The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus.

Bottle gourd (Lagenaria siceraria) is an important vegetable crop as well as a rootstock for other cucurbit crops. In this study, we report a high-quality 313.4-Mb genome sequence of a bottle gourd inbred line, USVL1VR-Ls, with a scaffold N50 of 8.7 Mb and the longest of 19.0 Mb. About 98.3% of the assembled scaffolds are anchored to the 11 pseudomolecules. Our comparative genomic analysis identifies chromosome-level syntenic relationships between bottle gourd and other cucurbits, as well as lineage-specific gene family expansions in bottle gourd. We reconstructed the genome of the most recent common ancestor of Cucurbitaceae, which revealed that the ancestral Cucurbitaceae karyotypes consisted of 12 protochromosomes with 18 534 protogenes. The 12 protochromosomes are largely retained in the modern melon genome, while have undergone different degrees of shuffling events in other investigated cucurbit genomes. The 11 bottle gourd chromosomes derive from the ancestral Cucurbitaceae karyotypes followed by 19 chromosomal fissions and 20 fusions. The bottle gourd genome sequence has facilitated the mapping of a dominant monogenic locus, Prs, conferring Papaya ring-spot virus (PRSV) resistance in bottle gourd, to a 317.8-kb region on chromosome 1. We have developed a cleaved amplified polymorphic sequence (CAPS) marker tightly linked to the Prs locus and demonstrated its potential application in marker-assisted selection of PRSV resistance in bottle gourd. This study provides insights into the paleohistory of Cucurbitaceae genome evolution, and the high-quality genome sequence of bottle gourd provides a useful resource for plant comparative genomics studies and cucurbit improvement.

A systems approach demonstrating sphingolipid-dependent transcription in stress responses.

Microarray hybridization allows genome-wide screening of changes in mRNA levels under stress conditions. In Saccharomyces cerevisiae, this approach has demonstrated that responses to heat stress, oxidative stress, nutrient deprivation, and other stress signals are highly overlapping and mRNA levels of a core group of genes, termed 'Environmental Stress Response' (ESR) genes, respond similarly to many stressors. In addition to changes in mRNA levels, stress responses induce wide changes in cell metabolic pathways and metabolite levels. Microarrays coupled with chemical inhibition of these pathways and/or using organisms with genetic mutations in enzymes in the pathways of interest allow determination of the roles of specific metabolites in gene expression. In cases where high-throughput '-omics' strategies are available for determining changes in a spectrum of metabolites, these datasets can be integrated with gene expression data to obtain a systems view of regulations and functions of a given pathway. We have used these approaches to determine the regulation and functions of sphingolipid synthesis in Saccharomyces cerevisiae. Microarray hybridization and sphingolipidomic analysis experiments were performed on two yeast strains bearing mutations in enzymes of sphingolipid metabolism (and their respective parental strains), under normal conditions and during heat stress. These strategies have revealed diverse roles for sphingolipids in regulating stress response genes, and moreover, could be applied to numerous biological systems and thus provide a method to elucidate activities for a vast array of biomolecules, the metabolic pathways by which they are generated, and their cellular functions.