*3.2.1. Potato genome*

The draft sequence of 844 Mb genome of a homozygous double-monoploid genotype named DM (DM1-3 516R44) was sequenced using three methods, namely, Sanger method, Roche/454 Pyrosequencing, and Illumina sequencing-by-synthesis method and assembled using the SOAPdenovo assembly algorithm (PGSC; The Potato Genome Sequencing Consortium, 2011) [6]. A heterozygous diploid line, i.e., RH (RH89-039-16) was also sequenced using shotgun sequencing of BACs and WGS, and its reads were mapped to the reference assembly of DM genome (http://potatogenome.net). About 86% of the genome was anchored and assembled into pseudomolecules. A total of 39,031 protein-coding genes were obtained; of them, 90% were located on 12 pseudomolecules. To overcome the problem of heterozygosity and inbreeding depression, which is the major drawback in potato improvement using traditional breeding practices, the researchers selected a homozygous, double-monoploid form, referred as DM for sequencing and integrated with sequence data of heterozygous diploid line RH. The potato genome was the first among the asterid species to be sequenced, and a total of 2642 high-confidence asterid-specific and 3372 potato lineage-specific genes were identified and also found the collinearity with 97.5% identity between DM and RH genome. Furthermore, they identified 3.67 million SNPs and 275 gene-specific presence/absence variations and concluded that the homozygous alleles were the reason for the reduced level of vigor in DM line. They also studied the evolution of tuber development, which revealed that about 15,235 genes were found to be expressed in developing tubers.

#### *3.2.2. Tomato genome*

scriptome profiling in two *C. annuum* varieties resulted in 279,221 and 316,357 sequenced reads with a total of 120.44 and 142.54 Mb of sequence data. A total of 9701 and 12,741 potential SNPs

Eggplant or brinjal (*S. melongena* L.), an autogamous diploid (2*n* = 2*x* = 24), is the third most important vegetable crop from the genus *Solanum* after potato (*S. tuberosum*) and tomato (*S. lycopersicum*). The eggplant is widely grown in Asia, the Middle and Near East, Southern Europe, and Africa [54]. The eggplant fruit serves as an excellent source of antioxidants like anthocyanin and phenolics [55, 56] and the tolerance to abiotic and biotic stresses [57]. Therefore, several genetic studies have been carried out from the last two decades targeting various fruit traits such as size/shape and color. Moreover, the different origin of eggplant from other Solanaceae spp. makes it an important crop for comparative and evolutionary studies. In this regard, various aspects have been focused by researchers such as the develop‐ ment of genetic resources like molecular markers and genetic map that have been utilized for comparative analysis with other spp. of the Solanaceae family. The eggplant belongs to the *Leptostemonum* clade, which is far lagged behind the potato and tomato (potato clade) in terms of the development of genomic resources as only a total of 226,664 nucleotide sequences were available in NCBI database, of which majority (98,086) were obtained from ESTs generated by Fukuoka et al. [58]. These 98,086 ESTs were assembled into 16,245 unigenes that covered only a limited portion of eggplant transcriptome. Later, transcriptome sequencing was carried out using Illumina sequencing and reads were assembled into contigs using Trinity program [59]. Of these, 80% (27,393) of unigenes showed matches with the sequences available in NCBI nr database. A total of 29,717 genes were functionally annotated. A comparison of eggplant with 11 plant proteomes resulted in 276 high-confidence single-copy orthologous groups and revealed that eggplant and its wild *Leptostemonum* clade relative "turkey berry" split ~6.66 million years ago in the late Miocene and the *Leptostemonum* split ~15.75 Mya from the potato

were identified [53].

254 Next Generation Sequencing - Advances, Applications and Challenges

clade in the middle Miocene.

*3.2.1. Potato genome*

**3.2. Whole genome and transcriptome sequencing of Solanaceae spp.**

ment, and comparative study of genome evolution between different species.

Whole genome sequencing of a species reveals the structural organization of genome, includ‐ ing a number of protein-coding and non-protein-coding genes and repetitive elements and serves as the basis for finding genome-wide analysis of genetic variation, QTL mapping, diversity analysis, association mapping of agronomically important traits for crop improve‐

The draft sequence of 844 Mb genome of a homozygous double-monoploid genotype named DM (DM1-3 516R44) was sequenced using three methods, namely, Sanger method, Roche/454 Pyrosequencing, and Illumina sequencing-by-synthesis method and assembled using the SOAPdenovo assembly algorithm (PGSC; The Potato Genome Sequencing Consortium, 2011) [6]. A heterozygous diploid line, i.e., RH (RH89-039-16) was also sequenced using shotgun

*3.1.4. Eggplant*

In the year 2012, the Tomato Genome Consortium (TGC, 2012) [5] reported the draft genome sequence of inbred cultivar of tomato "Heinz 1706" using a combination of NGS technologies (454/Roche GS FLX, Illumina Genome Analyser, and SOLiD sequencing). They predicted the genome size of 900 Mb, which were assembled in 91 scaffolds aligned to 12 chromosomes. The data revealed only 0.6% nucleotide divergence (in two tomato genotypes) compared to 8% divergence with potato. The alignment of tomato–potato orthologous regions confirmed nine largeinversionsduringevolution.Theypredictedabout34,727(intomato)and35,004(inpotato) protein-coding genes. The analysis suggested that the genome triplications could have added new gene family members such as RIN (ripening-inhibitor), CNR (colorless nonripening), ACS (associatedwithethylene biosynthesis),PHYB1/PHYB2 forredlightphotoreceptors, andPSY1/ PSY2 (phytoene synthase) for lycopene biosynthesis that mediate important fruit-specific functions such as fleshiness and color. Further, the study reported the presence of noncoding RNAs (ncRNA) with the identification of 96 miRNA genes in tomato and 120 miRNA genes in potato genome. In another study, Aflitos et al. [60] performed the resequencing of 84 tomato accessions and explored the genetic variability present among those cultivated tomato and its wild progenitor. They identified more than 10 million SNPs in wild species, signifying the dramatic genetic erosion of tomato. Furthermore, through comparative sequence alignment, group-, species-, and accession-specific polymorphism was observed, which may be linked to agronomically important fruit traits. Such information may be easily used by recent highthroughput genotyping methods for the detection of genetic variability across extensive populations. The genomic information provided by these projects could be used for compara‐ tive genetic and genomic studies and in-depth sequence analysis in Solanaceae.

#### *3.2.3. Pepper genome*

The recent advancement in the sequencing and development of NGS technologies has accelerated the genetics and genomics studies of capsicum. Recently, a draft genome sequence of a diploid hot pepper, i.e., "*C. annum* cv 'CM334'" (Criollo de Morelos 334), was published [7]. The variety CM334 has been utilized in breeding practices as it showed resistance against *Phytophthora capsici*, pepper mottle virus, and root-knot nematodes. The authors reported sequencing a total of 650.2 Gb pepper genome, which is approximately equal to 186.6× genome coverage of 3.48 Gb estimated *C. annuum* genome by utilizing Illumina platform. Filtered reads were assembled into 37,989 scaffolds using SOAPdenovo and SPACE (total 3.06 Gb). Anchor‐ ing of those contigs on high-density genetic map could assembled 86% of the (2.63 Gb; 1357 scaffolds) scaffolds onto 12 pseudomolecules of capsicum genome. A total of 34,903 proteincoding genes were identified using the PGA annotation pipeline. The comparative analysis showed a high level of conservation with its closest relative, i.e., tomato, as 17,397 orthologous gene sets were identified, and their expression studies revealed that 8.8% of them showed expression in leaf tissue and 46.4% were found to be expressed in pericarp tissue. As the pepper genome is four times larger than tomato, the genome size increment seen is mainly due to the presence of a large number of repetitive elements such as LTR retrotransposons. Of the reported retrotransposons, the Gypsy family was found to present 12-fold more than the Copia family when compared to another genome such as tomato, maize, and barley. Moreover, the expression analysis of different capsaicinoid pathway genes showed that all genes were expressed at 16 DPA, 25 DPA, and mature green stages of pepper fruit, but their orthologous genes hardly showed any expression in tomato and potato fruits. This study confirms the specificity of capsaicinoid pathway in the development of pungent flavor in pepper fruit.

To provide a better understanding of evolution and domestication of capsicum, Qin et al. [61] reported two reference genome sequences of cultivated Zunla-1 (*C. annuum* L.) and wild Chiltepin (*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 intronoverlapping 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*.
