Browsing by Author "Choudhary, S"

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Molecular basis of transitivity in plant RNA silencing
(Springer, 2019) Choudhary, S; Thakur, S; Bhardwaj, Pankaj
The discovery of small RNAs has offered exciting opportunities in manipulating gene expression. The non-coding RNAs cause target gene inactivation at the transcriptional, post-transcriptional or translational level. In addition to the default silencing approach, they provide another mode of gene regulation by transitivity. Here, gradual amplification in effector RNAs number allows regulation of genes other than the original target and causes the outspread of silencing from its origin to aid a robust response. Unlike the short-range cell-to-cell movement of silencing signal (through plasmodesmata), little is known of the mediators of systemic silencing (usually through phloem). Through the present review, we combine the reports available so far to better understand the characteristics of secondary silencing, factors involved, and summarize the instances where it has been employed in plants. Understanding the molecular mechanism behind transitivity has led to the designing of efficient transgenes for targeted gene inactivation, utilized in silencing of a multigene family, and in the field of functional genomics. Studies uncovering the origin of distinct secondary silencing pathways in plants have been exploited for developing artificial RNA silencing methods such as hairpin RNA, artificial microRNA, intrinsic direct repeat, inverted repeat, artificial trans-acting siRNA, phased siRNA, and virus-induced gene silencing. The techniques have facilitated the spread of traits such as pathogenic resistance or alter plant growth and development features. The mechanism of reprogramming in the silencing machinery and the consequent genetic manipulation through transitive RNA is still not completely understood and its exploitation in crop improvement programmes is still in a developing phase. © 2019, Springer Nature B.V.
Transcriptome characterization and development of functional polymorphic SSR marker resource for Himalayan endangered species, Taxus contorta (Griff)
(Elsevier, 2019) Majeed, A; Singh, A; Choudhary, S; Bhardwaj, Pankaj
Taxus contorta is an important medicinal plant currently listed as endangered in IUCN Red Data List. It produces an anticancer drug, paclitaxel which is well known in the industrial sector. Due to habitat destruction and overexploitation, it is at the verge of extinction. Genomic and transcriptomic data for this species is scarce which has hampered its genomic studies. Moreover, large scale polymorphic informative codominant marker resource is also scarce which hinders its population and landscape genetic analysis. Here, we generated a reference transcriptome for this species which would facilitate the understanding of the functional elements and promote genomic research in this species. Also, a robust polymorphic SSR marker resource was characterized which can be used in conservation of this species. More than 100 million paired end raw reads were obtained through Illumina sequencing. A total of 129,869 unigenes with mean sequence length of 1244 nt were obtained from 209,860 de novo assembled transcripts. Of these, 35,752 transcripts were assigned 5971 unique GO terms. Around 40,386 transcripts were found to have 2163 unique Pfam Ids. Pathway analysis against KEGG database yielded 3721 unique enzyme numbers. Screening of the transcripts for microsatellite regions yielded 7041 SSRs. Among the 100 SSRs selected for characterization on 30 genotypes, 37 polymorphic markers showed a total of 214 alleles with mean of 5.78 alleles per locus. Mean effective number of alleles (Ne) was found to be 3.64 and average PIC value of 0.64 was observed. Observed heterozygosity (0.57) was found to be lower than expected (0.69). This effective polymorphic SSR marker resource will act as valuable tool for deciphering its genetic diversity. © 2019 Elsevier B.V.