Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom)

Abstract

Elettaria cardamomum (L.) Maton, known as ‘queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild) and SRX1141276 (cultivars). The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

“…A total of 58,278,226 clean and high-quality reads with a 94.25% Q30 level, which ensures the quality of sequencing. In the present study, the N50 sizes of generated unigenes (2002 bp) were obviously longer than those in the Zingiberaceae family, such as A. villosum (N50 = 1381 bp) [ 15 ], C. wenyujin (N50 = 1566 bp) [ 40 ], Curcuma longa (N50 = 1515 bp) [ 41 ], Curcuma alismatifolia (N50 = 1501 bp) [ 42 ], Zingiber officinale (N50 = 1077 bp) [ 43 ], and Elettaria cardamomum (N50 = 616–664 bp) [ 44 ].…”

A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges

“…Transcriptomic studies on leaves, stems, flowers, flower buds, capsule rot disease ( Nadiya et al, 2017 ; Mathew et al, 2019 ), mosaic virus disease ( Khan et al, 2020 ) of small cardamom, and Chirke disease ( Mathew et al, 2020 ) of large cardamom are reported. In turmeric species ( C. longa ), inter-cultivar differential gene expression in rhizomes of Nattu, Erode, Mysore, and Suvarna, along with SNP discovery, has been described ( Annadurai et al, 2013 ; Sahoo et al, 2016 ).…”

Omics Technologies to Enhance Plant Based Functional Foods: An Overview

“…The biological properties of curcumin were explored by using protein expression studies ( Fang et al, 2011 ). The functional component of cardamom ( Elettaria cardamomum ) is d-limonene with antibacterial, anti-inflammatory, analgesic, and antispasmodic activities ( Nadiya et al, 2017 ). Similarly, eugenol and eugenyl acetate, the functional components of clove ( Syzygium aromaticum ) are natural oxidants ( Lee and Shibamoto, 2001 ).…”

“…In garlic and turmeric ( Curcuma longa ), genetic engineering approaches were utilized for developing herbicide tolerant plants ( Park et al, 2002 ; Shirgurkar et al, 2006 ). Although there are some reports on the transcriptome of black pepper fruits ( Hu et al, 2015 ), ginseng (Panax ginseng) ( Rai et al, 2016 ), and cardamom ( Nadiya et al, 2017 ) to study global transcriptome, there are no reports related to functional components in most of the spices. There is tremendous potential to use genomics approaches including trait mapping, transcriptomics, whole-genome studies and allele mining in case of spices to demonstrate and increase the functional components.…”