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

Scientific Reports
Sima TaheriParisa Azizi

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. Thre...Continue Reading

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Citations

Apr 8, 2020·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Wenli AnXiasheng Zheng
Oct 10, 2020·Frontiers in Genetics·Harun KarcιSalih Kafkas

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Methods Mentioned

BETA
RNA-seq
Illumina sequencing
one hybrid
electrophoresis
PCR

Software Mentioned

Numerical Taxonomy and Multivariate Analysis System ( NTSYSpc
Trinity
BLASTX
script MIcroSAtellite
NTSYSpc
MISA
BLAST
POPGENE32
Perl
Blast2GO

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