The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing

Abstract

Strawberry ( Fragaria x ananassa ) is an allopolyploid species with diverse and complex transcripts. The regulatory mechanisms of fruit development and maturation have been extensively studied; however, little is known about the signaling mechanisms that direct this process in octoploid strawberry ( Fragaria x ananassa ). Here, we used long-read sequencing (LRS) technology and RNA-seq analysis to investigate the diversity and complexity of the polyploid transcriptome and differentially expressed transcripts along four successive fruit developmental stages of cultivated strawberry. We obtained a reference transcriptome with 119,897 unique full-length isoforms, including 2017 new isoforms and 2510 long noncoding RNAs. Based on the genome of the plausible progenitor ( Fragaria vesca ), 20,229 alternative splicing (AS) events were identified. Using this transcriptome, we found 17,485 differentially expressed transcripts during strawberry fruit development, including 527 transcription factors (TFs) belonging to 41 families. The expression profiles of all members of the auxin, ABA pathway, and anthocyanin biosynthesis gene families were also examined, and many of them were highly expressed at the ripe fruit stage, strongly indicating that the role of those genes is in the regulation of fruit ripening. We produce a high-quality reference transcriptome for octoploid strawberry, including much of the full-length transcript diversity, to help understand the regulatory mechanisms of fruit development and maturation of polyploid species, particularly via elucidation of the biochemical pathways involved in auxin, ABA, and anthocyanin biosynthesis.

Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress

“…Here, we characterized AS in autotetraploid Italian ryegrass using PacBio ISO-seq. In common with results with respect to cotton [24], rice [26], strawberry [29], and switchgrass [55], the retained intron events contributed the most AS events. In addition, the percentage of unique isoforms is greater than those of other species; it appeared that polyploidy also played an important role in increasing the transcript diversity of Italian ryegrass [56].…”

“…In the past decade, next-generation sequencing (NGS) technology has been widely used for genetic discovery and research [29], and the well-known short-read RNA-seq has become an integral part in evaluating whole RNA expression patterns [30]. However, the sequenced fragments of NGS are usually between 50 and 300 bp, and this was insufficient in the accurate reconstruction and reliable expression estimation of transcript variants, especially for species with low-quality genomes or even without reference genomes [31].…”

Genomic structure and transcript analysis of the Rapid Alkalinization Factor (RALF) gene family during host-pathogen crosstalk in Fragaria vesca and Fragaria x ananassa strawberry

“…Nucleotide sequences of the 15 F. vesca RALF members (both previous and new found ones), were used as query for BLASTx on the F. × ananassa cv. Camarosa Genome v1.0.a1 proteome [37] to find octoploid RALF orthologs. Sequences of F. × ananassa RALF peptides were aligned with MUSCLE [38] and the phylogeny was inferred using the Maximum Likelihood method and JTT matrix-based model [39].…”

The transcriptional landscape of cultivated strawberry (Fragraia×ananassa) and its diploid ancestor (Fragraia×vesca) during fruit development

“…The AS could create new isoforms and hence change the proteins, and also could regulate transcripts expression level through triggering nonsense-mediated decay (NMD) pathway degradation 8 . The AS events of diploid and octoploid strawberry have been identified 9,10 , but we do not know the difference between them, especially in the process of fruit development.…”