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De novo transcriptome assembly and mining of EST-SSR markers in Gloriosa superba. 2020

Moumita Das, and Soumya Prakash Sahu, and Archana Tiwari
School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Bhopal 462 033, India. drmoumitadas1@gmail.com.

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.

UI MeSH Term Description Entries
D005819 Genetic Markers A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event. Chromosome Markers,DNA Markers,Markers, DNA,Markers, Genetic,Genetic Marker,Marker, Genetic,Chromosome Marker,DNA Marker,Marker, Chromosome,Marker, DNA,Markers, Chromosome
D000070437 Colchicaceae A family in the order Liliales.
D059014 High-Throughput Nucleotide Sequencing Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc. High-Throughput Sequencing,Illumina Sequencing,Ion Proton Sequencing,Ion Torrent Sequencing,Next-Generation Sequencing,Deep Sequencing,High-Throughput DNA Sequencing,High-Throughput RNA Sequencing,Massively-Parallel Sequencing,Pyrosequencing,DNA Sequencing, High-Throughput,High Throughput DNA Sequencing,High Throughput Nucleotide Sequencing,High Throughput RNA Sequencing,High Throughput Sequencing,Massively Parallel Sequencing,Next Generation Sequencing,Nucleotide Sequencing, High-Throughput,RNA Sequencing, High-Throughput,Sequencing, Deep,Sequencing, High-Throughput,Sequencing, High-Throughput DNA,Sequencing, High-Throughput Nucleotide,Sequencing, High-Throughput RNA,Sequencing, Illumina,Sequencing, Ion Proton,Sequencing, Ion Torrent,Sequencing, Massively-Parallel,Sequencing, Next-Generation
D059467 Transcriptome The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells. Transcriptomes,Gene Expression Profiles,Gene Expression Signatures,Transcriptome Profiles,Expression Profile, Gene,Expression Profiles, Gene,Expression Signature, Gene,Expression Signatures, Gene,Gene Expression Profile,Gene Expression Signature,Profile, Gene Expression,Profile, Transcriptome,Profiles, Gene Expression,Profiles, Transcriptome,Signature, Gene Expression,Signatures, Gene Expression,Transcriptome Profile
D018506 Gene Expression Regulation, Plant Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants. Plant Gene Expression Regulation,Regulation of Gene Expression, Plant,Regulation, Gene Expression, Plant
D018895 Microsatellite Repeats A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs). Microsatellite Markers,Pentanucleotide Repeats,Simple Repetitive Sequence,Tetranucleotide Repeats,Microsatellites,Short Tandem Repeats,Simple Sequence Repeats,Marker, Microsatellite,Markers, Microsatellite,Microsatellite,Microsatellite Marker,Microsatellite Repeat,Pentanucleotide Repeat,Repeat, Microsatellite,Repeat, Pentanucleotide,Repeat, Short Tandem,Repeat, Simple Sequence,Repeat, Tetranucleotide,Repeats, Microsatellite,Repeats, Pentanucleotide,Repeats, Short Tandem,Repeats, Simple Sequence,Repeats, Tetranucleotide,Repetitive Sequence, Simple,Repetitive Sequences, Simple,Sequence Repeat, Simple,Sequence Repeats, Simple,Sequence, Simple Repetitive,Sequences, Simple Repetitive,Short Tandem Repeat,Simple Repetitive Sequences,Simple Sequence Repeat,Tandem Repeat, Short,Tandem Repeats, Short,Tetranucleotide Repeat
D020224 Expressed Sequence Tags Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived. ESTs,Expressed Sequence Tag,Sequence Tag, Expressed,Sequence Tags, Expressed,Tag, Expressed Sequence,Tags, Expressed Sequence

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