The Cucumber Genome—An Update

Abstract

Cucumber, Cucumis sativus L. (2n = 2x = 14), is both an economically and biologically important vegetable crop. Cucumber was the first horticultural crop with a publicly released genome. Draft genomes with varying qualities of four cucumber genotypes (‘9930’, ‘Gy14’, B10, and PI 183967) were developed using Illumina short-read sequencing or 454 technologies. In recent years, high throughput long-read sequencing and new scaffolding technologies have significantly improved assembly quality of genomes. The low cost of sequencing also allows most crops to afford a draft genome. In cucumber, using single molecule, real-time (SMRT), and Illumina sequencing and 10 × Genomics and Hi-C scaffolding methods, new versions of genome assemblies have been developed for both 9930 (v3.0) and B10 (v3.0). In this chapter, I will summarize major improvements and new insights from these new assemblies. I will also review recent progress in cucumber organelle genomes. I will discuss the cucumber genome in the context of comparative analysis with other cucurbits, cucumber genome evolution, domestication, and population genomics perspectives.