Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L

Abstract

Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%) followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsESTSSRs resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics studies in Allium species.

Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (<i>Carica papaya</i> L.)

“…In mononucleotides repeats, the most abundant motif was A/T (69.3%), which is similar with previous reports on Allium sativum [54] and Humulus lupulus [56]. In dinucleotides, AG/CT motif (61%) was most abundant in this study.…”

“…The frequency of mononucleotide was found to be highest (94.7%) as compared to other repeat types in our study which is similar to previous report of papaya in which mononucleotides contributed maximum (69.1%) [40]. The abundance of mononucleotide repeats in assembled ESTs suggests that they are present within the expressed regions and not at the end of the mRNA sequences [54]. Mononucleotide repeats have been used to study the population genetic in chloroplast genomes [55].…”

Omics approaches inAlliumresearch: Progress and way ahead

“…Similarly, microsatellite, SNP, and indel markers were discovered from the transcriptome data of garlic ( Havey & Ahn, 2016 ; Chand et al, 2015 ). Tsukazaki et al (2015) used the transcriptome shotgun assembly and Illumina HiSeq 2000 for RNA-seq analyses in A. fistulosum .…”

In silico analysis of onion chitinases using transcriptome data

“…The availability of EST data in public databases like dbEST facilitates the mining, prediction and characterization of candidate genes by computational biological methods. Several genes having vital functional attributes in processes like seed development [ 12 ], plant growth [ 13 ], and defense response [ 14 , 15 ], microsatellites [ 16 ], and micro-RNAs [ 17 ] have been identified using mining of dbESTs and genome survey sequences (dbGSS) sequences. In the current work, an EST mining-based identification of chitinases in A. cepa has been carried out using already reported plant chitinase sequences as bait.…”