Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.)

Publication Type:Journal Article
Year of Publication:2013
Authors:Zhang, J-Y, Lee, Y-C, Torres-Jerez, I, Wang, M, Yin, Y, Chou, W-C, He, J, Shen, H, Srivastava, AC, Pennacchio, C, Lindquist, E, Grimwood, J, Schmutz, J, Xu, Y, Sharma, M, Sharma, R, Bartley, LE, Ronald, PC, Saha, MC, Dixon, RA, Tang, Y, Udvardi, MK
Journal:The Plant Journal
Volume:74
Issue:1
Date Published:2013
ISBN Number:1365-313X
Keywords:bioenergy, genomics, Panicum, Panicum virgatum, switchgrass, technical advance, transcript sequence, transcriptome
Abstract:

Switchgrass (Panicum virgatum L.) is a perennial C4 grass with the potential to become a major bioenergy crop. To help realize this potential, a set of RNA-based resources were developed. Expressed sequence tags (ESTs) were generated from two tetraploid switchgrass genotypes, Alamo AP13 and Summer VS16. Over 11.5 million high-quality ESTs were generated with 454 sequencing technology, and an additional 169 079 Sanger sequences were obtained from the 5′ and 3′ ends of 93 312 clones from normalized, full-length-enriched cDNA libraries. AP13 and VS16 ESTs were assembled into 77 854 and 30 524 unique transcripts (unitranscripts), respectively, using the Newbler and pave programs. Published Sanger-ESTs (544 225) from Alamo, Kanlow, and 15 other cultivars were integrated with the AP13 and VS16 assemblies to create a universal switchgrass gene index (PviUT1.2) with 128 058 unitranscripts, which were annotated for function. An Affymetrix cDNA microarray chip (Pvi_cDNAa520831) containing 122 973 probe sets was designed from PviUT1.2 sequences, and used to develop a Gene Expression Atlas for switchgrass (PviGEA). The PviGEA contains quantitative transcript data for all major organ systems of switchgrass throughout development. We developed a web server that enables flexible, multifaceted analyses of PviGEA transcript data. The PviGEA was used to identify representatives of all known genes in the phenylpropanoid–monolignol biosynthesis pathway.

URL:http://dx.doi.org/10.1111/tpj.12104
Short Title:The Plant Journal
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