title: Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.).
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.
authors.affiliation: Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA.
authors.forename: Ji-Yi
authors.initials: JY
authors.lastname: Zhang
authors.forename: Yi-Ching
authors.initials: YC
authors.lastname: Lee
authors.forename: Ivone
authors.initials: I
authors.lastname: Torres-Jerez
authors.forename: Mingyi
authors.initials: M
authors.lastname: Wang
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Yin
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Chou
authors.forename: Ji
authors.initials: J
authors.lastname: He
authors.forename: Hui
authors.initials: H
authors.lastname: Shen
authors.forename: Avinash C
authors.initials: AC
authors.lastname: Srivastava
authors.forename: Christa
authors.initials: C
authors.lastname: Pennacchio
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
authors.forename: Manoj
authors.initials: M
authors.lastname: Sharma
authors.forename: Rita
authors.initials: R
authors.lastname: Sharma
authors.forename: Laura E
authors.initials: LE
authors.lastname: Bartley
authors.forename: Pamela C
authors.initials: PC
authors.lastname: Ronald
authors.forename: Malay C
authors.initials: MC
authors.lastname: Saha
authors.forename: Richard A
authors.initials: RA
authors.lastname: Dixon
authors.forename: Yuhong
authors.initials: Y
authors.lastname: Tang
authors.forename: Michael K
authors.initials: MK
authors.lastname: Udvardi
mesh_terms: D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D015723:Gene Library; D018745:Genome, Plant; D005838:Genotype; D020407:Internet; D008897:Panicum / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant