Sequencing, assembly, annotation, and gene expression: novel insights into browning-resistant Luffa cylindrica

Ya-Hui Wang; Xiao-Hong Liu; Rong-Rong Zhang; Zhi-Ming Yan; Ai-Sheng Xiong; Xiao-Jun Su

doi:10.7717/peerj.9661

Sequencing, assembly, annotation, and gene expression: novel insights into browning-resistant Luffa cylindrica

PeerJ. 2020 Aug 10:8:e9661. doi: 10.7717/peerj.9661. eCollection 2020.

Authors

Ya-Hui Wang^#^{1

2}, Xiao-Hong Liu^#¹, Rong-Rong Zhang², Zhi-Ming Yan³, Ai-Sheng Xiong², Xiao-Jun Su¹

Affiliations

¹ Institute of Vegetable Crops, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
² State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
³ Jiangsu Vocational College of Agriculture and Forestry, Jurong, China.

^# Contributed equally.

Abstract

Luffa is a kind of melon crop widely cultivated in temperate regions worldwide. Browning is one of the serious factors affecting the quality of Luffa. Therefore, the molecular mechanism of Luffa browning is of great significance to study. However, the molecular diversity of Luffa cultivars with different browning-resistant abilities has not been well elucidated. In our study, we used high-throughput sequencing to determine the transcriptome of two Luffa cylindrica cultivars '2D-2' and '35D-7'. A total of 115,099 unigenes were clustered, of which 22,607 were differentially expression genes (DEGs). Of these DEGs, 65 encoding polyphenol oxidase, peroxidase, or ascorbate peroxidase were further analyzed. The quantitative real-time PCR (RT-qPCR) data indicated that the expression levels of the LcPPO gene (Accession No.: Cluster-21832.13892) was significantly higher in '35D-7' compared with that in '2D-2'. Several POD genes (Accession No.: Cluster-21832.19847, Cluster-21832.30619 and Cluster-48491.2) were also upregulated. Analysis of the plantTFDB database indicated that some transcription factors such as WRKY gene family may also participate in the regulation of Luffa browning. The results indicated that the divergence of genes expression related to enzymatic reaction may lead to the different browning resistances of Luffa. Our study will provide a theoretical basis for breeding of browning-resistant Luffa.

Keywords: Browning; Expression; Luffa; Polyphenol oxidase; Transcriptome.

Grants and funding

The research was supported by the grants from the Suzhou Agricultural Science and Technology Innovation Project (Research on the application of key agricultural technologies) (SNG2018061). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.