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

Huazhao Yuan,Fuhua Pang,Mizhen Zhao,Jin Xia,Hongmei Yu,Xinjie Shen,Jing Wang,Tao Huang

doi:10.1038/s41438-019-0126-6

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.

Highlights

Cultivated strawberry (Fragaria x ananassa) is an economically important soft fruit species that is grown commercially around the world[1]
To identify key genes involved in strawberry fruit development, we identified 15,514 (12.94% SMLR isoforms) differential expression isoforms in six combinations (GF-WF, GF-TS, GF-red fruit (RF), WF-TS, WF-RF, TS-RF) based on the RNA-seq data (Supplementary Information 3)
Over the past decade, nextgeneration sequencing (NGS) technology has become an integral part of genetic research and discovery

Summary

Introduction

Cultivated strawberry (Fragaria x ananassa) is an economically important soft fruit species that is grown commercially around the world[1]. Strawberry is a typical nonclimacteric fruit, as the respiratory burst and rise in ethylene production are absent during ripening[5]. It is believed that auxin and ABA, rather than ethylene, play essential roles in the regulation of strawberry fruit ripening[6,7,8]. Cultivated strawberry (Fragaria x ananassa) originated in the 1700s from a natural hybridization between two octoploid strawberries, F. virginiana and F. chiloensis[9]. There is no high-quality reference genome or annotation for Fragaria x ananassa due to heterozygosity and complexity of the polyploid genome, and only a virtual reference draft genome is available[10]. Polyploidy and alternative splicing can greatly increase transcript diversity in eukaryotes[11]

Methods

Results

Conclusion