Vol. 7, Issue 4 (2019)
Development and validation of simple sequence repeat markers from genome of ajwain (Trachyspermum ammi L.)
Author(s): Mayur R Jogarana, Rushita V Bhadani, Harshita J Kachhadiya, Abhijeeta K Nandha, Manthan Kapuria, Antala Virali and Tomar RS
Abstract: Ajwain (Trachyspermum ammi L.) is an annual herbaceous plant belonging to the highly valued medicinally important family, Apiaceae.In present study, Ion Torrent Genome Sequencing (Ion S5) technology was used to generate ajwain draft genome using genotype Gujarat Ajwain 1. Gujarat Ajwain 1 genotype was sequenced using next generation sequencing platform Ion S5 which yielded 8.4 Gb of raw data. After trimming of reads, the quality data were of 28,450,128 bp with average read length of 193.8 bp. The average percentage of quality filtered read was 99.43%. The de novo assembly yielded assembled reads of 499,199,313 bp and number of contigs were 788,836. In the assembly the N25, N50, N75 contig size were 1151 bp, 644 bp and 416 bp respectively. Based on the contig length more than 5000 sequences were generated from which 425 sequences were selected for further analysis. In Blast 2GO analysis, 425 sequence were functionally annotated out of which 22 showed positive interpro. While 414 got Blast hits, of which 408 and 339 sequence were mapped and annotated, respectively. During the gene ontology, total 33594 GO IDs were found, which were grouped in to biological process, cellular components and molecular function, respectively. Out of 425 sequences scanned 17 showed positive InterPro result while 408 did not showed any InterPro results. KEGG pathway rewarded that among all sequences the maximum sequence was in Purine metabolism (63). KEGG analysis created the enzymes ID of which maximum enzymes count ID were found in the pathway of Diterpenoid biosynthesis, which was 12 while for other pathway few enzyme ID count were found. From the sequenced genome a total of 228 SSRs were identified with the Tm range of 56-62 °C and GC% of 40-70%. The length of SSR primer was between 18-23 bp and the product size in the range of 100-300 bp. The percentage of dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, hexanucleotide repeats comprised 26.31%, 27.9%, 35.52%, 7.89% and 3.07%, respectively. Validation of selected 25 SSR primers was carried out in 5 different genotypes of ajwain namely Ajmer ajwain-1, Ajmer Aawain-2, Ajmer ajwain-93, Gujarat ajwain-1, Gujarat ajwain-2. Out of 25 primers 19 primers were amplified to produce a total 24 band. The largest amplicon of 734 bp was amplified by SSR primer AJ 12 and smallest fragment of 58 bp was applied by SSR primer AJ16. The polymorphic primer can be used in genetic diversity analysis of Ajwain and its relatives.
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How to cite this article:
Mayur R Jogarana, Rushita V Bhadani, Harshita J Kachhadiya, Abhijeeta K Nandha, Manthan Kapuria, Antala Virali, Tomar RS. Development and validation of simple sequence repeat markers from genome of ajwain (Trachyspermum ammi L.). Int J Chem Stud 2019;7(4):426-432.
