Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes

The majority of nematodes are gonochoristic (dioecious) with distinct male and female sexes, but the best-studied species, Caenorhabditis elegans, is a self-fertile hermaphrodite. The sequencing of the genomes of C. elegans and a second hermaphrodite, C. briggsae, was facilitated in part by the low amount of natural heterozygosity, which typifies selfing species. Ongoing genome projects for gonochoristic Caenorhabditis species seek to approximate this condition by intense inbreeding prior to sequencing. Here we show that despite this inbreeding, the heterozygous fraction of the whole genome shotgun assemblies of three gonochoristic Caenorhabditis species, C. brenneri, C. remanei, and C. japonica, is considerable. We first demonstrate experimentally that independently assembled sequence variants in C. remanei and C. brenneri are allelic. We then present gene-based approaches for recognizing heterozygous regions of WGS assemblies. We also develop a simple method for quantifying heterozygosity that can be applied to assemblies lacking gene annotations. Consistently we find that ∼10% and 30% of the C. remanei and C. brenneri genomes, respectively, are represented by two alleles in the assemblies. Heterozygosity is restricted to autosomes and its retention is accompanied by substantial inbreeding depression, suggesting that it is caused by multiple recessive deleterious alleles and not merely by chance. Both the overall amount and chromosomal distribution of heterozygous DNA is highly variable between assemblies of close relatives produced by identical methodologies, and allele frequencies have continued to change after strains were sequenced. Our results highlight the impact of mating systems on genome sequencing projects

Comparison of Winter Strawberry Production in a Commercial Heated High Tunnel versus a University Greenhouse

For the past 4 years, the University of Nebraska strawberry team has worked to develop low cost, sustainable methods for farmers and growers to produce strawberries in a double polyethylene greenhouse during the winter. This past year, this growing system was adapted to become a commercial grower’s heated high tunnel for the winter/spring of 2013-14. The idea was to scale up to a farm-size demonstration and compare it to the university greenhouse production system with a goal to expand marketing opportunities for strawberries into the winter season

University Research on Winter Growing of Container-Grown Strawberries Translates to Grower\u27s Farm Trial

Strawberries are only seasonally available in Nebraska (NE). If an affordable heated structure can be designed, then opportunity exists to increase on-farm income by producing strawberries off-season during high-value market periods. A series of university greenhouse trials were conducted from 2010 to 2012. The varieties Evie-2 and Seascape were identified as being most productive under a low technology growing scheme. A new research project, which ran from fall to late spring (2013–2014), was designed to determine if this production scheme would translate to a commercial grower. Varieties Seascape and Evie-2 (each at two grades indicated by +) and San Andreas plants were grown simultaneously at the university research greenhouse and a cooperative specialty crop grower greenhouse, similar structures and production timelines. Top performers for both experiment locations were ‘Evie-2ʹ, and ‘Evie-2+’ plants, with average harvest berry weights (marketable) per plant (pp) of over 0.454 kg, and ‘Seascape’ with 0.390 kg. ‘Seascape+’ plants performed well at the cooperator location (0.399 kg pp), but not at the university location. ‘San Andreas’ plants performed well at the university location with 0.454 kg pp but not at the cooperator location. Productivity was greatest during the winter-spring season, which accounted for more than 82% of the total berry mass harvested at the cooperator site and 88% at the university site. The results support the concept that the growing system used within a controlled university research setting is representative of the crop productivity a specialty crop grower might expect, particularly when strawberries are grown in late winter and early spring. However, securing low fuel costs, eliminating delivery and having a secondary market for culls is key for profitability