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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 was 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. 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.
Data in Brief
Transcriptome proling of Elettaria cardamomum (L.) Maton
(small cardamom)
F. Nadiya
a
, N. Anjali
a
, Jinu Thomas
a
, A. Gangaprasad
b
, K.K. Sabu
a,
a
Biotechnology and Bioinformatics Division, Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram 695562, India
b
Department of Botany, University of Kerala, Thiruvananthapuram 695581, India
abstractarticle info
Article history:
Received 16 December 2016
Accepted 24 December 2016
Available online 31 December 2016
Elettaria cardamomum (L.) Maton, known as queen of spices, is a perennial herbaceous monocot of the family
Zingiberaceae, native to southern India. Cardamomis an economically valuable spice crop andused widely in cu-
linary 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 ve cultivar genotypes of carda-
mom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for ap-
proximately 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 ltered 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 unigeneswere functionally annotated using several databases including PlantCyc for pathwayan-
notation. This work represents the rst 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.
© 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords:
Transcriptome proling
Elettaria cardamomum
Cardamom
Ion proton sequencing
RNA seq
Specications
Organism/cell
line/tissue
Wild and cultivar Elettaria cardamomum (L.) Maton
Sex Monoecious
Sequencer or
array type
Ion Proton System
Data format Raw data in BAM le
Experimental
factors
Transcriptome sequencing of tissues of wild and cultivar
cardamom
Experimental
features
Freshly collected leaf, stem, ower, ower buds and young
fruits were used for RNA isolation, tissues were pooled, RNA
seq libraries representing two genotypes of cardamom were
sequenced and de novo assembled
Consent NA
Sample source
location
JNTBGRI, Cardamom germplasm conservatory
1. Direct link to deposited data
http://www.ncbi.nlm.nih.gov/sra/SRX1141276[accn]
http://www.ncbi.nlm.nih.gov/sra/SRX1141272[accn]
2. Introduction
Elettaria cardamo mum (L.) Maton or small cardamom, belongs to the
family Zingiberaceae, is a potential spice crop due to its unique aromatic
avor and multiple health benets. Cardamom seeds and fruits are the
economically signicant parts and effectively used as a traditional med-
icine, food additive and avoring agent [1]. The essential oil component
extracted from the fruits of cardamom was reported to possess antibac-
terial, anti-inammatory, analgesic, and antispasmodic activities [2,3].
In the cardamom essential oil, the bioactive component d- limonene
was reported to possess chemopreventive property towards colon can-
cer, mammary, lung, liver, skin and stomach cancers in rodents [46].
Hence better understanding of genes and pathways associated with
the biosynthesis of the active compounds in cardamom might be bene-
cial for therapeutic purposes as well as selectionof superior genotypes.
Since there are no genomic and transcriptome data of cardamom avail-
able in any of the publicly available databases, the data we presented
Genomics Data 11 (2017) 102103
Corresponding author.
E-mail addresses: nadiyashiyas@yahoo.com (F. Nadiya), anjalinair20@gmail.com
(N. Anjali), jinutchirayath@gmail.com (J. Thomas), agangaprasad@yahoo.com
(A. Gangaprasad), sabu@jntbgri.res.in (K.K. Sabu).
http://dx.doi.org/10.1016/j.gdata.2016.12.013
2213-5960/© 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Contents lists available at ScienceDirect
Genomics Data
journal homepage: www.elsevier.com/locate/gdata
here provide information on potential genes coding for enzymes re-
sponsible for pharmaceutically valuable bioproducts.
3. Experimental design, materials and methods
3.1. Plant material
Fresh leaf, stem, ower, ower bud and young fruit were collected
from wild and ve cultivar accessions (including landraces and released
varieties) of cardamom growing in the JNTBGRI cardamom conservato-
ry. The tissues were immediately frozen in liquid nitrogen and kept as
such until processing.
3.2. Total RNA isolation and transcriptome sequencing
Total RNA was isolated from all tissues of cardamom using RNeasy
plant mini kit combined with modied CTAB method [7]. Quantication
and quality analysis were done using 2100 BioAnalyzer (Agilent Tech-
nologies). The tissues of wild cardamom were pooled as one sample
and the tissues from all cultivars were pooled as second sample
representing wild and cultivar genotypes of cardamom. Two sets of
total RNA were puried and cDNA library was constructed using Ion
Total RNA seq Kit V2 according to manufacturer's instructions. The puri-
ed libraries were submitted to RNA sequencing with the Ion Proton se-
quencer. RNA seq generated a total of 22,811,983 (92 base) and
24,889,197 (75 base) raw reads accounting for approximately 8.21
and 7.65 GB of sequence data for wild and cultivar genotypes of carda-
mom respectively.
3.3. De novo transcriptome assembly and functional annotation
The raw reads were preprocessed to remove low quality bases,
tRNAs and rRNAs. De novo assembly was performed with MIRA (Mim-
icking Intelligent Read Assembly) program [8] which assembles read
pairs from partial path into contigs. The transcriptome assembly gener-
ated 112,208 and 264,161 contigs for wild and cultivar genotypes and to
generate a comprehensive reference transcriptome a combined
assembly was performed which yielded 178,745 contigs (Table 1). We
annotated the assembled transcripts to NCBI non redundant (NR) pro-
tein database, Swissprot, TrEMBL, pfam, PlantCyc, KOG and TAIR10 da-
tabases. We also identied the differential expression analysis of
signicant genes inwild and cultivar genotypes of cardamom.The infor-
mation we provided might be useful in molecular marker development,
SNP identication, genetic manipulation of specic genes to enhance
the production of desired compounds and breeding for developing
novel elite cultivars.
Conict of interest
The authors declare that they have no competing interests.
Acknowledgements
The authors thank the Director of the Jawaharlal Nehru Tropical
Botanic Garden & Research Institute (JNTBGRI) for providing the neces-
sary facilities and nancial assistance through Plan Project (P114) to
carry out this research work. Thanks are due to the Kerala State Council
for Science, Technology, and Environment (KSCSTE) for granting Re-
search Fellowship to Nadiya, F. (010-52/FSHP/10/CSTE) to conduct
this study. We acknowledge the permission granted by Kerala Forest
Department for collecting the plant samples. Thanks are due to Shafeek,
S. and Vishnu, J. S. for assistance rendered for the study. We are grateful
to the staff at the Centre for Cellular and Molecular Platforms (C-CAMP,
Bangalore, India) for performing high throughput sequencing. We are
also thankful to Indian Cardamom Research Institute and Cardamom
ResearchCentre in Kerala, India for providing necessary cardamom cul-
tivars used in the present study.
References
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Table 1
Read and assembly statistics of cardamom transcriptome.
Plant material Cultivar Wild
Total number of raw reads 24,889,197 22,811,983
Total number of bases 1,856,105,873 2,105,322,150
N20 1,518,466,470 1,719,212,155
GC% 55 55
Read length 73 bp 92 bp
Reads after adapter removal and quality trimming 18,921,421 17,515,399
Total contigs 264,161 112,208
Largest contig 1489 1263
N50 contig size 616 664
Average consensus quality 26 26
Contigs with reads without quality values 0 0
Maximum coverage (total) 24,835 17,774
Total size of assembly 16 MB 43 MB
103F. Nadiya et al. / Genomics Data 11 (2017) 102103
... E. cardamomum, popularly known as "Queen of spices" for its unique aromatic flavour is frequently used in Arab, Scandinavian as well as western cuisines. Cardamomum is the third most expensive spice in the world after saffron and vanilla [9][10][11] . The essential oil obtained from the species is reported to have various biological properties such as antioxidant, antimicrobial, analgesic, anti-inflammatory and anticancer activities 10,12,13 . ...
... Cardamomum is the third most expensive spice in the world after saffron and vanilla [9][10][11] . The essential oil obtained from the species is reported to have various biological properties such as antioxidant, antimicrobial, analgesic, anti-inflammatory and anticancer activities 10,12,13 . Some studies in the past have revealed that E. cardamomum is an important source of phenolic compounds, flavonoids, terpenoids, sterols and lipids 7,14 . ...
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We present an EST sequence assembler that specializes in reconstruction of pristine mRNA transcripts, while at the same time detecting and classifying single nucleotide polymorphisms (SNPs) occuring in different variations thereof. The assembler uses iterative multipass strategies centered on high-confidence regions within sequences and has a fallback strategy for using low-confidence regions when needed. It features special functions to assemble high numbers of highly similar sequences without prior masking, an automatic editor that edits and analyzes alignments by inspecting the underlying traces, and detection and classification of sequence properties like SNPs with a high specificity and a sensitivity down to one mutation per sequence. In addition, it includes possibilities to use incorrectly preprocessed sequences, routines to make use of additional sequencing information such as base-error probabilities, template insert sizes, strain information, etc., and functions to detect and resolve possible misassemblies. The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments.
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Oxygen-free radicals, more generally known as reactive oxygen species (ROS) along with reactive nitrogen species (RNS) are well recognised for playing a dual role as both deleterious and beneficial species. The "two-faced" character of ROS is substantiated by growing body of evidence that ROS within cells act as secondary messengers in intracellular signalling cascades, which induce and maintain the oncogenic phenotype of cancer cells, however, ROS can also induce cellular senescence and apoptosis and can therefore function as anti-tumourigenic species. The cumulative production of ROS/RNS through either endogenous or exogenous insults is termed oxidative stress and is common for many types of cancer cell that are linked with altered redox regulation of cellular signalling pathways. Oxidative stress induces a cellular redox imbalance which has been found to be present in various cancer cells compared with normal cells; the redox imbalance thus may be related to oncogenic stimulation. DNA mutation is a critical step in carcinogenesis and elevated levels of oxidative DNA lesions (8-OH-G) have been noted in various tumours, strongly implicating such damage in the etiology of cancer. It appears that the DNA damage is predominantly linked with the initiation process. This review examines the evidence for involvement of the oxidative stress in the carcinogenesis process. Attention is focused on structural, chemical and biochemical aspects of free radicals, the endogenous and exogenous sources of their generation, the metal (iron, copper, chromium, cobalt, vanadium, cadmium, arsenic, nickel)-mediated formation of free radicals (e.g. Fenton chemistry), the DNA damage (both mitochondrial and nuclear), the damage to lipids and proteins by free radicals, the phenomenon of oxidative stress, cancer and the redox environment of a cell, the mechanisms of carcinogenesis and the role of signalling cascades by ROS; in particular, ROS activation of AP-1 (activator protein) and NF-kappaB (nuclear factor kappa B) signal transduction pathways, which in turn lead to the transcription of genes involved in cell growth regulatory pathways. The role of enzymatic (superoxide dismutase (Cu, Zn-SOD, Mn-SOD), catalase, glutathione peroxidase) and non-enzymatic antioxidants (Vitamin C, Vitamin E, carotenoids, thiol antioxidants (glutathione, thioredoxin and lipoic acid), flavonoids, selenium and others) in the process of carcinogenesis as well as the antioxidant interactions with various regulatory factors, including Ref-1, NF-kappaB, AP-1 are also reviewed.
High-quality RNA extraction from small cardamom tissues rich in polysaccharides and polyphenols Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
  • F Nadiya
  • N Anjali
  • A Gangaprasad
  • K K Sabu
  • B Chevreux
  • T Pfisterer
  • B Drescher
  • A J Driesel
  • W E G Müller
  • T Wetter
  • S Suhai
[7] F. Nadiya, N. Anjali, A. Gangaprasad, K.K. Sabu, High-quality RNA extraction from small cardamom tissues rich in polysaccharides and polyphenols., Anal. Biochem. 485 (2015) 25–27. doi:10.1016/j.ab.2015.05.017. [8] B. Chevreux, T. Pfisterer, B. Drescher, A.J. Driesel, W.E.G. Müller, T. Wetter, S. Suhai, Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs, Genome Res. 14 (2004) 1147–1159.