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

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

Ya-Hui Wang #  1   2 , Xiao-Hong Liu #  1 , Rong-Rong Zhang  2 , Zhi-Ming Yan  3 , Ai-Sheng Xiong  2 , Xiao-Jun Su  1
Affiliations

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

Ya-Hui Wang et al. PeerJ. .

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.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Sequence length distribution of the Luffa unigene library.
Figure 2
Figure 2. Species distribution of the Luffa unigene library against the NR database.
Figure 3
Figure 3. COG function classification of the Luffa unigene library.
Figure 4
Figure 4. GO enrichment analysis of the DEGs identified in the unigene libraries between two Luffa cultivars.
Figure 5
Figure 5. Statistics of KEGG enrichment of the DEGs identified in the unigene libraries between two Luffa cultivars.
Figure 6
Figure 6. Heatmap of the expression levels of browning-related genes identified in the DEGs.
(A) Polyphenol oxidase, (B) peroxidase, (C) ascorbate peroxidase. Heat maps were created by the log2 relative abundance of the DEGs. Blue and orange represent low and high expression, respectively. Black represents no expression detected.
Figure 7
Figure 7. Expression levels of browning-related genes.
The unigene ‘Cluster-21832.13892’ (A) was identified as LcPPO encoding polyphenol oxidase. The unigenes ‘Cluster-21832.19847’, ‘Cluster-21832.30619’, ‘Cluster-2183.38395’, ‘Cluster-23349.0’, ‘Cluster-2660.0’, ‘Cluster-48491.2’ and ‘Cluster-5215.0’ (B-H) were identified as LcPODs encoding peroxidase. The unigenes ‘Cluster-19973.6’, ‘Cluster-21832.12599’, ‘Cluster-21832.17816’ and ‘Cluster-21832.12605’ (I-L) were identified as LcAPXs encoding ascorbate peroxidase.
Figure 8
Figure 8. Simplified diagram of differences between browning resistant and browning prone Luffa cultivars.
See this image and copyright information in PMC

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