Next-Generation Genomics and Omics in Crop Enhancement and Sustainable Agriculture

For centuries, agriculture has served as the foundation of human civilization, providing food, raw materials, and livelihoods to millions worldwide. Traditional breeding methods, based on repeated selection, often take years to develop improved plant varieties. However, their limitations in enhancing yield and resilience have led to the emergence of next-generation sequencing (NGS) technologies as powerful tools in modern agriculture. Incorporating both second- and third-generation platforms, NGS has revolutionized agricultural genomics by enabling high-throughput and cost-effective analysis of entire genomes, exomes, mRNA, small RNAs, and other non-coding RNAs. NGS allows the simultaneous sequencing of millions of DNA fragments, offering in-depth insights into genome architecture, genetic variations, gene expression patterns, and epigenetic modifications. Combining genomic, transcriptomic, and metabolomic data, a multi-omics approach provides a comprehensive understanding of plant growth, stress responses, and adaptation mechanisms. This comprehensive strategy is vital for enhancing crop yield, improving stress tolerance, and accelerating breeding programs, thus contributing to long-term agricultural sustainability and global food security. This chapter reviews key sequencing technologies, recent advances, and emerging trends in agricultural genomics. It also discusses the technical and analytical challenges of NGS and highlights its transformative role in crop improvement and the future of plant breeding.

Nadiya, F., Sabu, K.K., Rajalakshmi, R. (2026). Next-Generation Genomics and Omics in Crop Enhancement and Sustainable Agriculture. In: Al-Khayri, J.M., Yatoo, A.M., Jain, S.M., Penna, S. (eds) Handbook of Agricultural Technologies. Springer, Singapore. https://doi.org/10.1007/978-981-99-0862-2_72-1 

Safeguarding Andaman flora: new plant biorepository strengthens global genome conservation

Highlights

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  First plant biorepository established for the Andaman Islands under the GGI-Gardens programme.
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  Collection includes 45 species from 44 genera and 33 families, exceeding project targets.
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  Eleven threatened species, including Cycas zeylanica and Bentinckia nicobarica, are safeguarded.
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  Over half of the genera collected are new to the Global Genome Biodiversity Network (GGBN).
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  Strengthens global genomic conservation capacity while addressing urgent regional threats.
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• Read full article at https://doi.org/10.1016/j.pld.2025.10.001
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Comparative study of DNA and RNA extraction methods for high-quality nucleic acid isolation from Cullenia exarillata

Isolation of high-quality DNA and RNA from plants with high polysaccharide and secondary metabolite content is typically difficult, particularly in the case of trees.  Metabolites commonly undergo co-precipitation with RNA and DNA, resulting in degradation of their quality. Cullenia exarillata leaf samples were subjected to various DNA and RNA extraction techniques, and the resulting data were compared and analysed. The isolation of high-quality DNA and RNA is crucial for the advancement of molecular and biotechnological techniques that aim to preserve the endemic status of C. exarillata and this research is to establish an efficient procedure for extracting DNA and RNA from C. exarillata. This method will make molecular and genomic research easier in forestry and conservation fields. In this research, we evaluated various methods for extracting high quality DNA and total RNA from C. exarillata tree, incorporating minor modifications in standard procedure. To acquire DNA and RNA of superior quality, a comparison was made between conventional DNA and RNA extraction methods and a variety of commercial kits that revealed the conventional technique yielded DNA samples of superior purity and concentration. It was discovered that combining modified commercial and conventional procedures yielded RNA with exceptionally high concentration and purity. The Agilent 2100 Bioanalyzer and NanoDrop spectrophotometer ensure the impeccable purity of the nucleic acids generated via these procedures. Additionally, the application of agarose gel electrophoresis unveiled unique bands. Further investigation was conducted to validate the purity and amplification of the DNA and RNA that were collected.  This study clarifies a method for extracting sufficient and high-quality amounts of DNA and RNA from C. exarillata; future research on this plant will greatly benefit from knowing this information.

Full article link: https://cellmolbiol.org/index.php/CMB/article/view/5841

Citation: Revathy S, Sabu K K, Anilkumar S (2025). Comparative study of DNA and RNA extraction methods for high-quality nucleic acid isolation from Cullenia exarillata A. Robyns. Cellular and molecular biology, 71(6), 54–61. https://doi.org/10.14715/cmb/2025.71.6.7

The Cardamom Genome (Book)

 Overview

Editors: K. K. Sabu, Chittaranjan Kole

• Written by globally reputed experts on cardamom genetics, genomics, transcriptomics, and breeding
• Is the first one compiling advances in genomics and metabolic profiling of cardamom
• Presents an overview of advanced techniques of biotechnology and genome profiling in cardamom

About this book

This book is the first comprehensive compilation of elucidation of the genome of cardamom (Elettaria cardamomum Maton) and its genetic improvement. It includes reviews on the genetic resources, genetics and breeding and in vitro culture in cardamom and molecular characterization of phylogenetic relationship of cardamom of Columbia and Costa Rica.  This book presents deliberations on the whole genome sequencing and SSR markers of small cardamom. It also enumerates on the genetics and genomics of biotic stress and host-pathogen interaction, genomics of flavors, and transcriptomics resources and their implications and finally functional regulation of mRNAs in cardamom. Altogether, the book contains about 150 pages over 10 chapters authored by globally reputed experts on the relevant field in this crop. The book is useful to the students, teachers, and scientists in the academia and relevant private companies interested in classical genetics and breeding, molecular genetics, structural genomics, functional genomics, plant pathology and plant physiology of cardamom.

Visit book page online at https://link.springer.com/book/10.1007/978-3-031-71829-8

In Vitro Anti Angiogenetic Activity of Traditional Plants Saraca asoca, Glycyrrhizia glabra and Curcuma longa Beneficial for Endometriosis Treatment

The development of angiogenesis plays an essential role in the growth and survival of endometriosis. The aim was to determine the in vitro anti-angiogenic effect of Saraca asoca, Glycyrrhiza glabra, and Curcuma longa ethanolic extract in chick embryos by emphasizing its total phenolic and flavonoid contents in the sample. It was determined by Folin-Ciocalteu and aluminum chloride methods respectively. Anti-angiogenesis assay was done in chorioallantoic membrane. The high amount of total phenol and flavonoid was obtained from all three plant extracts and may be responsible for the bioactivity of the crude extract. Saraca asoca exhibits high phenolic content and anti-angiogenic activity followed by Curcuma longa with rich flavonoid and Glycyrrhiza glabra showed moderate activity for all the assays. A significant anti-angiogenic effect was observed for Saraca asoca (73.65+0.021) % and Curcuma longa (67.65+0.024) % than reference drug dienogest (62.42+0.02) % in the study. Search for new therapeutic agents with anti-angiogenic potential rich in plant secondary metabolites like phenols and flavonoids are need of the hour. The results successfully reveal that the abovementioned plants used in traditional medicines could be used for treating angiogenesis-related diseases like endometriosis.

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Identification of dominant housekeeping genes to normalize mRNA level in dioecious Palmyra palm

Suchilkumar Soorya, Thacheril Sukumaran Swapna, Senan Siju and Sabu Kalluvettankuzhy Krishnan Nair

Res. J. Biotech.; Vol. 19(1); 10-21; doi: https://doi.org/10.25303/1901rjbt01021; (2024)

Abstract
A stable housekeeping gene is required for precise and consistent qPCR data analysis. Palmyra palm is an important tropical dioecious tree crop with diverse uses. However, no reliable gene expression studies or housekeeping gene standardization have been documented, which limit crop improvement and utilization. In this work, four frequently used statistical tools such as RefFinder, NormFinder, Delta CT method and BestKeeper were applied to evaluate the constancy and fluctuation in expression of a chosen 10 internal control genes such as NADH dehydrogenase subunit 5-like (NAD5), β-actin, ACTIN CRD, alpha-tubulin, UBCE, EIF, EF2, AP1, GAPDH and UBQ2 in both vegetative and reproductive tissues of dioecious Palmyra palm. Six flower tissues and two leaf tissues from male and female palms were used in this study. The findings indicated that NAD5-2 is the most reliable and constant housekeeping gene expressed during Palmyra palm flower development. The AGAMOUS and SEEDSTICK genes expression pattern in the flower development were used to validate the normalized expression of the four housekeeping genes that were chosen in order to further support the stability of those genes. Our results will be useful for further research on gene transcription level in Palmyra palms and also the above mentioned tool is very useful for the normalization of housekeeping genes of biological samples with different experimental conditions.

Growth promoting effects of endophytic fungus Piriformospora indica in small cardamom (Elettaria cardamomum Maton)

Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of a wide range of host plants and provides various benefits to the plants. Cardamom (Elettaria cardamomum Maton) is an economically valuable spice crop of the tropics. In this work, we describe differentially expressed transcripts responding to P. indica root colonization in small cardamom for elucidation of molecular basis of growth and development. During the study, a wild genotype of cardamom was propagated under in vitro conditions using full strength Murashige and Skoog medium supplemented with 1 mg l⁻¹ BAP (for shoot induction) and basal MS liquid medium (for root induction). Cardamom plantlets were co-cultivated with P. indica. Microscopic observation confirmed the presence of P. indica inside the roots of cardamom plantlets. Growth parameters of control and P. indica colonized plantlets were observed for three months at an interval of 15 days. P. indica colonization resulted in a significant increase in the morpho-physiological traits of the host plant. The growth enhancement was visible after 15 days of co-culture. There was a significant increase (p < 0.05) in the number and length of leaves, height of the plant and chlorophyll content in P. indica colonized plants compared to non-colonized control plant. In addition to this, the expression levels of auxin, nitrate reductase, vegetative storage protein and phosphate transporter genes were upregulated by 3.45, 3.26, 1.62 and 1.19 times respectively by the co-cultivation of P. indica in cardamom plantlets.

Anjana H. N., K. N. Anith, Sabu K K. 2023. Growth promoting effects of endophytic fungus Piriformospora indica in small cardamom (Elettaria cardamomum Maton). 2023. Symbiosis. DOI: 10.1007/s13199-023-00949-1

Expression profiling of stress responsive genes in cell suspension of Elettaria cardamomum (L.) Maton under abiotic stress

Cardamom is an economically important spice, valued for its multiple utility from culinary to medical purposes. The plant is highly susceptible to both abiotic and biotic stresses. Despite the fact that several studies focusing on stress in cardamom have been conducted; a molecular analysis at the cellular level has not been reported. This study highlights the molecular response of homogenous population of cardamom cell suspension following the temperature and drought stresses for a short period of time (20 mins). Temperature stress at 30, 35, and 40°C caused a significant increase in the transient expression of genes, sHSP 17.8 and sHSP 17.9, which are molecular chaperones involved in protein folding coping with the heat stress response of plants. Drought stress with various concentrations of PEG 6000 has demonstrated only a little increase in the expression of transcription factors, WRKY 35 and WRKY 71. The study implies that sHSP 17.8 and sHSP 17.9 play a crucial role during heat stress, which is a major limiting factor for the cultivation of cardamom in lower altitudes where atmospheric temperature is usually high. But WRKY 35 and WRKY 71 genes are found not to have a high impact at the cellular level in response to drought stress in cardamom when it is exposed to a brief duration of drought. Understanding the molecular mechanism underlying abiotic stress response in cardamom will aid in developing elite varieties adaptable to lower altitudes and to cope with the frequent climatic variations.

Cite this article

Soumya S. Dharan and K.K. Sabu. Expression profiling of stress responsive genes in cell suspension of Elettaria cardamomum (L.) Maton under abiotic stress. Journal of Plantation Crops 2023, 51(1): 23-30. https://doi.org/10.25081/jpc.2023.v51.i1.8188

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Phytochemical Profiling and Biological Effects of Glycyrrhiza glabra L.

Glycyrrhiza glabra L. commonly known as licorice belonging to the family Leguminosae is an ayurvedic medicinal plant having substantial pharmacological properties such as anti-inflammatory and anticancer effects. Analysed ethnopharmacological studies show phytochemical and biological activities of the plant extract and serve as a resource for studying anti- endometriosis. According to WHO, 176 million women in the world are affected with endometriosis condition and up to 30-50% of women may experience infertility. Our study aims to evaluate in vitro activity of ethanolic extract of Glycyrrhiza glabra in different cell lines, DPPH assay and HPLC studies in order to propose it to be an effective remedy in endometriosis treatment. In vitro cytotoxic assessment of the extract was determined in estrogenic (MCF 7), non-estrogenic (MDAMB 231) and endometrial cancer cell lines (Ishikawa) along with its safety assessment in normal cell lines (L929). The extract of G. glabra exhibited DPPH radical scavenging activity with 77.09% inhibition in 100 μg concentration. Cytotoxic activity of extract in MCF 7, MDAMB 231, endometrial cancer cells- Ishikawa and significant cell viability in normal L929 cell line shows promising effect of the extract and suggests it as a possible therapeutic adjuvant for treating endometriosis.

Reshmi Nair R J, Lakshmi S, Suja K P and K K Sabu. 2023. Phytochemical Profiling and Biological Effects of Glycyrrhiza glabra. Research Journal of Biotechnology 18(5): 1-7. Published on 13 April 2023. https://doi.org/10.25303/1805rjbt01007

Unraveling microRNA mediated gene regulation in Centella asiatica (L.) Urb. by high-throughput sequencing based small-RNA profiling

Centella asiatica is a widely spread herb mostly found in the tropics having extensive medicinal values. Here, we report for the first time, transcriptome-wide characterization of miRNA profile from the leaves of C. asiatica using high-throughput Illumina sequencing. We identified 227 conserved and 109 putative novel miRNAs. Computational screening revealed potential mRNA targets for both the conserved and novel miRNAs encoding diverse transcription factors and enzymes involved in plant development, disease resistance, metabolic and signaling pathways. Gene ontology annotation and KEGG analysis revealed the miRNA targets to be involved in a wide range of metabolomic and regulatory pathways. The differential expression of the miRNA encoding genes in diverse tissues was determined by real-time PCR analysis. We also found that gene expression levels of miR156, 159 and 1171 was reduced in salicylic acid treated axenic shoot cultures of C. asiatica compared to its control. Furthermore, RLM-RACE experiments mapped miRNA-mediated cleavage at two of the mRNA targets. The present study represents the large-scale identification of microRNAs from C. asiatica and contributes to the base for the up-coming studies on miRNA-mediated gene regulation of plant secondary metabolite pathways in particular Gouri Priya Ranjith, Jisha Satheesan, K K Sabu. 2023. Unraveling microRNA mediated gene regulation in Centella asiatica (L.) Urb. by high-throughput sequencing based small-RNA profiling. Tropical Plant Biology, Springer. https://10.1007/s12042-023-09342-0

A short review on the identification of ABCDE genes in monocot plants

Soorya S, Swapna TS, Sabu KK. 2022. A short review on the identification of ABCDE genes in monocot plants. Journal of Tropical Life Science 12(3): 423 – 433.

https://doi.org/10.11594/jtls.12.03.15

One of the most important divisions in the plant kingdom is the monocotyledon division of angiosperms. More than 60,000 monocot spp. have been identified, the majority of which are economically important, such as the Poaceae, Orchidaceae, Arecaceae, Liliaceae, and certain other families. The involvement of the ABCDE model of floral organ determination during flower development is a growing area of research in the field of molecular biology due to the diversity in the floral morphology of monocots. The MADS-box gene family is a large molecular transcript family that helps identifies specific proteins involved in floral development. It is classified into several classes based on its function. The review aimed to evaluate the significance of ABCDE genes for floral development and subsequent organ identification, which have been discovered in a range of monocot plants, as well as the functions of these genes in determining the sex of dioecious plants. We sought to summarise the MADS-box gene responsible for flower initiation and floral whorl differentiation reported in economically valuable monocotyledonous plants.

Impact of mannitol and poly ethylene glycol 6000 induced water deficit on plant biomass and major secondary metabolites in Centella asiatica (L.) Urb. in vitro

Jisha S, Aiswarya S, Gouri PR, Manikantan K & Sabu KK. 2022. Impact of mannitol and poly ethylene glycol 6000 induced water deficit on plant biomass and major secondary metabolites in Centella asiatica (L.) Urb. in vitro. Indian Journal of Experimental Biology Vol. 60, March 2022, pp. 184-191.

Low water potential related stresses are regulated by modifying water uptake and loss to avoid low water potential, accumulating solutes which in turn enhance active principles and its gene expressions. Present study examined effect of in vitro induced absorption of mannitol and PEG (poly ethelene glycol) 6000 in Indian pennywort, Centella asiatica (L.) Urb., neutraceutical plant, evidenced by phenotypic, molecular and phytochemical analyses. Both mannitol and PEG 6000 induce water deficit conditions in plants and retarded normal plant biomass in terms of fresh and dry weights. These effects were significantly less severe in plants subjected to mannitol, compared to PEG. PEG and mannitol imposed water deficit, resulted in decline in major active compound, asiaticoside evidenced by HPTLC of asiaticoside content. Differential expression of some selected key genes in the asiaticoside pathway including squalene synthase and β amyrin synthase by qPCR, confirmed decrease in transcript level expression of asiaticoside, whereas upregulated transcript level expression was observed in cycloartenol synthase for synthesis of phytosterols. Estimation of total flavonoids and phenolics under different water deficit conditions were found declined. In conclusion, water deficit by mannitol and PEG 6000 can significantly affects processes associated with biomass growth and ability to synthesize secondary metabolites in C. asiatica.

Download/Read article at http://nopr.niscair.res.in/handle/123456789/59289

Genetic diversity and structure revealed by genomic microsatellite markers in Centella asiatica (L.) Urb., a plant with medicinal potential

 Abstract

Background: Around the world, medicinal plants are utilised for various purposes. Centella asiatica is one of the important medicinal plants widely used in many medicinal systems. Nevertheless, analysis of the genetic diversity would pave the way for its most suitable utilisation.

Methods and results: The present study analyses the genetic diversity and structure of eighty C. asiatica accessions collected from the southern states of India, using ten genomic microsatellite markers. The mean Nei’s gene diversity (0.46) indicates considerable genetic diversity. Analysis of molecular variance (82.48%) exhibited significant genetic variance between samples within the population. The cluster analysis brought out the structure of the analysed populations as three subpopulations based on the genetic differentiation.

Conclusions: The study showed significant intra-population variation, predominant inbreeding and population differentiation in C. asiatica. The findings will help better understanding of the genetic structure and gene pool of the plant.

Full article link: https://rdcu.be/cAvFI

Impact of potential stimulants on asiaticoside and madecassoside levels and expression of triterpenoid-related genes in axenic shoot cultures of Centella asiatica (L.) Urb

Gouri Priya Ranjith, S. Jisha, Achutan Sudarsanan Hemanthakumar, Chinthu V. Saji, Rajesh A. Shenoi, Kallevettankuzhy Krishnannair Sabu

Phytochemistry, Volume 186, 2021, 112735

The triterpenoid saponins, asiaticoside and madecassoside from Centella asiatica (L.) Urb. are known to have a wide range of applications in pharmaceutical and cosmetic industries. The effect of addition of Potential Metabolite Stimulants (PMSs) - casein acid hydrolysate, meat peptone, salicylic acid, copper sulphate, and silver nitrate, on the concentrations of these saponins and transcript levels of associated genes encoding important biosynthetic enzymes, was assessed in axenic shoot cultures of C. asiatica. Among the stimulants, silver nitrate induced asiaticoside content approximately 6-fold increase in madecassoside levels, after three weeks post-treatment with a decrease in biomass compared to its control. Gene expression analysis of essential genes involved in triterpenoid synthesis such as β-amyrin synthase showed an upregulation of approximately 50-fold at the third week of silver nitrate treatment compared to control. These findings suggest that silver nitrate can act as a metabolite stimulant, to enhance the formation of triterpenoids in axenic shoot culture of C. asiatica, which could be utilized in studying the regulation of terpenoid biosynthesis and biotechnological application for the increased production of these bioactive molecules.

https://doi.org/10.1016/j.phytochem.2021.112735

Phytochemical profiling and antioxidant activities of different parts of Artocarpus heterophyllus Lam. (Moraceae): A review on current status of knowledge

Artocarpus heterophyllus Lam. (Jackfruit tree) is one of the most ancient fruits indigenous to Western Ghats of India. They are large edible summer fruits and are good source of nutritional and antioxidant components which hold their potential for nutraceutical development. The present review attempts to document reports on the chemical and pharmacological investigations carried out with jackfruit. Research shows that the fruit contains a huge amount of phytochemicals such as phenolics, flavonoids, terpenoids, steroids, glycosides, saponins, alkaloids, and tannins which exhibit antioxidant properties. Diversity of secondary metabolites present in the jackfruit shows that it is a functionally, nutritionally, and medicinally important fruit. Detailed studies are essential for awareness among people for the proper use of jackfruit as a functional food and utilize the medicinal uses of jackfruit.

Sreeja Devi P S, Neethu S Kumar, K K Sabu. 2021. Phytochemical profiling and antioxidant activities of different parts of Artocarpus heterophyllus Lam. (Moraceae): A review on current status of knowledge. Future Journal of Pharmaceutical Sciences 7, Article number: 30. Published: 28 January 2021. https://doi.org/10.1186/s43094-021-00178-7

Genetic resources of Asian Palmyrah palm (Borassus flabellifer L.): A comprehensive review on diversity, characterization and utilization

Asian palmyrah palm (Borassus flabellifer L.) is a multipurpose, economically important tree widely distributed in the Indian subcontinent and Southeast Asia. The multifaceted uses (~800 uses) of the tree as food, wood and medicine make it a viable industrial crop. However, the dioecious nature of the tree coupled with long juvenile phase (12–20 years to initiate flowering), long stature and considerable variations in the productivity of male and female trees necessitates the application of new biotechnological tools for crop improvement. This review provides comprehensive information on the extent of genetic diversity of the crop, problems associated with palmyrah cultivation along with its multifaceted application and research gaps to be addressed for the effective utilization and conservation of palmyrah palm genetic resources.

Siju S. and K. K. Sabu. 2021. Genetic resources of Asian Palmyrah palm (Borassus flabellifer L.): A comprehensive review on diversity, characterization and utilization. Plant Genetic Resources. Published online: 08 January 2021. https://doi.org/10.1017/S1479262120000477

Dataset on Discovery of MicroRNAs in Centella asiatica (L.) Urb.

Gouri, P. R., Jisha, S., and K. K. Sabu. 2020. Dataset on Discovery of MicroRNAs in Centella asiatica (L.) Urb. Data in Brief 106451. Available online 22 October 2020. https://doi.org/10.1016/j.dib.2020.106451

MicroRNAs (miRNAs) are small (21–24 nucleotides), non-coding, riboregulators that regulate gene expression in eukaryotes. Pentacyclic triterpenoid saponins and sapogenins known as centellosides of the plant Centella asiatica (L.) Urb. are known for their broad spectrum medicinal properties. Two C. asiatica accessions viz.,CA301 and CA308 were selected for the miRNAome profiling. Total RNA isolated from fresh young leaves of both accessions along with their replicas was used for library construction. Illumina® sequencing of the four small RNA libraries generated a total of 59,234,923; 58,487,817; 59,520,376; 64,093,228 raw reads. The raw reads were quality filtered and used for the prediction of conserved and novel miRNAs. A total of 227 conserved and 109 novel microRNAs were identified from the libraries. Target gene prediction done using psRNAtarget and PANTHER™GO helped in localization of predicted targets. KEGG (Kyoto Encyclopedia for Genes and Genomes) was used for pathway prediction of the targets of predicted miRNAs. The present study provides first elaborated glimpse of miRNA pool of C. asiatica. The outcome of this research could help understand miRNA dependent regulation of centelloside biosynthesis and to design further metabolic engineering experiments to enhance their content in this important medicinal plant.

Role of miRNAs in biotic and abiotic stress management in crop plants

Anjali N & Sabu K K (2020). Role of miRNAs in biotic and abiotic stress management in crop plants. In: Sustainable Agriculture in the Era of Climate Change. Edited by R. Roychowdhury (Springer New York, USA). Pp. 513-532. https://doi.org/10.1007/978-3-030-45669-6_22

MicroRNAs (miRNAs) are endogenous, 18–25 nucleotide in length, and noncoding RNAs found in animals, plants, and in some viruses. They have been recognized as an important class of gene expression regulators and are involved in a multitude of biological processes in plants, including organ differentiation and development, metabolism, and response to biotic and abiotic stress factors, to mention a few. The method of action of miRNA is by binding to a ribonucleoprotein complex which is incorporated with a protein of Argonaute family. This RNA-induced silencing complex (RISC) targets the mRNA and inhibits its expression by degrading mRNA or by translational repression. It has been reported that posttranscriptional regulation mediated by miRNAs has important roles in adverse stress conditions. Some miRNAs respond to a number of abiotic and biotic stresses, and some others are stress specific. Not only characterization of miRNAs but also identification of their targets is crucial in this field of research. The participation of miRNAs in a species-specific manner to biotic and abiotic stress responses reveals the functional diversification of miRNAs among plant species and highlights the importance of conducting miRNA studies in diverse plant species. MicroRNA-based genetic modification technology is a very powerful technique to develop high-yielding crops which can resist biotic and abiotic stress factors.

Data on Large cardamom transcriptome associated with Chirke disease

Mary Mathew K, Renjanan Reshma, M Geethu, Varghese Rithin, Swapna Sasidharan, P P Gouthaman, K K Sabu, F Nadiya, Noushad Muhammad Ali, Dharan S Soumya, R Prakashkumar, A B Remashree. 2019. Data on Large cardamom transcriptome associated with Chirke disease. Data in Brief 29: 10504. https://doi.org/10.1016/j.dib.2019.105047

Abstract
Large cardamom (Amomum subulatum Roxburg), is an ancient spice native to North-Eastern India and Southeast Asia, which belongs to the family Zingiberaceae under the order Scitaminae. Large cardamom is mostly affected by a viral disease termed Chirke caused by Large Cardamom Chirke Virus (LCCV). These disease has spread due to drastic changes in the ecosystem, inadequate rain in dry months and absence of good agricultural practices by the farmers resulting in aphid infestations. In the present study, using HiSeq™ 2000 RNA sequencing technology transcriptome sequencing was performed for both control (disease not expressed) and diseased large cardamom leaf tissues. RNA-seq generated 77260968 (7.72 GB) and 72239708 (7.22 GB) paired raw reads for large cardamom control and diseased samples respectively. The raw data were submitted to the NCBI SRA database under the accession numbers SRX2529373 and SRX2529372 and the assembled transcriptomes were submitted to TSA under the accession numbers GIAV01000000 and GIAW01000000 for the control and diseased samples respectively. The raw reads were quality trimmed and assembled de novo using TRINITY assembler which created 156822 (control) and 148953 (diseased) contigs with N50 values 2107 (control) and 2182 (diseased). The data were used to identify the significantly differentially expressed genes between control and diseased samples.

Data on small cardamom transcriptome associated with capsule rot disease

Mary Mathew K, Renjanan Reshma, M. Geethu, Varghese Rithin, K.K. Sabu, F. Nadiya, Muhammad Ali Noushad, Soumya S. Dharan, Y.S. Rao, A.B. Remashree. 2019. Data on small cardamom transcriptome associated with capsule rot disease. Data in Brief 27: 104625. https://doi.org/10.1016/j.dib.2019.104625

Abstract
Small cardamom (Elettaria cardamomum (L.) Maton, also known as the ‘Queen of Spices’ is a rhizomatous herbaceous monocot from the family Zingiberaceae. In the present study, using HiSeq™ 2000 RNA sequencing technology, transcriptome sequencing was performed for both control and disease stressed small cardamom leaf tissues. RNA-seq generated 46,931,637 (101 base) and 31,682,496 (101 base) raw reads and totally 9.93GB and 6.63GB of sequence data for cardamom control and stressed samples respectively. The raw data were submitted to NCBI SRA database of under the accession numbers SRX2512359 and SRX2512358 for the control and diseased samples respectively. The raw reads were quality filtered and assembled using TRINITY de novo assembler which created 1,11,495 (control) and 91,096 (diseased) contigs with N50 values 3013 (control) and 2729 (stressed). The data was further used to identify significantly differentially expressed unigenes between control and stressed samples. Assembled unigenes were further annotated and evaluated in silico to predict the function using publicly available databases and gene annotation tools.