SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

Hongjun Yang; Danping Xu; Zhihang Zhuo; Jiameng Hu; Baoqian Lu

doi:10.7717/peerj.9133

SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

PeerJ. 2020 May 21:8:e9133. doi: 10.7717/peerj.9133. eCollection 2020.

Authors

Hongjun Yang¹, Danping Xu², Zhihang Zhuo^{1

3}, Jiameng Hu¹, Baoqian Lu⁴

Affiliations

¹ Key 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, China.
² Sichuan Provincial Key Laboratory of Agricultural Products Processing and Preservative, College of Food Science, Sichuan Agricultural University, Yaan, Sichuan, China.
³ Key Laboratory of Integrated Pest Management on Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
⁴ Key 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, China.

Abstract

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.

Keywords: Different developmental stage; Full-length transcriptome; Illumina RNA-seq; PacBio Iso-Seq; Rhynchophorus ferrugineus.

Grants and funding

This work was supported by the Hainan Natural Science Foundation Project (NO. 319QN163), The Fund Project of Key Laboratory of Integrated Pest Management on Crops in South China, Ministry of Agriculture, P. R. China (NO. SCIPM2018-04) and the Research Initiation Project of Hainan University (NO. KYQD[ZR]1823). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.