Comparative full-length transcriptome analysis by Oxford Nanopore Technologies reveals genes involved in anthocyanin accumulation in storage roots of sweet potatoes (Ipomoea batatas L.)

Jun Xiong; Xiuhua Tang; Minzheng Wei; Wenjin Yu

doi:10.7717/peerj.13688

Comparative full-length transcriptome analysis by Oxford Nanopore Technologies reveals genes involved in anthocyanin accumulation in storage roots of sweet potatoes (Ipomoea batatas L.)

PeerJ. 2022 Jul 12:10:e13688. doi: 10.7717/peerj.13688. eCollection 2022.

Authors

Jun Xiong^{1

2}, Xiuhua Tang², Minzheng Wei², Wenjin Yu¹

Affiliations

¹ Agricultural College, Guangxi University, Nanning, China.
² Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.

Abstract

Background: Storage roots of sweet potatoes (Ipomoea batatas L.) with different colors vary in anthocyanin content, indicating different economically agronomic trait. As the newest DNA/RNA sequencing technology, Oxford Nanopore Technologies (ONT) have been applied in rapid transcriptome sequencing for investigation of genes related to nutrient metabolism. At present, few reports concern full-length transcriptome analysis based on ONT for study on the molecular mechanism of anthocyanin accumulation leading to color change of tuberous roots of sweet potato cultivars.

Results: The storage roots of purple-fleshed sweet potato (PFSP) and white-fleshed sweet potato (WFSP) at different developmental stages were subjected to anthocyanin content comparison by UV-visible spectroscopy as well as transcriptome analysis at ONT MinION platform. UV-visible spectrophotometric measurements demonstrated the anthocyanin content of PFSP was much higher than that of WFSP. ONT RNA-Seq results showed each sample generated average 2.75 GB clean data with Full-Length Percentage (FL%) over 70% and the length of N50 ranged from 1,192 to 1,395 bp, indicating reliable data for transcriptome analysis. Subsequent analysis illustrated intron retention was the most prominent splicing event present in the resulting transcripts. As compared PFSP with WFSP at the relative developmental stages with the highest (PH vs. WH) and the lowest (PL vs. WL) anthocyanin content, 282 and 216 genes were up-regulated and two and 11 genes were down-regulated respectively. The differential expression genes involved in flavonoid biosynthesis pathway include CCoAOMT, PpLDOX, DFR, Cytochrome P450, CHI, and CHS. The genes encoding oxygenase superfamily were significantly up-regulated when compared PFSP with WFSP at the relative developmental stages.

Conclusions: Comparative full-length transcriptome analysis based on ONT serves as an effective approach to detect the differences in anthocyanin accumulation in the storage roots of different sweet potato cultivars at transcript level, with noting that some key genes can now be closely related to flavonoids biosynthesis. This study helps to improve understanding of molecular mechanism for anthocyanin accumulation in sweet potatoes and also provides a theoretical basis for high-quality sweet potato breeding.

Keywords: Anthocyanin; Full-length transcriptome; Oxford Nanopore Technologies; Storage roots; Sweet potato.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anthocyanins / genetics
Gene Expression Profiling
Ipomoea batatas* / genetics
Nanopores*
Plant Breeding
Solanum tuberosum* / genetics
Technology
Transcriptome / genetics

Substances

Anthocyanins

Grants and funding

This research was funded by the Fundamental Research Fund of Guangxi Academy of Agriculture Sciences (2021YT060) and the Guangxi Key Research and Development Plan Project (GuiKe AB16380085; GuiKe AB18221101). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.