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PubMed | University of America, University of Texas at Arlington, University of Colorado at Denver and United States Geological Survey Fort Collins Science Center
Type: Journal Article | Journal: PloS one | Year: 2014

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clarks Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.


Castoe T.A.,Aurora University | Poole A.W.,Aurora University | de Koning A.P.J.,Aurora University | Jones K.L.,Aurora University | And 7 more authors.
PLoS ONE | Year: 2012

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample - a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable. © 2012 Castoe et al.


Graham J.,Colorado State University | Jarnevich C.S.,United States Geological Survey Fort Collins Science Center | Simpson A.,U.S. Geological Survey | Newman G.J.,Colorado State University | Stohlgren T.J.,United States Geological Survey Fort Collins Science Center
Frontiers of Earth Science | Year: 2011

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance. © 2011 Higher Education Press and Springer-Verlag Berlin Heidelberg.


English N.B.,Los Alamos National Laboratory | McDowell N.G.,Los Alamos National Laboratory | Allen C.D.,United States Geological Survey Fort Collins Science Center | Mora C.,Los Alamos National Laboratory
Rapid Communications in Mass Spectrometry | Year: 2011

Tree-ring carbon and oxygen isotope ratios from live and recently dead trees may reveal important mechanisms of tree mortality. However, wood decay in dead trees may alter the δ 13C and δ 18O values of whole wood obscuring the isotopic signal associated with factors leading up to and including physiological death. We examined whole sapwood and α-cellulose from live and dead specimens of ponderosa pine (Pinus ponderosa), one-seed juniper (Juniperous monosperma), piñon pine (Pinus edulis) and white fir (Abies concolor), including those with fungal growth and beetle frass in the wood, to determine if α-cellulose extraction is necessary for the accurate interpretation of isotopic compositions in the dead trees. We found that the offset between the δ 13C or δ 18O values of α-cellulose and whole wood was the same for both live and dead trees across a large range of inter-annual and regional climate differences. The method of α-cellulose extraction, whether Leavitt-Danzer or Standard Brendel modified for small samples, imparts significant differences in the δ 13C (up to 0.4%) and δ 18O (up to 1.2%) of α-cellulose, as reported by other studies. There was no effect of beetle frass or blue-stain fungus (Ophiostoma) on the δ 13C and δ 18O of whole wood or α-cellulose. The relationships between whole wood and α-cellulose δ 13C for ponderosa, piñon and juniper yielded slopes of ∼1, while the relationship between δ 18O of whole wood and α-cellulose was less clear. We conclude that there are few analytical or sampling obstacles to retrospective studies of isotopic patterns of tree mortality in forests of the western United States. © 2011 by John Wiley & Sons, Ltd.

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