De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock

Abstract

Field pennycress (Thlaspi arvense L.) has potential as an oilseed crop that may be grown during fall (autumn) and winter months in the Midwestern United States and harvested in the early spring as a biodiesel feedstock. There has been little agronomic improvement in pennycress through traditional breeding. Recent advances in genomic technologies allow for the development of genomic tools to enable rapid improvements to be made through genomic assisted breeding. Here we report an annotated transcriptome assembly for pennycress. RNA was isolated from representative plant tissues, and 203 million unique Illumina RNA-seq reads were produced and used in the transcriptome assembly. The draft transcriptome assembly consists of 33 873 contigs with a mean length of 1242 bp. A global comparison of homology between the pennycress and Arabidopsis transcriptomes, along with four other Brassicaceae species, revealed a high level of global sequence conservation within the family. The final assembly was functionally annotated, allowing for the identification of putative genes controlling important agronomic traits such as flowering and glucosinolate metabolism. Identification of these genes leads to testable hypotheses concerning their conserved function and to rational strategies to improve agronomic properties in pennycress. Future work to characterize isoform variation between diverse pennycress lines and develop a draft genome sequence for pennycress will further direct trait improvement.

Emergence of field pennycress (Thlaspi arvense L.): Comparison of two accessions and modelling

“…Its growth characteristics make it suitable as a winter crop in Mediterranean climates (Zanetti et al, 2013), where it could be alternated with irrigated crops, as proposed for other crop species by Meza et al (2008). As a winter annual, it can also double as a cover-crop to sequester excess soil nitrogen, reduce erosion, provide spring cover, and suppress other weeds (Dorn et al, 2013).…”

De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification

“…Fortunately, with the advent of next-generation sequencing (NGS) technology in recent years, genomic information in previously uncharacterized systems can be generated (Grabherr et al 2011). Currently, high-throughput RNA sequencing (RNA-Seq) has emerged as a powerful and cost-efficient tool for transcriptome analysis, and it has also been used for transcript profiling in various nonmodel plant species, including potato (Solanum tuberosum L.) (Zhang et al 2014), pennycress (Thlaspi arvense) (Dorn et al 2013), sweet potato (Ipomoea batatas) (Firon et al 2013) and radish (Raphanus sativus L.) (Wang et al 2012a).…”

“…Thus, it is necessary to reconstruct the flowering pathway in Arabidopsis using the deduced peptides from the transcriptome assembly (Dorn et al 2013). Using TBLASTN, at least 55 known Arabidopsis (or other phylogenetically related species) homologous genes involved in four floral pathways (the photoperiod, vernalization, autonomous and gibberellin (GA)-signaling pathway) were identified in our transcripts databases (Haas et al 2013).…”

Sustainable commercialization of new crops for the agricultural bioeconomy

“…The goal is to identify new desirable phenotypes, as well as desirable mutations in key genes of interest. Pennycress is closely related to the model plant species Arabidopsis thaliana; thus, many of the lessons learned from the billions of dollars and decades spent on Arabidopsis research can now be directly applied to the development of this new crop species (Dorn et al, 2013(Dorn et al, , 2015Sedbrook et al, 2014). With the genomic resources now in hand for pennycress, the use of new plant breeding technologies such as genome editing are feasible (Hartung and Schiemann, 2014;Sedbrook et al, 2014 Release of commercially viable germplasm depends on progress on many traits, as noted above.…”

“…To date, the first pennycress transcriptome (Dorn et al, 2013) and genome (Dorn et al, 2015) sequences have been released. These genomic resources are driving a mutation breeding approach to target the key traits previously mentioned, including ethyl methanesulfonate, fast neutron, and gamma ray mutagenesis.…”