SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)
Background Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study,...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2020-05-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/9133.pdf |
| _version_ | 1797425525242724352 |
|---|---|
| author | Hongjun Yang Danping Xu Zhihang Zhuo Jiameng Hu Baoqian Lu |
| author_facet | Hongjun Yang Danping Xu Zhihang Zhuo Jiameng Hu Baoqian Lu |
| author_sort | Hongjun Yang |
| collection | DOAJ |
| description | Background Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus. |
| first_indexed | 2024-03-09T08:17:23Z |
| format | Article |
| id | doaj.art-2266ae5167854be6af452e5b8e8605a0 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:17:23Z |
| publishDate | 2020-05-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-2266ae5167854be6af452e5b8e8605a02023-12-02T22:01:01ZengPeerJ Inc.PeerJ2167-83592020-05-018e913310.7717/peerj.9133SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)Hongjun Yang0Danping Xu1Zhihang Zhuo2Jiameng Hu3Baoqian Lu4Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, ChinaSichuan Provincial Key Laboratory of Agricultural Products Processing and Preservative, College of Food Science, Sichuan Agricultural University, Yaan, Sichuan, ChinaKey Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, ChinaKey Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, ChinaKey Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture China, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, ChinaBackground Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.https://peerj.com/articles/9133.pdfRhynchophorus ferrugineusDifferent developmental stagePacBio Iso-SeqIllumina RNA-seqFull-length transcriptome |
| spellingShingle | Hongjun Yang Danping Xu Zhihang Zhuo Jiameng Hu Baoqian Lu SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) PeerJ Rhynchophorus ferrugineus Different developmental stage PacBio Iso-Seq Illumina RNA-seq Full-length transcriptome |
| title | SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) |
| title_full | SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) |
| title_fullStr | SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) |
| title_full_unstemmed | SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) |
| title_short | SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) |
| title_sort | smrt sequencing of the full length transcriptome of the rhynchophorus ferrugineus coleoptera curculionidae |
| topic | Rhynchophorus ferrugineus Different developmental stage PacBio Iso-Seq Illumina RNA-seq Full-length transcriptome |
| url | https://peerj.com/articles/9133.pdf |
| work_keys_str_mv | AT hongjunyang smrtsequencingofthefulllengthtranscriptomeoftherhynchophorusferrugineuscoleopteracurculionidae AT danpingxu smrtsequencingofthefulllengthtranscriptomeoftherhynchophorusferrugineuscoleopteracurculionidae AT zhihangzhuo smrtsequencingofthefulllengthtranscriptomeoftherhynchophorusferrugineuscoleopteracurculionidae AT jiamenghu smrtsequencingofthefulllengthtranscriptomeoftherhynchophorusferrugineuscoleopteracurculionidae AT baoqianlu smrtsequencingofthefulllengthtranscriptomeoftherhynchophorusferrugineuscoleopteracurculionidae |