Genome-wide gene expression profiling of the melon fly, Zeugodacus cucurbitae, during thirteen life stages

Abstract

The melon fly, Zeugodacus cucurbitae (Coquillett), is an important destructive pest worldwide. Functional studies of the genes associated with development and reproduction during different life stages are limited in Z. cucurbitae. There have yet to be comprehensive transcriptomic resources for genetic and functional genomic studies to identify the molecular mechanisms related to its development and reproduction. In this study, we comprehensively sequenced the transcriptomes of four different developmental stages: egg, larva, pupa, and adults. Using the Illumina RNA-Seq technology, we constructed 52 libraries from 13 stages with four biological replicates in each and generated 435.61 Gb clean reads. We comprehensively characterized the transcriptomes with highcoverage mapping to the reference genome. A total of 13,760 genes were mapped to the reference genome, and another 4481 genes were characterized as new genes. Finally, 14,931 genes (81.85%) were functionally annotated against six annotation databases. This study provides the first comprehensive transcriptome data of all developmental stages of Z. cucurbitae, and will serve as a valuable resource for future genetic and functional studies. These results indicated that sequencing quality was high. Clean reads were separately aligned to the reference genome using HISAT2 33 .Transcriptome quality assessment. The saturation of sequencing was also analyzed using RSeQC 2.3.6 package, and the data showed a high saturation of each sample sequencing (Fig. 3a). Most of the reads were mapped to the coding sequence region (Fig. 3b). The alignment of the superreads to the reference genome resulted in a total of 41,530 transcripts, and 34.03% were longer than 2700 bp, and 75.96% were longer than 900 bp (Fig. 3c). Analyses of the structures of the transcripts suggested that 11,506 transcripts were potential novel transcript isoforms (Fig. 3d), and 22,068 transcripts were completely matched to the exons.

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

“…The lncRNAs in Z. cucurbitae were undocumented, so we identified these lncRNAs and studied their expression in adult tissues by RNA-Seq. Our transcriptome data were of high quality as illustrated by the relatively large Q30 percentages [30]. No "N" base was detected in any of the samples.…”

“…Our transcriptome data were of high quality as illustrated by the relatively large Q30 percentages [ 30 ]. No “N” base was detected in any of the samples.…”

“…Melon flies were collected as pupae from Hainan Academy of Agricultural Sciences (20.01°N; 110.37°E), Haikou, Hainan Province, China, in 2016, and reared in an environmental chamber at 26°C-27°C and 65-75% relative humidity (RH) under a 14:10 h (light: dark) photoperiod in a temperature-controlled insectary [30]. Newly emerged melon fly adults were sexed and reared separately.…”

“…The genome of Z. cucurbitae has been sequenced and released [29], which provides sequence information for gene annotation and functional research. The genome-wide expression of genes during the developmental stages has also been analyzed by RNA-seq [30]. However, there is no information about lncRNAs or functional studies in Z. cucurbitae.…”

Transcriptomic Profiling of Various Developmental Stages of Aphis Aurantii to Provide a Genetic Resource for Gene Expression and SSR Analysis

“…For instance, RNA-Seq was used to elucidate the underlying molecular mechanisms of metamorphic development of Henosepilachna vigintioctopunctata (Zhang et al, 2018 ). Using available insect genomes, comparative transcriptome analysis was conducted to analyze gene expression during all developmental stages of Zeugodacus cucurbitae (Wei et al, 2020 ), Bactrocera dorsalis (Liu et al, 2020 ). In addition, gene expression has been studied by RNA-Seq in multiple tissues to identify tissue-specific genes involved in female fertility in B. dorsalis [e.g., vitellogenin and vitelline membrane protein in female (Wei et al, 2018 , 2019 )].…”