De novo assembly of wheat root transcriptomes and transcriptional signature of longitudinal differentiation

Abstract

Hidden underground, root systems constitute an important part of the plant for its development, nourishment and sensing the soil environment around it, but we know very little about its genetic regulation in crop plants like wheat. In the present study, we de novo assembled the root transcriptomes in reference cultivar Chinese Spring from RNA-seq reads generated by the 454-GS-FLX and HiSeq platforms. The FLX reads were assembled into 24,986 transcripts with completeness of 54.84%, and the HiSeq reads were assembled into 91,543 high-confidence protein-coding transcripts, 2,404 low-confidence protein-coding transcripts, and 13,181 non-coding transcripts with the completeness of >90%. Combining the FLX and HiSeq assemblies, we assembled a root transcriptome of 92,335 ORF-containing transcripts. Approximately 7% of the coding transcripts and ~2% non-coding transcripts are not present in the current wheat genome assembly. Functional annotation of both assemblies showed similar gene ontology patterns and that ~7% coding and >5% non-coding transcripts are root-specific. Transcription quantification identified 1,728 differentially expressed transcripts between root tips and maturation zone, and functional annotation of these transcripts captured a transcriptional signature of longitudinal development of wheat root. With the transcriptomic resources developed, this study provided the first view of wheat root transcriptome under different developmental zones and laid a foundation for molecular studies of wheat root development and growth using a reverse genetic approach.

Physiological and Transcriptomic Characterization of Sea-Wheatgrass-Derived Waterlogging Tolerance in Wheat

“…Twelve RNA samples (two genotypes × two treatments × three samples per genotype) were submitted to Novogene Inc. (Sacramento, CA, USA) for constructing 12 paired-end (PE) RNA-seq libraries and producing ~20 million pairs of 150 bp reads per library for Tt139 and ~40 million reads for Amph819 on the HiSeq2000 sequencing platform (Illumina, San Diego, CA, USA). The processing of the raw reads was conducted following the procedure described by Challa and Li [ 35 ]. The transcript abundances were calculated by the RNA-seq quantification program Kallisto [ 36 ] using the International Wheat Genome Sequencing Consortium (IWGSC) reference genome assembly RefSeqv2.0 and the gene models v2.0 [ 37 , 38 ].…”

“…Briefly, the log-transformed transcript abundances were normalized using the trimmed mean of M-values method, and the differentially expressed genes (DEGs) were identified by comparing the transcript abundances of stagnant condition samples vs. the aerated condition samples from Tt139 and Amph819. The DEGs with at least two-fold change and a p -value of <10 −3 were selected for annotations using the BLASTp against the NCBI-nr database, Interpro, and the GO term annotations as described by Challa and Li [ 35 ]. The GO terms were enriched against the total GO terms in the genome and filtered by adjusted p -value of 0.05.…”

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)

“…To address this, experimental systems have been developed which allow access to growing roots during the imposition of water stress, both for transcriptomic and physiological analyses. These include hydroponic systems, with osmotic stress being imposed using high molecular weight polyethylene glycol (PEG) [18–21] and the use of other suitable soil, sand [4, 13, 22, 23] and non-soil based hydrated media such as vermiculite [24–28], from which roots can be isolated relatively rapidly while minimising mechanical damage, at least for simpler root systems.…”