Generation and Characterisation of a Reference Transcriptome for Phalaris (Phalaris aquatica L.)

Abstract

Phalaris aquatica is a cool-season perennial grass species that is extensively cultivated in Australia, with additional usage in other areas of the world. Phalaris displays a number of desirable agronomic characteristics, although unfavourable traits include excessive seed shattering, sensitivity to aluminium toxicity, and several toxicosis syndromes. Varietal development has to date been based on traditional selection methods, but would benefit from the application of genomics-based approaches, which require the development of large-scale sequence resources. Due to a large nuclear DNA content, methods that target the expressed component of the genome and reduce the complexity of analysis are most amenable to current sequencing technologies. A reference unigene set has been developed by transcriptome sequencing of multiple tissues from a single plant belonging to the variety Landmaster. Comparisons have been made to gene complements from related species, as well as reference protein databases, and patterns of gene expression in different tissues have been evaluated. A number of candidate genes relevant to removal of undesirable attributes have been identified. The reference unigene set will provide the basis for detailed studies of differential gene expression and identification of candidate genes for potential transgenic deployment, as well as a critical resource for genotypic analysis to support future genomics-assisted breeding activities for phalaris improvement.

Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis

“…A higher N50 is likely due to the presence of untranslated regions (UTRs) in this study as compared to previous datasets. In terms of functional characterisation of the transcripts, 64% of Cannbio’ transcripts were assigned at least one GO term, which is comparable with other published plant transcriptome studies 32,36,37 .…”

“…Not all contigs and scaffolds from the generated transcriptome assembly were annotated based on similarity search to known protein of UniRef100 database which could represent the presence of pseudogenes, or repetitive elements, or genes with disrupted function which were discarded from the assembly. Moreover, the subset of transcripts was found to be from non-plant origin and this level of contamination was found to be comparable in other plant datasets 32 which could indicate the presence of microbial communities in the rhizosphere, and in planta. Cannbio’s transcripts had the highest number of similarity matches to Trema orientalis and Parasponia andersonii , which is consistent with known phylogenetic relations, as all belong to the Cannabaceae 33 .…”

Genotyping‐by‐sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels

“…Approximately 500–800 million sequence reads from a range of tissues are sufficient to generate a reference which can be relatively easily assembled, as shown by Baillie et al . (), Shinozuka et al . () and Sudheesh et al .…”

“…In all instances, visualization of alignments was performed using Tablet (Milne et al ., ). For lentil, perennial ryegrass and phalaris, reference transcriptomes have already been described (Baillie et al ., ; Shinozuka et al ., ; Sudheesh et al ., ). To provide a common standard across all species, the CDS file from the canola reference genome sequence (Chalhoub et al ., ) was used as a proxy for a reference transcriptome.…”

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses

“…In a comparative transcriptome analysis, a stress-responsive protein has been identified in Lolium/Festuca species ( Czaban et al, 2015 ). Recently, transcriptome analyses were done to study dwarfism to enhance dwarfing breeding in Kentucky bluegrass ( Gan et al, 2016 ), drought stress response in creeping bentgrass ( Ma et al, 2017 ), water stress ( Talukder et al, 2015 ), lead (pb) stress ( Li et al, 2017 ), and endophyte response in tall fescue ( Dinkins et al, 2017 ), and to develop a unigene reference as a molecular breeding resource in Phalaris ( Baillie et al, 2017 ). Markers developed from the reference transcript corresponding to the protein might be useful for MAS for stress tolerance.…”