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.

Transcriptome mining for EST-INDELs and development of EST-SSR markers in turmeric

Sabu K. K., M. D. Shehenaz and J. Amrutha. 2018. Transcriptome mining for EST-INDELs and development of EST-SSR markers in turmeric (Curcuma longa L.). International Journal of Agriculture, Environment and Biotechnology 11(3): 487-492. http://ndpublisher.in/countpdfdownload.php?id=3040&pdf=IJAEBv11n3i.pdf

ABSTRACT
Curcuma longa L. commonly known as turmeric is used as a culinary spice in India and many Asian countries. Turmeric has anti-fungal, anti-bacterial, anti-malarial and anti-cancer properties to mention a few. We have analyzed the transcriptome of C. longa retrieved from NCBI SRA database (SRR495223) for the development and validation of EST-SSR markers and identification of EST-InDels to be used for C. longa and related genera. A total of 337 primers were developed and 20 primers having the rating of 100% with the help of NetPrimer were selected and used for PCR validation in C. longa, Amomum subulatum Roxb. (large cardamom) and Elettaria cardamomum (L.) Maton (small cardamom). It was found that around 50% primers generated PCR products in both types of cardamom and 85% in C. longa. The developed primers worked with curcuma, large cardamom and small cardamom plants at varying levels. Besides, the transcriptome analysis detected high amount of deletion and 18 addition of bases which could be screened through the development of CAPS markers using the tool SNP2CAPS and it was found that 93 restriction enzyme can be used for screening these InDels.

Highlights

• Transcriptome sequence of Curcuma longa was used for the development of EST-SSR markers.
• The EST-SSR primers were validated in Curcuma longa and its related taxa such as Amomum subulatum and Elettaria cardamomum
• EST-InDels were also successfully identified in the transcriptome sequences of Curcuma longa.

Keywords: Curcuma longa, EST-SSR, EST-InDel, PCR, ClustalW, WebSat, NetPrimer, SNP2CAPS

Agri Gene

Volume 8, June 2018, Pages 18-27

Genome-wide differential expression profiling in wild and cultivar genotypes of cardamom reveals regulation of key pathways in plant growth and development

Author links open overlay panelNadiyaF.a  AnjaliN.a   JinuThomasa  Gangaprasad A.b  SabuK.K.a

https://doi.org/10.1016/j.aggene.2018.03.002

Highlights

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Transcriptome sequencing data of five cultivars and a wild genotype of cardamom was used to find the differential expression profiling of the cultivar and wild genotypes of cardamom.

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Differential expression profiling of the cultivar and wild genotypes of cardamom exhibited 132 unigenes as differentially expressed (log2>4) with 105 up regulated and 27 down regulated genes in cultivars comparing with its wild genotype.

•

This work represents the first report on differential expression profiling and functional annotation of wild and cultivar genotypes which will enhance the genomic resources of the species.

Abstract

Cardamom (Elettaria cardamomum Maton) is an economically valuable spice crop and the essential oil of cardamom possesses splendid medicinal properties. To get insight into the domestication related traits and varied gene regulation, differential expression profiling of wild and cultivar cardamom was performed by analyzing the transcriptome data available for cardamom. Functional annotation using seven different publicly available databases identified significant genes coding for enzymes participating in monoterpenoid biosynthesis. Differential expression profile of cultivar and wild genotypes of cardamom exhibited 132 unigenes as differentially expressed (log2 > 4) with 105 up regulated and 27 down regulated genes in cultivars comparing with its wild genotype. Expression analysis showed wild cardamom has increased drought stress tolerance, defense response, and various plant growth regulations. Most of the genes coding for enzymes participating in flavanoid biosynthesis were up regulated, while resistance related genes (cinnamoyl CoA reductase) and few genes involved in the monoterpenoid biosynthetic pathway were down regulated in cultivars when compared to its wild progenitor. Transcriptome data were validated and correlated using qPCR using 10 randomly selected differentially expressed genes. Our study is the first application of next generation RNA-seq to explore the genes involved in various metabolic pathways and quantification of transcript expression levels in cultivar and wild cardamom genotypes.

Keywords

Cardamom, 

Transcriptome, 

Differential expression, 

Up regulation, 

Down regulation, 

Essential oil biosynthesis

Biodiversity Mining Through Transcriptome Analysis

Secondary metabolites or chemical constituents of plants are functional products synthesized through more complex multienzymatic secondary metabolite pathways. The release of few secondary metabolites is related to the exertion of morphological differentiation and maturation during plant development. Secondary metabolite compounds designate huge chemical diversity, i.e., each plant possesses its own complex diverse set of metabolites. This diversity imparts analytical challenges, characterization of a number of metabolites in parallel, and quantification of particular compound of interest. These compounds itself are related to significant plant traits (color and fragrance of flowers, taste and color of food, and resistance toward pests and pathogens) and also for the synthesis of fine chemicals such as medicines (anticancer, anti-inflammatory, antioxidants, etc.), flavors, fragrances, dyes, insecticides, pheromones, and antimicrobial agents. The emergence of cost-effective high throughput sequencing or next-generation sequencing (NGS) technology quickly expanded transcriptome information of several plant species, which could be analyzed for quick identification of previously unknown genes and enzymes and elucidation of biosynthetic pathways. The present chapter details diverse secondary metabolites, gene expression patterns, molecular basis of chemical diversity of the compounds, and application of NGS based transcriptome profiling for biosynthetic pathway elucidation.

Citation: Sabu, K. K. and F. Nadiya. 2017. Biodiversity Mining Through Transcriptome Analysis. In: Bioresources and Bioprocess in Biotechnology, Volume 1: Status and Strategies for Exploration, Part II. Eds. Sabu A, N.S. Pradeep, S. Shiburaj. pp 207-246. doi: 10.1007/978-981-10-3573-9_10. Springer, Singapore.

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

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. 

Citation
Nadiya, F., N. Anjali, Jinu Thomas, A. Gangaprasad, K. K. Sabu. 2017. Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom). Genomics Data Vol 11: 102–103. doi: 10.1016/j.gdata.2016.12.013

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Associative transcriptomics of traits in the polyploid crop species Brassica napus

Association genetics can quickly and efficiently delineate regions of the genome that control traits and provide markers to accelerate breeding by marker-assisted selection. But most crops are polyploid, making it difficult to identify the required markers and to assemble a genome sequence to order those markers. To circumvent this difficulty, John Innes Centre has developed associative transcriptomics, which uses transcriptome sequencing to identify and score molecular markers (SNPs) representing variation in both gene sequences and gene expression, and correlate this with trait variation. Applying the method in the recently formed tetraploid crop Brassica napus, the research team at JIC (Harper AL, Trick M, Higgins J, Fraser F, Clissold L, Wells R, Hattori C, Werner P, Bancroft I.) has identified genomic deletions that underlie two quantitative trait loci for glucosinolate content of seeds. The deleted regions contained orthologs of the transcription factor HAG1 (At5g61420), which controls aliphatic glucosinolate biosynthesis in Arabidopsis thaliana. This approach facilitates the application of association genetics in a broad range of crops, even those with complex genomes.

See the abstract at Pubmed