Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms <i>(Bombyx mori)</i>
RNA sequencing was used to assemble transcriptome data for Philippine-reared silkworm and compare gene expression profiles of strains reared in high- and low-temperature environments. RNA was isolated from the silk glands of fifth instar larvae and mRNA-enriched libraries were sequenced using Illumi...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-07-01
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| Series: | Insects |
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| Online Access: | https://www.mdpi.com/2075-4450/13/8/669 |
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| author | Pauline Nicole O. de la Peña Adria Gabrielle D. Lao Ma. Anita M. Bautista |
| author_facet | Pauline Nicole O. de la Peña Adria Gabrielle D. Lao Ma. Anita M. Bautista |
| author_sort | Pauline Nicole O. de la Peña |
| collection | DOAJ |
| description | RNA sequencing was used to assemble transcriptome data for Philippine-reared silkworm and compare gene expression profiles of strains reared in high- and low-temperature environments. RNA was isolated from the silk glands of fifth instar larvae and mRNA-enriched libraries were sequenced using Illumina NextSeq 500. Transcriptome reads were assembled using reference-based and de novo assemblers, and assemblies were evaluated using different metrics for transcriptome quality, including the read mapping rate, E90N50, RSEM-eval, and the presence of single-copy orthologs. All transcriptome assemblies were able to reconstruct >40,000 transcripts. Differential expression analysis found 476 differentially expressed genes (DEGs; 222 upregulated, 254 downregulated) in strains reared in different temperatures. Among the top DEGs were myrosinase, heat shock proteins, serine protease inhibitors, dehydrogenases, and regulators of the juvenile hormone. Validation of some of the top DEGs using qPCR supported the findings of the in silico analysis. GO term enrichment analysis reveals an overrepresentation of GO terms related to nucleotide metabolism and biosynthesis, lipid and carbohydrate metabolic processes, regulation of transcription, nucleotide binding, protein binding, metal binding, catalytic activity, oxidoreductase activity, and hydrolase activity. The data provided here will serve as a resource for improving local strains and increasing silk production of Philippine-reared <i>B. mori</i> strains. |
| first_indexed | 2024-03-09T04:17:37Z |
| format | Article |
| id | doaj.art-0de31efa66074663b20ca3e10b5fe97d |
| institution | Directory Open Access Journal |
| issn | 2075-4450 |
| language | English |
| last_indexed | 2024-03-09T04:17:37Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Insects |
| spelling | doaj.art-0de31efa66074663b20ca3e10b5fe97d2023-12-03T13:51:12ZengMDPI AGInsects2075-44502022-07-0113866910.3390/insects13080669Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms <i>(Bombyx mori)</i>Pauline Nicole O. de la Peña0Adria Gabrielle D. Lao1Ma. Anita M. Bautista2National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, PhilippinesNational Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, PhilippinesNational Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, PhilippinesRNA sequencing was used to assemble transcriptome data for Philippine-reared silkworm and compare gene expression profiles of strains reared in high- and low-temperature environments. RNA was isolated from the silk glands of fifth instar larvae and mRNA-enriched libraries were sequenced using Illumina NextSeq 500. Transcriptome reads were assembled using reference-based and de novo assemblers, and assemblies were evaluated using different metrics for transcriptome quality, including the read mapping rate, E90N50, RSEM-eval, and the presence of single-copy orthologs. All transcriptome assemblies were able to reconstruct >40,000 transcripts. Differential expression analysis found 476 differentially expressed genes (DEGs; 222 upregulated, 254 downregulated) in strains reared in different temperatures. Among the top DEGs were myrosinase, heat shock proteins, serine protease inhibitors, dehydrogenases, and regulators of the juvenile hormone. Validation of some of the top DEGs using qPCR supported the findings of the in silico analysis. GO term enrichment analysis reveals an overrepresentation of GO terms related to nucleotide metabolism and biosynthesis, lipid and carbohydrate metabolic processes, regulation of transcription, nucleotide binding, protein binding, metal binding, catalytic activity, oxidoreductase activity, and hydrolase activity. The data provided here will serve as a resource for improving local strains and increasing silk production of Philippine-reared <i>B. mori</i> strains.https://www.mdpi.com/2075-4450/13/8/669silkworm<i>Bombyx mori</i>RNA-seqsilk glandtranscriptome analysis |
| spellingShingle | Pauline Nicole O. de la Peña Adria Gabrielle D. Lao Ma. Anita M. Bautista Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms <i>(Bombyx mori)</i> Insects silkworm <i>Bombyx mori</i> RNA-seq silk gland transcriptome analysis |
| title | Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms <i>(Bombyx mori)</i> |
| title_full | Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms <i>(Bombyx mori)</i> |
| title_fullStr | Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms <i>(Bombyx mori)</i> |
| title_full_unstemmed | Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms <i>(Bombyx mori)</i> |
| title_short | Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms <i>(Bombyx mori)</i> |
| title_sort | global profiling of genes expressed in the silk glands of philippine reared mulberry silkworms i bombyx mori i |
| topic | silkworm <i>Bombyx mori</i> RNA-seq silk gland transcriptome analysis |
| url | https://www.mdpi.com/2075-4450/13/8/669 |
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