De novo transcriptome assembly and mining of EST-SSR markers in Gloriosa superba

• Published in: Journal of genetics Vol. 99; no. 1
• Main Authors: Das, Moumita, Sahu, Soumya Prakash, Tiwari, Archana
• Format: Journal Article
• Language: English
• Published: New Delhi Springer India 01-12-2020; Springer; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Biomedical and Life Sciences; Cancer; Colchicine; Ecotypes; Evolutionary Biology; Expressed sequence tags; Gene expression; Genes; Genetic diversity; Gloriosa superba; Gout; Inflammatory diseases; Life Sciences; Microbial Genetics and Genomics; Mineral industry; Mining industry; NR protein; Oncology, Experimental; Plant Genetics and Genomics; Research Article; Trinucleotide repeat diseases; Trinucleotide repeats; assembly; expresses sequence tag-derived simple sequence repeat marker; colchicine; .
• ISSN: 0022-1333; 0973-7731
• DOI: 10.1007/s12041-020-01235-5

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.