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DOI: https://doi.org/10.1016/j.jgeb.2024.100393
English
eng
Prajapati, Malyaj R.
Contributor
<div id="as005" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="st010" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Background</h3><div class="u-margin-s-bottom" id="sp0005" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;"><span style="margin: 0px; padding: 0px;">The cabbage <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/webworm" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">webworm</a>, </span><em style="margin: 0px; padding: 0px;">Hellula undalis</em><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"> (Fabricius) (Lepidoptera: Pyralidae), is a significant pest of <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/brassica" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">brassicas</a> and other cruciferous plants in warm regions worldwide. </span><a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/transcriptome" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Transcriptome</a> analysis is valuable for investigation of molecular mechanisms underlying the insect development and reproduction. </span><em style="margin: 0px; padding: 0px;">De novo</em><span style="margin: 0px; padding: 0px;"> assembly is particularly useful for acquiring complete <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/transcriptome" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">transcriptome</a> information of insect species when there is no reference genome available. In case of </span><em style="margin: 0px; padding: 0px;">Hellula undalis</em><span style="margin: 0px; padding: 0px;">, only 17 nucleotide records are currently available throughout NCBI nucleotide database. Genes associated with metabolic processes, general development, reproduction, defense and <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/functional-genomics" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">functional genomics</a> were not previously predicted in the </span><em style="margin: 0px; padding: 0px;">Hellula undalis</em> at the genomic level.</div></div><div id="as010" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="st015" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Methods & Results</h3><div class="u-margin-s-bottom" id="sp0010" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;">To address this issue, we constructed <em style="margin: 0px; padding: 0px;">Hellula undalis</em><span style="margin: 0px; padding: 0px;"> transcriptome using Illumina NovaSeq6000 technology. Approximately 48 million 150 bp paired-end reads were obtained from sequencing. A total of 30,451 <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/contig" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">contigs</a> were generated by </span><em style="margin: 0px; padding: 0px;">de novo</em><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"> assembly of sample and were compared with the sequences in the NCBI non-redundant <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/protein-database" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">protein database</a> (Nr). In total, 71 % of contigs were matched to known proteins in public databases including Nr, </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gene-ontology" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Gene Ontology</a> (GO), and Cluster Orthologous Gene Database (COG), and then, contigs were mapped to 123 via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we compared the ortholog </span><a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/multigene-family" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">gene family</a> of the </span><em style="margin: 0px; padding: 0px;">Hullula undalis,</em> transcriptome to <span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/spodoptera-frugiperda" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Spodoptera frugiperda</a></span><em style="margin: 0px; padding: 0px;">, spodotera litura</em></span> and <span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/spodoptera-littoralis" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">spodoptera littoralis</a></span></span> and found that 391 orthologous gene families are specific to <em style="margin: 0px; padding: 0px;">Hullula undalis</em>. A total of 1,913 potential SSRs was discovered in <em style="margin: 0px; padding: 0px;">Hullula undalis</em> contigs.</div></div><div id="as015" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="st020" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Conclusions</h3><div class="u-margin-s-bottom" id="sp0015" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;">This study is the first transcriptome data for <em style="margin: 0px; padding: 0px;">Hullula undalis.</em> Additionally, it serves as a valuable resource for identifying target genes and developing effective and environmentally friendly strategies for pest control.</div></div>
Elsevier
December 2024
pdf
Journal of Genetic Engineering and Biotechnology
De novo transcriptome assembly, annotation and SSR mining data of Hellula undalis (Fabr.) (Lepidoptera: Pyralidae), the cabbage webworm
mixed material
Elsevier