Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Abstract

Background: Although the reference genome of Solanum tuberosum group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research and its subsequent applications in breeding. Results: For the DM genome assembly, two only partially-overlapping gene models exist di ering in a unique set of genes and intron/exon structure predictions. First step was to merge and manually curate the merged gene model, creating a union of genes in Phureja sca old. We next compiled available RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using CLC, Trinity, Velvet, and rnaSPAdes de novo assemblers using di erent settings to test for optimal outcome. In addition, for cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. Revised EvidentialGene redundancy-reducing pipeline was employed to produce accurate and complete cultivar-speci c transcriptomes from assemblers output, as well as to attain the pan-transcriptome. Due to being the most diverse dataset in terms of tissues (stem, seedlings and roots) and experimental conditions, cv. Désirée was the most complete transcriptome (95.8% BUSCO completeness). For cv. Rywal and breeding clone PW363 data were available for leaf samples only and the resulting transcriptomes were less complete than cv. Désirée (89.8% and 89.3% BUSCO completeness, respectively). Cross comparison of these cultivar-speci c transcriptomes and merged DM gene model suggests that the core potato transcriptome is comprised of 16,339 genes. The pan-transcriptome contains a total of 95,779 transcripts, of which 54,614 transcripts are not present in the Phureja genome. These represent the variants of the novel genes found in the potato pan-genome. Conclusions: Our analysis shows that the available gene model of double-monoploid potato from group Phureja is, to some degree, not complete. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput -omics analyses, and future breeding programmes.

Precision transcriptomics of viral foci reveals the spatial regulation of immune‐signaling genes and identifies RBOHD as an important player in the incompatible interaction between potato virus Y and potato

“…Quality control was performed in clc genomics workbench 12.0 (Qiagen). The merging of overlapping pairs, the mapping of reads to the potato genome (Petek et al ., 2020) and read counting were performed in both clc genomics and star . Differential expression analysis was performed in r (R Core Team, 2020; version 3.2.2), using the r package limma (Ritchie et al ., 2015), trimmed mean of M values (TMM) normalization and voom function.…”

Plant Molecular Responses to Potato Virus Y: A Continuum of Outcomes from Sensitivity and Tolerance to Resistance

“…tuberosum were sequenced (The Potato Genome Sequencing Consortium, 2011, https://www.plantbreeding.wur.nl/Solyntus/). In addition, the pan-transcriptome constructed from several potato cultivars is available [31].…”

A mini-TGA protein, lacking a functional DNA-binding domain, modulates gene expression through heterogeneous association with transcription factors

“…All primers and probes used for qPCR analysis together with the target gene IDs are listed in Supplementary Table 11. New qPCR assays, targeting StPRX07 , StPRX15 , StPRX46 , StTGA2.1 and StPti5 were designed with Primer Express v2.0 (Applied Biosystems, USA), using the sequences from the potato reference genome 88 , cultivar Rywal cds, and cultivar Rywal and cultivar Désirée reference transcriptomes 89 .…”

“…The presence of contaminant organism reads was determined using Centrifuge 91 . Reads were mapped to the reference group Phureja DM1-3 potato genome v4.04 88 using the merged PGSC and ITAG genome annotation 89 and counted using STAR 92 with default parameters. Differential expression analysis was performed in R using the limma package 93 .…”