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

• DOI: 10.1111/tpj.12104
• Publication Date: 2013-01-05T16:52:36Z
• Authors: Ji‐Yi Zhang; Yi‐Ching Lee; Ivone Torres‐Jerez; Mingyi Wang; Yanbin Yin; Wen‐Chi Chou; Ji He; Hui Shen; Avinash C. Srivas...; Christa Pennacchio; Erika Lindquist; Jane Grimwood; Jeremy Schmutz; Ying Xu; Manoj Sharma; Rita Sharma; Laura E. Bartley; Pamela C. Ronald; Malay C. Saha; Richard A. Dixon; Yuhong Tang; Michael K. Udvardi
• Keywords: Expressed Sequence Tags; 2. Zero hunger; Internet; 0303 health sciences; Genotype; Sequence Analysis, DNA; 15. Life on land; Panicum; 03 medical and health sciences; RNA, Plant; RNA, Messenger; Databases, Nucleic Acid; Genome, Plant; Gene Library

SummarySwitchgrass (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.