Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The Survival of <i>Pinus ponderosa</i> Saplings Subjected to Increasing Levels of Fire Behavior and Impacts on Post-Fire Growth

Improved predictions of tree species mortality and growth metrics following fires are important to assess fire impacts on forest succession, and ultimately forest growth and yield. Recent studies have shown that North American conifers exhibit a &#8216;toxicological dose-response&#8217; relationship between fire behavior and the resultant mortality or recovery of the trees. Prior studies have not been conclusive due to potential pseudo-replication in the experimental design and time-limited observations. We explored whether dose-response relationships are observed in ponderosa pine (Pinus ponderosa) saplings exposed to surface fires of increasing fire behavior (as quantified by Fire Radiative Energy&#8212;FRE). We confirmed equivalent dose-response relationships to the prior studies that were focused on other conifer species. The post-fire growth in the saplings that survived the fires decreased with increasing FRE dosages, while the percentage mortality in the sapling dosage groups increased with the amount of FRE applied. Furthermore, as with lodgepole pine (Pinus contorta), a low FRE dosage could be applied that did not yield mortality in any of the replicates (r = 10). These results suggest that land management agencies could use planned burns to reduce fire hazard while still maintaining a crop of young saplings. Incorporation of these results into earth-system models and growth and yield models could help reduce uncertainties associated with the impacts of fire on timber growth, forest resilience, carbon dynamics, and ecosystem economics

Dataset associated with “Genomic‐based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America"

The dataset contains SSR marker data for the purpose of measuring population structure and relatedness among populations of Bassica scoparia (kochia) from across the western USA and Canada, collected from 2007-2015. The dataset also contains scripts to run the analyses described in the publication.Genomic-based epidemiology can provide insight into the origins and spread of herbicide resistance mechanisms in weeds. We used kochia (Bassia scoparia) populations resistant to the herbicide glyphosate from across western North America to test the alternative hypotheses that 1) a single EPSPS gene duplication event occurred initially in the Central Great Plains and then subsequently spread to all other geographical areas now exhibiting glyphosate-resistant kochia populations or that 2) gene duplication occurred multiple times in independent events in a case of parallel evolution. We used qPCR markers previously developed for measuring the structure of the EPSPS tandem duplication to investigate whether all glyphosate-resistant individuals had the same EPSPS repeat structure. We also investigated population structure using simple sequence repeat (SSR) markers to determine the relatedness of kochia populations from across the Central Great Plains, Northern Plains, and the Pacific Northwest. We found that the original EPSPS duplication genotype was predominant in the Central Great Plains where glyphosate resistance was first reported. We identified two additional EPSPS-duplication genotypes, one having geographic associations with the Northern Plains and the other to the Pacific Northwest. The EPSPS duplication genotype from the Pacific Northwest seems likely to represent a second, independent evolutionary origin of a resistance allele. We found evidence of gene flow across populations and a general lack of population structure. The results support at least two independent evolutionary origins of glyphosate resistance in kochia, followed by substantial and mostly geographically localized gene flow to spread the resistance alleles into diverse genetic backgrounds.The work was supported by USDA National Institute of Food and Agriculture grant number 2012-67013-19347 to PW, Western Sugar Joint Research Committee, Snake River Sugar Beet Research and Seed Alliance, Colorado Wheat Administrative Committee, USDA-NIFA Hatch project COL00783 at Colorado State University, and USDA National Institute of Food and Agriculture through the Western Integrated Pest Management Center, grant number 2018-70006-28881 to support the Western IPM Kochia Work Group