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Sequence Databases and Online Tools for Capsicum Research

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The Capsicum Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

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Abstract

Pepper is an important vegetable crop in terms of economic value and unique biological features, such as diversity in fruit morphology and capsaicin biosynthesis. Understanding pepper gene function is essential to explore the mechanisms how these unique features were developed in pepper and improve pepper agricultural traits with modern biotechnologies. Pepper has a very big genome of more than 3.5 Gb nucleotides, which is even more than the human genome. Maturation of high-throughput DNA sequencing technologies has made it possible for researchers to start decoding the pepper genome and investigate gene expression pattern genome-wide. In this chapter, we summarize various sequence databases generated for pepper studies and various online tools that are available for pepper research. Currently, six capsicum draft genomes and a pangenome with 383 pepper cultivars were published. These genomes were sequenced by Illumina-sequencing platform and provided very important foundation for further genome and transcriptome studies. Several hundred pepper transcriptome databases including both mRNA and small RNA were generated using sanger, 454 and Illumina platforms for different research objectives ranging from marker discovery, hormone signaling, pathogen resistance to database construction. Finally, we introduced several online resources for pepper genome, transcriptome data access and analyses. These sequence data and online tools will be useful for dissecting pepper gene function. Even though, significant progress has been made in generating pepper sequence databases and online tools in the past few years, large gaps exist comparing to the data and tools available for other plant species. More attention needs to be paid into this line of research in future for the pepper research community.

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Acknowledgements

This work is funded by the start fund provided by Huazhong Agricultural University to Li F (2013RC001).

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Authors and Affiliations

  1. Key Laboratory of Horticultural Plant Biology (MOE), College of Horticultural and Forestry Sciences, Huazhong Agricultural University, Wuhan, China

    Feng Li, Minglei Liu & Yingjia Zhou

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  1. Feng Li
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  2. Minglei Liu
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  3. Yingjia Zhou
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Correspondence to Feng Li .

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Editors and Affiliations

  1. School of Life Sciences, Jawaharlal Nehru University, New Delhi, India

    Nirala Ramchiary

  2. Raja Ramanna Fellow, Department of Atomic Energy, Government of India, ICAR-National Research Center on Plant Biotechnology, New Delhi, India

    Chittaranjan Kole

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Li, F., Liu, M., Zhou, Y. (2019). Sequence Databases and Online Tools for Capsicum Research. In: Ramchiary, N., Kole, C. (eds) The Capsicum Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-97217-6_14

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