Thousands of Pristionchus pacificus orphan genes were integrated into developmental networks that respond to diverse environmental microbiota.

Adaptation of organisms to environmental change may be facilitated by the creation of new genes. New genes without homologs in other lineages are known as taxonomically-restricted orphan genes and may result from divergence or de novo formation. Previously, we have extensively characterized the evolution and origin of such orphan genes in the nematode model organism Pristionchus pacificus. Here, we employ large-scale transcriptomics to establish potential functional associations and to measure the degree of transcriptional plasticity among orphan genes. Specifically, we analyzed 24 RNA-seq samples from adult P. pacificus worms raised on 24 different monoxenic bacterial cultures. Based on coexpression analysis, we identified 28 large modules that harbor 3,727 diplogastrid-specific orphan genes and that respond dynamically to different bacteria. These coexpression modules have distinct regulatory architecture and also exhibit differential expression patterns across development suggesting a link between bacterial response networks and development. Phylostratigraphy revealed a considerably high number of family- and even species-specific orphan genes in certain coexpression modules. This suggests that new genes are not attached randomly to existing cellular networks and that integration can happen very fast. Integrative analysis of protein domains, gene expression and ortholog data facilitated the assignments of biological labels for 22 coexpression modules with one of the largest, fast-evolving module being associated with spermatogenesis. In summary, this work presents the first functional annotation for thousands of P. pacificus orphan genes and reveals insights into their integration into environmentally responsive gene networks.

Response of Tomato Genotypes under Different High Temperatures in Field and Greenhouse Conditions.

Heat stress is one of the production constraints for tomato (Solanum lycopersicum L.) due to unfavorable, above optimum temperatures. This research was undertaken to evaluate growth and fruit yield of tomato genotypes under three contrasting growing conditions (i.e., optimal temperature in field-, high temperature in field- and high temperature in greenhouse conditions) to determine their relative heat tolerance. Eleven tomato genotypes, including two local check varieties, were evaluated, and data on growth and yield were measured and analyzed. The interactions between the genotypes and growing conditions for all yield traits were significant. In general, the performance of tomato under optimal temperature field conditions was better than under high temperature field- and greenhouse conditions. Genotypes CLN1621L, CLN2026D, CLN3212C, and KK1 had consistently greater fruit yield per plant in all growing conditions. Although the local genotype, Neang Tamm, had lower yield under optimal conditions, it performed moderately well under high temperature field- and high temperature greenhouse conditions, and yield decrease under high temperature condition was minimal. Genotype CLN1621L had stable fruit setting compared to other genotypes under high temperature conditions. Since fruit setting and yield are important traits for heat tolerance, genotypes CLN1621L and Neang Tamm are potential candidates for breeding programs focused on improved yield and heat stress tolerance.