dissolved oxygen, temperature, and pressure. Although the adaptations that allow these hitchhikers to mitigate the impacts of such extreme environmental conditions remain unknown, we discuss these findings in the framework of the ecophysiology of deep diving and the hitchhiker‐host fidelity.
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Project description:BackgroundDe novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes. De novo short-read assemblers commonly use de Bruijn graphs, where nodes are sequences of equal length k, also known as k-mers. Edges in this graph are established between nodes that overlap by [Formula: see text] bases, and nodes along unambiguous walks in the graph are subsequently merged. The selection of k is influenced by multiple factors, and optimizing this value results in a trade-off between graph connectivity and sequence contiguity. Ideally, multiple k sizes should be used, so lower values can provide good connectivity in lesser covered regions and higher values can increase contiguity in well-covered regions. However, current approaches that use multiple k values do not address the scalability issues inherent to the assembly of large genomes.ResultsHere we present RResolver, a scalable algorithm that takes a short-read de Bruijn graph assembly with a starting k as input and uses a k value closer to that of the read length to resolve repeats. RResolver builds a Bloom filter of sequencing reads which is used to evaluate the assembly graph path support at branching points and removes paths with insufficient support. RResolver runs efficiently, taking only 26 min on average for an ABySS human assembly with 48 threads and 60 GiB memory. Across all experiments, compared to a baseline assembly, RResolver improves scaffold contiguity (NGA50) by up to 15% and reduces misassemblies by up to 12%.ConclusionsRResolver adds a missing component to scalable de Bruijn graph genome assembly. By improving the initial and fundamental graph traversal outcome, all downstream ABySS algorithms greatly benefit by working with a more accurate and less complex representation of the genome. The RResolver code is integrated into ABySS and is available at https://github.com/bcgsc/abyss/tree/master/RResolver .
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Project description:Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of individual human genomes to catalog natural genetic variation. To address this limitation, we developed ABySS (Assembly By Short Sequences), a parallelized sequence assembler. As a demonstration of the capability of our software, we assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina, Inc. Approximately 2.76 million contigs > or =100 base pairs (bp) in length were created with an N50 size of 1499 bp, representing 68% of the reference human genome. Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes.
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