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

文献类型： 外文期刊

作者： Yuan, Huazhao 1 ; Yu, Hongmei 1 ; Huang, Tao 2 ; Shen, Xinjie 3 ; Xia, Jin 1 ; Pang, Fuhua 1 ; Wang, Jing 1 ; Zhao, Mizhe 1 ;

作者机构： 1.Jiangsu Acad Agr Sci, Inst Pomol, Jiangsu Key Lab Hort Crop Genet Improvement, Nanjing 210014, Jiangsu, Peoples R China

2.Biomarker Technol Corp, Beijing 101300, Peoples R China

3.Chinese Acad Agr Sci, Oil Crops Res Inst, Minist Agr Peoples Republ China, Key Lab Biol & Genet Improvement Oil Crops, Wuhan 430062, Hubei, Peoples R China

期刊名称：HORTICULTURE RESEARCH （ 影响因子：6.793； 五年影响因子：6.589 ）

ISSN： 2052-7276

年卷期： 2019 年 6 卷

页码：

收录情况： SCI

摘要： 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.

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