*3.2.4. Eggplant genome*

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.

256 Next Generation Sequencing - Advances, Applications and Challenges

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*.

To elucidate the genome structure and complexity, a draft genome sequence of eggplant has recently been published in which the whole genome shotgun sequencing of eggplant variety named as "Nakate-Shinkuro" was carried out using HiSeq 2000 sequencer (Illumina) [62]. The high-quality reads were assembled using SOAPdenovo v1.05 into 1,321,157 scaffolds and presented a draft genome assembly "SME\_r2.5.1" that spanned approximately 74% (833.1 Mb) of the total 1127 Mb of the eggplant genome. Also, transcriptome sequencing of "AE-P03" and "LS1934" was carried out using Roche/454 FLX sequencer (Roche Diagnostics, Basel, Switzer‐ land). By merging the two data sets, a hybrid assembly was produced using PCAP.rep that constituted 81,273 hybrid scaffolds of a total of 836.8 Mb in size. They predicted about 42,035 protein-coding genes in SME\_r2.5.1 by Augustus 2.7. A total of 16,573 genes were located on superscaffolds and showed an orthologous relationship with tomato.
