skip to main content

Attention:

The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 11:00 PM ET on Thursday, June 13 until 2:00 AM ET on Friday, June 14 due to maintenance. We apologize for the inconvenience.


Search for: All records

Creators/Authors contains: "Sullivan, A. P."

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Background High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. Findings We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. Conclusions These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology. 
    more » « less
  2. Abstract

    As part of the WINTER (Wintertime Investigation of Transport, Emissions, and Reactivity) campaign, a Particle‐into‐Liquid Sampler with a fraction collector was flown aboard the National Center for Atmospheric Research C‐130 aircraft. Two‐minute integrated liquid samples containing dissolved fine particulate matter (PM1) species were collected and analyzed off‐line for the smoke marker levoglucosan using high‐performance anion‐exchange chromatography‐pulsed amperometric detection to compare levoglucosan with aerosol mass spectrometer (AMS) biomass burning markers and investigate the contribution from residential burning during the study. Levoglucosan was correlated with AMS organic aerosol (R2 = 0.49) and with carbon monoxide (CO;R2 = 0.51) for all flights. Levoglucosan was not correlated with the inorganic smoke marker water‐soluble potassium but was correlated with the AMS markers ∆C2H4O2+(high resolution,R2 = 0.60) and ∆m/z60 (unit mass resolution,R2 = 0.61). However, at low levoglucosan, AMS markers deviated potentially due to interferences from other sources or differences with the species captured by the AMS markers. Analysis of levoglucosan changes relative to carbon monoxide as plumes advected from source regions showed no systematic levoglucosan loss for plumes up to 20 hr old. Based on literature residential burning source ratios and measured levoglucosan, contributions of organic carbon (OC) due to residential burning were estimated. The contribution ranged from ~30 to 100% of the OC, with significant variability depending on the source ratio used; however, the results show that biomass burning was a significant PM1OC source across the entire sampling region. A GEOS‐Chem model simulation predicted significantly less smoke contribution.

     
    more » « less