De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing

Sima Taheri,Thohirah Lee Abdullah,Chee How Teo,Stefaan P O Werbrouck,Mahbod Sahebi,Parisa Azizi,M Y Rafii,Jennifer Ann Harikrishna

doi:10.1038/s41598-019-39944-2

Abstract

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, ‘Chiang Mai Pink’ and ‘UB Snow 701’, to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.

Highlights

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia
We report the first analysis of transcriptome data from C. alismatifolia, a perennial ornamental bulb plant with long vase life and easy growth habits
In spite of significant advances in DNA/RNA sequencing technologies and progress in developing SSR markers, there is a lack of genetic information to develop molecular markers for assessment of genetic diversity of C. alismatifolia populations compared to that in other ornamental plant species

Summary

Introduction

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Open flowers are small with purple flag petals (Fig. 1) To improve this species, traditional breeding programmes have been launched in previous studies[1]. The advent of NGS technologies, such as sequencing by synthesis (e.g., Illumina) can simplify the creation of an enormous amount of genomic or transcriptome sequence data, allowing cost-effective and efficient development of molecular markers, including SSR markers[20]

Methods

Results

Conclusion