De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

Abstract

Background Arundo donax has attracted renewed interest as a potential candidate energy crop for use in biomass-to-liquid fuel conversion processes and biorefineries. This is due to its high productivity, adaptability to marginal land conditions, and suitability for biofuel and biomaterial production. Despite its importance, the genomic resources currently available for supporting the improvement of this species are still limited.ResultsWe used RNA sequencing (RNA-Seq) to de novo assemble and characterize the A. donax leaf transcriptome. The sequencing generated 1249 million clean reads that were assembled using single-k-mer and multi-k-mer approaches into 62,596 unique sequences (unitranscripts) with an N50 of 1134 bp. TransDecoder and Trinotate software suites were used to obtain putative coding sequences and annotate them by mapping to UniProtKB/Swiss-Prot and UniRef90 databases, searching for known transcripts, proteins, protein domains, and signal peptides. Furthermore, the unitranscripts were annotated by mapping them to the NCBI non-redundant, GO and KEGG pathway databases using Blast2GO. The transcriptome was also characterized by BLAST searches to investigate homologous transcripts of key genes involved in important metabolic pathways, such as lignin, cellulose, purine, and thiamine biosynthesis and carbon fixation. Moreover, a set of homologous transcripts of key genes involved in stomatal development and of genes coding for stress-associated proteins (SAPs) were identified. Additionally, 8364 simple sequence repeat (SSR) markers were identified and surveyed. SSRs appeared more abundant in non-coding regions (63.18%) than in coding regions (36.82%). This SSR dataset represents the first marker catalogue of A. donax. 53 SSRs (PolySSRs) were then predicted to be polymorphic between ecotype-specific assemblies, suggesting genetic variability in the studied ecotypes.ConclusionsThis study provides the first publicly available leaf transcriptome for the A. donax bioenergy crop. The functional annotation and characterization of the transcriptome will be highly useful for providing insight into the molecular mechanisms underlying its extreme adaptability. The identification of homologous transcripts involved in key metabolic pathways offers a platform for directing future efforts in genetic improvement of this species. Finally, the identified SSRs will facilitate the harnessing of untapped genetic diversity. This transcriptome should be of value to ongoing functional genomics and genetic studies in this crop of paramount economic importance.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0828-7) contains supplementary material, which is available to authorized users.

RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’

“…This is not a grapevine-specific problem: results of recent plant transcriptome annotation efforts indicated that our knowledge of gene function in higher plants is still limited. For example, a recent transcriptome analysis in rose-scented geranium ( Pelargonium graveolens ) and giant cane ( Arundo donax ) found protein homology to only 66% and 55% of the transcripts [ 48 , 49 ], respectively. Collectively, plant de novo transcriptome analysis studies confirmed that, despite the wealth of genomics and bioinformatics resources accumulated, our understanding of plant biology is still hindered by our inability to assign even tentative function to a large number of plant genes.…”

Marginal Lands to Grow Novel Bio-Based Crops: A Plant Breeding Perspective

“…Herbaceous 7-61 Mutant and clone collections; leaf and shoot transcriptomic sequences; studies on genetic diversity (AFLP, RAPD, and microsatellites markers) Khudamrongsawat et al, 2004;Zegada-Lizarazu et al, 2010;Pilu et al, 2014;Barrero et al, 2015;Canavan et al, 2017;Evangelistella et al, 2017;Malone et al, 2017;Valli et al, 2017 Reed canarygrass (Phalaris arundinacea L.) Pocienë et al, 2013;Lord, 2015 Virginia mallow (Sida hermaphrodita)…”

Impact of high phosphorous and sodium on productivity and stress tolerance of Arundo donax plants

“…NAC and WRKY genes family are known to mediate water-(Hadiarto and Tran, 2011) and Na + -stress responses, as well as ABA signaling pathway in plants (Jiang et al ., 2017). Genes coding for stress-associated proteins (SAPs) are important regulators of multiple abiotic stress tolerance (Giri et al ., 2013) and found to be induced in water-stressed A. donax plants (Evangelistella et al ., 2017). However, only two SAPs were down-regulated in +Na and +NaP plants.…”

“…To this purpose, we used an integrated approach, combining physiological and biochemical measurements with transcriptomic analysis. Leaf and root transcriptomes of A. donax have been recently explored only in healthy plants (Sablok et al , 2014) and in plants exposed to drought stress (Fu et al , 2016; Evangelistella et al , 2017). Understanding, at molecular level, the response of A. donax to combined P and Na + stress is crucial for implementing adaptation strategies in order to achieve high biomass yield and productivity in marginal areas for agriculture.…”