Transcriptome analysis in the beet webworm, Spoladea recurvalis (Lepidoptera: Crambidae)

Abstract

The beet webworm, Spoladea recurvalis Fabricius, is a destructive pest on vegetable crops in tropics and subtropics; its main host plant is amaranth. It has become imperative to develop non-chemical methods to control S. recurvalis on amaranth. However, the lack of molecular information about this species has hindered the development of novel pest management strategies. In this study, high-throughput RNA sequencing covering de novo sequence assemblies, functional annotation of transcripts, gene function classification and enrichment was performed on S. recurvalis. Illumina sequencing generated a total of 120 435 transcript contigs ranging from 201 to 22 729 bases with a mean length of 688 bases. The assembled transcripts were subjected to Basic Local Alignment Search Tool-X (BLASTX) to obtain the annotations against non-redundant, Swiss-Prot, Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases. A subset of 58 225 transcript sequences returned hits from known proteins in the National Center for Biotechnology Information database, and the majority of the transcript sequences had the highest number of hits for Danaus plexippus (50.43%). A total of 1217 Gene Ontology-level 3 annotations were assigned to 51 805 transcripts, while 39 650 transcripts were predicted as functional protein-coding genes in the COG database and 20 037 transcripts were enriched to KEGG pathways. We identified 40 putative genes related to pheromone production and reception in S. recurvalis, with the expression of one gene between 0.29 and 1141.79 fragments per kilo base per million (FPKM) reads. The transcriptome sequence of S. recurvalis is a first step toward offering a comprehensive genomic resource which would enable better understanding of molecular mechanisms to enable development of effective pest management practices for this species.

Gut Microbial Dysbiosis Is Associated With Profibrotic Factors in Liver Fibrosis Mice

“…We used PICRUSt software for analysis. The COG database mainly contains information about bacteria and archaea genomes (Chang and Ramasamy, 2018). In CCl 4 -induced liver fibrosis mice, the enriched COG terms are as follows: "Secondary metabolites biosynthesis, transport and catabolism, " "Cytoskeleton, " and "Intracellular trafficking, secretion, and vesicular transport."…”

Transcriptome and gene expression analysis of three developmental stages of the coffee berry borer, Hypothenemus hampei

“…The availability of sequence databases is very useful for a better understanding of host-pathogen interactions 19 , feeding mechanisms 20 , development 21 , and defense pathways in phytophagous insects 22 . Additionally, a significant number of studies using transcriptomic-based approaches have focused on identifying genes involved in developmental processes, with expression profiles among different life stages reported in several insect species 21,23,24 . Recent studies have reported such gene expression analyses across different developmental stages in lepidopteran pests of global economic relevance 24–26 .…”

“…Additionally, a significant number of studies using transcriptomic-based approaches have focused on identifying genes involved in developmental processes, with expression profiles among different life stages reported in several insect species 21,23,24 . Recent studies have reported such gene expression analyses across different developmental stages in lepidopteran pests of global economic relevance 24–26 . Similarly, a number of such studies have been performed on coleopteran pests 21,27,28 .…”

Bacterial community mapping of the intestinal tract in acute pancreatitis rats based on 16S rDNA gene sequence analysis

“…The COG database consists of proteins from complete genomes of bacteria, archaea and eukaryotes, and each categorized COG term represents an ancient conserved domain. 30 As shown in Fig. 8A, the results proved that COG terms of differential ora in small intestine (p < 0.05) were mainly contained "[F] Nucleotide transport and metabolism", "[G] Carbohydrate transport and metabolism" and "[J] Translation, ribosomal structure and biogenesis".…”