De novo transcriptome assembly and mining of EST-SSR markers in Gloriosa superba
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Ó Indian Academy of Sciences (0123456789().,-volV) (0123456789().,-volV)
RESEARCH ARTICLE
De novo transcriptome assembly and mining of EST-SSR markers in Gloriosa superba MOUMITA DAS*
, SOUMYA PRAKASH SAHU and ARCHANA TIWARI
School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Bhopal 462 033, India *For correspondence. E-mail: [email protected]. Received 17 February 2020; revised 11 May 2020; accepted 30 June 2020 Abstract. Gloriosa superba is an economical source of pharmaceutical colchicine, which is a mitotic poison used to treat gout, cancer and inflammatory diseases. It is important to study the genetic variations in this plant, but the progress is impeded due to limited number of molecular markers. In this study, we developed the expressed sequence tag-derived simple sequence repeat (EST-SSR) markers from the transcriptome sequence of the leaf samples of three different ecotypes of G. superba. De novo assembly was performed on these sequencing data to generate a total of 65,579 unigenes and 38,200 coding sequences (CDSs). These CDSs were annotated using NCBI Nr protein database, gene ontology terms and KEGG pathways. Differential gene expression was studied to yield differences in these ecotypes at the molecular level. Finally, a total of 14,672 potential EST-SSRs were identified from these unigenes, among which the dinucleotide (5754, 39.22%) and trinucleotide (5421, 36.95%) repeats were most abundant types followed by mononucleotides (3213, 21.83%). The most frequent motifs were CT/GA (1392, 9.48%), AG/TC (1219, 8.31%), and GA/CT (1146, 7.82%) among the dinucleotide repeats and CCG/ CGG (1487, 10.13%), AGG/CCT (1421, 9.68%), AGC/CTG (697, 4.75%) and AAG/CTT (621, 4.23%) among the trinucleotide repeats. Polymorphism study using a random set of 20 newly developed EST-SSRs revealed polymorphic information content value ranging from 0 to 0.5926 with an average of 0.4021. The large-scale ESTs developed in the current study will be useful as a genomic resource for further investigation of the genetic variations in this species. Keywords.
colchicine; expresses sequence tag-derived simple sequence repeat marker; de novo assembly; Gloriosa superba.
Introduction Gloriosa superba is a perennial tuberous climbing herb, which belongs to the family Colchicaceae. Due to its climbing nature, it is commonly known as climbing lily. Some of the other vernacular names of this plant are glory lily, flame lily, creeping lily etc. This species is native to tropical Africa and Asia, and are distributed throughout the tropics as a pot plant (Ghosh et al. 2002). Of the eight different types of alkaloids that are found in the family Colchicaceae, colchicine and colchicoside alkaloids are All authors contributed to the study conception and design. Collection of plant material, RNA isolation and data analysis were performed by Soumya Prakash Sahu and Moumita Das. The first draft of the manuscript was written by Soumya Prakash Sahu and Moumita Das. Archana Tiwari and Moumita Das revised the manuscript and prepared
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