Genome Sequencing of Capsicum Species: Strategies, Assembly, and Annotation of Genes

Pepper (Capsicum spp.) belongs to the Solanaceae, which is an economically important family of flowering plants consisting of about 102 genera and over 2500 species. The Solanaceae family includes crops of agronomic importance for which the efforts in genome sequencing are ongoing by almost 10 years (https://www.solgenomics.net/organism/sol100/view). Since the beginning of 2014, various consortia have released the genome sequences of domesticated and wild Capsicum species. The first effort was focused on the whole-genome sequencing of Capsicum annuum CM334 and of Capsicum chinense PI159236, which were widely used as founders of mapping populations and carry important disease resistance traits. Just a couple of months later, the genome sequences of C. annuum Zunla-1 and of the wild species Chiltepin (C. annuum var. glabriusculum) were published. Both studies reported a pepper genome size of ~3–3.5 Gb, rich in repetitive elements (over 80%) with about 35 thousand genes. The improved version of the reference genome CM334 as well as of C. chinense PI159236 together with the sequencing of the domesticated Capsicum baccatum revealed evolutionary relationships and estimated lineage divergence times occurring in Capsicum. Recently, the linked-read sequencing technology has been applied for the sequencing of a C. annuum accession that was an F1 cross hybrid of CM334 and a non-pungent pepper breeding line. Furthermore, genome resequencing studies have been performed with the aim to analyze loci of interest related to biotic/abiotic stresses and to qualitative features. In this chapter, we provide an overview of the genome sequencing and annotation strategies and describe the main results disclosed by all the whole and targeted genome sequencing projects in Capsicum