Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic Biomass Crop

Abstract

Prairie cordgrass (Spartina pectinata Bosc ex Link) is being developed as a cellulosic biomass crop. Development of this species will require numerous steps, including breeding, agronomy, and characterization of the species genome. The research in this paper describes the fi rst investigation of the transcriptome of prairie cordgrass via Next Generation Sequencing Technology, 454 GS FLX. A total of 556,198 expressed sequence tags (ESTs) were produced from four prairie cordgrass tissues: roots, rhizomes, immature infl orescence, and hooks. These ESTs were assembled into 26,302 contigs and 71,103 singletons. From these data were identifi ed, EST-SSR (simple sequence repeat) regions and cell wall biosynthetic pathway genes suitable for the development of molecular markers which can aid the breeding process of prairie cordgrass by means of marker assisted selection. P RAIRIE CORDGRASS (PCG) is a native grass species of the North American Prairie and has recently gained attention as a species suitable for the production of cellulosic biomass for producing biofuel . PCG is a warm season, C 4 grass with a geographical range extending from Texas to the Arctic Circle (USDA-NRCS, 2008) and having the highest latitude of distribution of any C 4 species (Potter et al., 1995). PCG has been utilized ecologically for revegetation, stream bank stabilization, and habitat development. In addition, this species has been used as a forage species . PCG is able to survive in a wide variety of environmental conditions, from open arid prairies and high railroad embankments to wet areas with high salinity and insuffi cient aeration of the soils where neither switchgrass (Panicum virgatum L.) nor maize (Zea mays L.) can be grown to their full potential . Th e inherent tolerance of PCG to these environmental conditions will allow the production of cellulosic biomass from land that is unsuitable for conventional crop production.On the basis of these favorable growth characteristics, research attention is being directed toward the development of PCG as a cellulosic biomass crop species. Indubitably, genetic improvements will be made to PCG to enhance this species for utilization as a source for biomass. Th ese genetic changes could occur via conventional breeding and marker assisted selection breeding or by incorporation of favorable genes (or characteristics) through plant transformation techniques. To facilitate any genetic improvement in PCG, comprehensive knowledge of the genome and its gene expression profi ling is essential. Limited genetic studies have been performed in PCG to date. Genetic diversity of populations of PCG with amplifi ed fragment length polymorphisms (AFLP) has been studied (Moncada et al., 2007; J. Gonzalez, unpublished data). Th e development of molecular markers for breeding can be achieved rapidly by utilizing techniques such as enriched genomic libraries and parallel pyrosequencing techniques. Both of these methods can provide considerable amounts of information about the genome structure of this species...

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

“…Functional annotation could be assigned to 68.6% of the S. maritima contigs and 98.6% of the S. alterniflora contigs. Nonetheless, a large number of unique reads (singletons) were found, that is, 15% for our data set compared with other studies using the same assembler: 13% in S. pectinata (Gedye et al, 2010); 10-25% in Mytilus galloprovincialis (Craft et al, 2010); 8.8% in Palomero maize (Vega-Arreguin et al, 2009) and 7% in Amaranthus and Ginseng Délano-Frier et al, 2011). This could result from various causes such as the presence of rare transcripts from lowly expressed genes.…”

“…Before this study, only a limited number of Spartina ESTs were deposited in the NCBI EST database. If we exclude a recent transcriptome analysis in the tetraploid Spartina pectinata that generated 556 198 ESTs (Gedye et al, 2010), a few hundred sequences only were available for S. maritima (Chelaifa et al, 2010a) and S. alterniflora (Baisakh et al, 2008). Our work represents the first effort to analyze the transcriptome of the hexaploid Spartina species, resulting in a reference transcriptome of more than 16 700 annotated genes from leaves and roots.…”

“…As there is no reference genome for Spartina, we used information from several EST and protein databases for gene annotation, a procedure successfully employed for other non-model species (for example, Barakat et al, 2009;Gedye et al, 2010;Franssen et al, 2011;Garg et al, 2011). In de novo sequencing projects transcriptome coverage efficiency has been evaluated by comparing the number of unique genes to the nearest transcriptome available (Parchman et al, 2010).…”

“…GS Assembler version 2.3 (Roche, Inc.) was employed to assemble reads into contigs; this program was already successfully used for assembly in transcriptome analyses (Bellin et al (2009) in Vitis vinifera; Gedye et al (2010) in S. pectinata; Sun et al (2010) in Panax ginseng).…”

Desarrollo y aplicación de herramientas genómicas para la mejora de especies cucurbitáceas por calidad y resistencia a enfermedades.

“…Around Our assembled unigenes were also larger than those reported for other plant trancriptomes obtained using the GS FLX Titanium platform combined with Sanger (Li et al, 2010;Sun et al, 2010). These differences in length might also be due to the different assemblers used.…”