Dataset Information

Comparative Transcriptome Analysis of Henosepilachna vigintioctomaculata Reveals Critical Pathways during Development.

ABSTRACT: Henosepilachna vigintioctomaculata is distributed in several Asian countries. The larvae and adults often cause substantial economic losses to Solanaceae crops such as potato, tomato, eggplant, and Chinese boxthorn. Even though a chromosome-level genome has been documented, the expression profiles of genes involved in development are not determined. In this study, we constructed embryonic, larval, pupal, and adult transcriptomes, generated a comprehensive RNA-sequencing dataset including ~52 Gb of clean data, and identified 602,773,686 cleaned reads and 33,269 unigenes. A total of 18,192 unigenes were successfully annotated against NCBI nonredundant protein sequences, Swissprot, Eukaryotic Orthologous Groups, Gene Ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. There were 3580, 2040, 5160, 2496, 3008, and 3895 differentially expressed genes (DEGs) between adult/egg, egg/larval, larval/pupal, adult/pupal, egg/pupal, and adult/larval samples, respectively. GO and KEGG analyses of the DEGs highlighted several critical pathways associated with specific developing stages. This is the first comprehensive transcriptomic dataset encompassing all developmental stages in H. vigintioctomaculata. Our data may facilitate the exploitation of gene targets for pest control and can serve as a valuable gene resource for future molecular investigations.

SUBMITTER: Zhang YX

PROVIDER: S-EPMC11276636 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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Comparative Transcriptome Analysis of <i>Henosepilachna vigintioctomaculata</i> Reveals Critical Pathways during Development.

Zhang Yu-Xing YX Wu Yi-Kuan YK Liu Hai-Hui HH Li Wen-Ze WZ Jin Lin L Li Guo-Qing GQ

International journal of molecular sciences 20240709 14

<i>Henosepilachna vigintioctomaculata</i> is distributed in several Asian countries. The larvae and adults often cause substantial economic losses to Solanaceae crops such as potato, tomato, eggplant, and Chinese boxthorn. Even though a chromosome-level genome has been documented, the expression profiles of genes involved in development are not determined. In this study, we constructed embryonic, larval, pupal, and adult transcriptomes, generated a comprehensive RNA-sequencing dataset including ...[more]

PMID: 39062748

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Project description:Soybean is one of the important economic crops, which supplies a great deal of vegetable oil and proteins for human. The content of nutrients in different soybean seeds is different, which is related to the expression of multiple genes, but the mechanisms are complicated and still largely uncertain. In this study, to reveal the possible causes of the nutrients difference in soybeans A7 (containing low oil and high protein) and A35 (containing high oil and low protein), RNA-seq technology was performed to compare and identify the potential differential expressed genes (DEGs) at different seed developmental stages. The results showed that DEGs mainly presented at the early stages of seeds development and more DEGs were up-regulated at the early stage than the late stages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs have diverged in A7 and A35. In A7, the DEGs were mainly involved in cell cycle and stresses, while in A35 were the fatty acids and sugar metabolism. Specifically, when the DEGs contributing to oil and protein metabolic pathways were analyzed, the differences between A7 and A35 mainly presented in fatty acids metabolism and seeds storage proteins (SSPs) synthesis. Furthermore, the enzymes, fatty acid dehydrogenase 2, 3-ketoacyl-CoA synthase and 9S-lipoxygenase, in the synthesis and elongation pathways of fatty acids, were revealed probably to be involved in the oil content difference between A7 and A35, the SSPs content might be due to the transcription factors: Leafy Cotyledon 2 and Abscisic acid-intensitive 3, while the sugar transporter, SWEET10a, might contribute to both oil and protein content differences. Finally, six DEGs were selected to analyze their expression using qRT-PCR, and the results were consistent with the RNA-seq results. Generally, the study provided a comprehensive and dynamic expression trends for the seed development processes, and uncovered the potential DEGs for the differences of oil in A7 and A35.

Dataset Information

Comparative Transcriptome Analysis of Henosepilachna vigintioctomaculata Reveals Critical Pathways during Development.

Publications

Comparative Transcriptome Analysis of <i>Henosepilachna vigintioctomaculata</i> Reveals Critical Pathways during Development.

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