Reaping the Benefits of Next-generation Sequencing Technologies for Crop Improvement — Solanaceae

Next-generation sequencing (NGS) technologies make possible the sequencing of the whole genome of a species decoding a complete gene catalogue and transcriptome to al‐ low the study of expression pattern of entire genes. The huge data generated through whole genome and transcriptome sequencing not only provide a basis to study variation at gene sequence (such as single-nucleotide polymorphism and InDels) and expression level but also help to understand the evolutionary relationship between different crop species. Furthermore, NGS technologies have made possible the quick correlations of phenotypes with genotypes in different crop species, thereby increasing the precision of crop improvement. The Solanaceae family represents the third most economically impor‐ tant family after grasses and legumes due to high nutritional components. The current advances in NGS technology and their application in Solanaceae crops made several pro‐ gresses in the identification of genes responsible for economically important traits, devel‐ opment of molecular markers, and understanding the genome organization and evolution in Solanaceae crops. The combination of high-throughput NGS technologies with conventional crop breeding has been shown to be promising in the Solanaceae trans‐ lational genomics research. As a result, NGS technologies has been seen to be adopted in a large scale to study the molecular basis of fruit and tuber development, disease resist‐ ance, and increasing quantity and quality of crop production. ( C. annuum var. glabriusculum) pepper. They estimated the genome size of 3.26 Gb and 3.07 Gb, respectively. The reads were assembled in scaffolds comprising 3.48 and 3.35 Gb, respectively. They found different transposable elements (TEs) that covered ∼2.7 Gb (81%) of the genome and estimated that the pepper genome expanded ∼0.3 Mya. Approximately 79% of 3.48 Gb scaffolds contained 34,476 protein-coding genes that were anchored to chromo‐ somes by a high-density genetic map. Using an in-house-generated program, they identified 6527 long noncoding RNAs (lncRNAs), which comprised 5976 intergenic and 222 intron-overlapping lncRNAs. In addition, the sequencing of small RNAs from five different tissues allowed the identification of 5581 phased siRNAs. Based on plant micro-RNAs (miRNAs) miRBase database, a total of 176 miRNAs were discovered of which 35 were found to be specific to pepper. They also predicted 1104 target genes that have putative functions such as dihy‐ drolipoamide dehydrogenase ( Capana12g000245 ) and α-CT ( Capana09g001602 ) genes from capsaicinoid biosynthetic pathway, suggesting the regulation of capsaicinoid biosynthesis by miRNAs. Further, they identified 31% constitutively expressed genes and also 3670 genes that were showing tissue-specific expression. The annotation of these genes resulted in the identification of candidate genes for various traits. By a comparison of cultivated and wild pepper genomes with data of 20 resequencing accessions, they identified genes for domesti‐ cation, which revealed molecular footprints of artificial selection. Moreover, they identified 51 gene families involved in capsaicinoid biosynthesis, and based on the phylogenetic analysis, they concluded that independent pepper-specific duplications in 13 gene families had occurred compared with tomato, potato, and Arabidopsis