While microarray analyses are useful in revealing genes that are responsive to different conditions, identi fication of allelic variants from genes showing differen tial expression may enable their application in breeding by marker assisted selection. Recent developments in se quencing technology are making it possible to combine gene discovery thing with identification of allelic variation. Transcriptome sequencing or RNA sequencing is an approach for quantifying transcripts, in which RNA samples are converted to cDNA and sequenced, typically using high throughput methods. The resulting reads are then mapped against a reference genome se quence or assembled de novo to produce genome scale transcriptome maps consisting of the structure and abundance of each gene.
The abundance of each transcript is determined by counting the number of sequences mapped to the corresponding gene thus pro viding digital estimate of gene expression. The main advantages of RNA seq over microarray analysis are a. As RNA seq is based on counting sequences, cross hy bridisation problems associated with microarrays are Inhibitors,Modulators,Libraries avoided b. RNA seq has high dynamic range of detection i. e. very low and very high abundance tran scripts can be detected with RNA seq while microarrays lack sensitivity to detect genes expressed at either high or low levels. Using this technique Zenoni et al. detected several genes expressed during berry develop ment in Vitis vinifera. Similarly several protein coding genes related to xylem formation were identified in an Eucalyptus plantation tree using RNA seq.
RNA seq is also useful for identifying and estimating tran script abundances from Inhibitors,Modulators,Libraries alternatively spliced variants. By sequencing several individuals from different Inhibitors,Modulators,Libraries populations it is also possible to identify single nucleo tide polymorphisms from genes showing differ ential expression. In addition transcriptome sequencing can also be used to study the evolutionary selection patterns of genes by estimating nonsynonymous to synonymous substitution ratios. Novaes et al. have shown that most of the genes are under purifying selection by sequencing RNA from different tissues bulked from several individ ual trees in E. grandis. Combining gene discovery with analysis of selection signatures may provide insights into natural selection patterns under drought stress.
Eucalyptus camaldulensis is one of the most widely planted tree species in the world, and is Inhibitors,Modulators,Libraries grown ex tensively in plantations for pulp production in the tro pics of South and South East Asia. Water availability is the most important factor determining the establishment and composition of tree species in the dry tropics. The seedling stage is the critical period for Inhibitors,Modulators,Libraries survival http://www.selleckchem.com/products/Romidepsin-FK228.html and establishment of trees. In this study we analysed the physiological responses of seedlings of three E.