University of Nevada, Reno

About: University of Nevada, Reno is a education organization based out in Reno, Nevada, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 13561 authors who have published 28217 publications receiving 882002 citations. The organization is also known as: University of Nevada & Nevada State University.

Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing

Abstract: While genome assembly projects have been successful in a number of haploid or inbred species, one of the current main challenges is assembling non-inbred or rearranged heterozygous genomes. To address this critical need, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble Single Molecule Real-Time (SMRT(R)) Sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We demonstrate the quality of this approach by assembling new reference sequences for three heterozygous samples, including an F1 hybrid of the model species Arabidopsis thaliana, the widely cultivated V. vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata that have challenged short-read assembly approaches. The FALCON-based assemblies were substantially more contiguous and complete than alternate short or long-read approaches. The phased diploid assembly enabled the study of haplotype structures and heterozygosities between the homologous chromosomes, including identifying widespread heterozygous structural variations within the coding sequences.

Assessing the development of shorebird eggs using the flotation method: species-specific and generalized regression models

Abstract: ABSTRACT We modeled the relationship between egg flotation and age of a developing embryo for 24 species of shorebirds For 21 species, we used regression analyses to estimate hatching date by modeling egg angle and float height, measured as continuous variables, against embryo age For eggs early in incubation, we used linear regression analyses to predict hatching date from logit-transformed egg angles only For late incubation, we used multiple regression analyses to predict hatching date from both egg angles and float heights In 30 of 36 cases, these equations estimated hatching date to within four days of the true hatching date for each species After controlling for incubation duration and egg size, flotation patterns did not differ between shorebirds grouped by mass (≥100 g or <100 g) or taxonomy (Scolopacidae versus Charadriidae) Flotation progressed more rapidly in species in which both adults incubate the clutch versus species in which only one adult incubates the clutch, although thi