Transcriptome and gene expression analysis ofRhynchophorus ferrugineus(Coleoptera: Curculionidae) during developmental stages

Abstract

Background Red palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control. Methods In this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest. Results Sequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus.

Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest

“…In 2020, two additional transcriptomic studies were conducted with the aim of identifying RPW genes [ 64 , 65 ]. Both studies used the same PacBio long-read isoform sequencing (iso-seq) and Illumina RNA-seq data to generate a full-length transcriptome assembly of the RPW.…”

“…When mapping Illumina reads to the assembled transcripts, approximately 87%, 89%, 88%, and 88% of the short reads were mapped for male adults, female adults, pupae, and larvae, respectively. Expression analysis found that about 13.45% (8583) of genes are differentially expressed and engaged in metabolic pathways, organ tissue formation, and material transportation in peroxisomes [ 65 ]. Approximately 86% of the identified transcripts could be annotated using several public databases [ 64 ]; in addition, a total of 9618 long noncoding RNAs, 2084 transcription factors, and 2184 alternative splicing events were identified [ 64 ].…”

Transcriptome Analysis and Weighted Gene Co-expression Network Reveal Multitarget-Directed Antibacterial Mechanisms of Benzyl Isothiocyanate against Staphylococcus aureus

“…Genes with a similar color have similar expression patterns, which are often functionally correlated. Meanwhile, differential genes were clustered by relative expression level log 2 (ratios) by H-cluster, k -means, and SOM methods . The results showed that the gene expression patterns at different time points of 0.5 and 2 h were similar, but both of them much differed from the control (Figure C).…”

Alterations of the Gut Microbiota and Metabolomics Associated with the Different Growth Performances of Macrobrachium rosenbergii Families

“…Adenosine modulated a wide range of processes in many gastrointestinal cells [59], and was essential for ATP biosynthesis and CoA biosynthesis required for fatty acid metabolism [60]. Meanwhile, we found that 8(s)-hydroxy-(5z,9e,11z,14z)-eicosatetraenoic acid and 13(s)hotre, which participated in the "arachidonic acid metabolism" and "alpha-linolenic acid metabolism", were upregulated in Group H. "Arachidonic acid metabolism" and "alphalinolenic acid metabolism" are related to fatty acid metabolism [61]. Furthermore, Uengwetwanit et al [23] reported that shrimp growth and development were largely dependent on lipid metabolism.…”