Full length sequencing reveals novel transcripts of detoxification genes along with related alternative splicing events and lncRNAs in Phyllotreta striolata

Guang Mao Shen; Shi Yuan Ou; Chu He; Jie Liu; Lin He

doi:10.1371/journal.pone.0248749

Full length sequencing reveals novel transcripts of detoxification genes along with related alternative splicing events and lncRNAs in Phyllotreta striolata

PLoS One. 2021 Mar 24;16(3):e0248749. doi: 10.1371/journal.pone.0248749. eCollection 2021.

Authors

Guang Mao Shen^{1

2

3}, Shi Yuan Ou^{1

2

3}, Chu He¹, Jie Liu^{1

2

3}, Lin He^{1

2

3}

Affiliations

¹ Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.
² Academy of Agricultural Sciences, Southwest University, Chongqing, China.
³ State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China.

Abstract

The striped flea beetle, Phyllotreta striolata (Fabricius), damages crops in the Brassicaceae. The genetic data for this pest are insufficient to reveal its insecticide resistance mechanisms or to develop molecular markers for resistance monitoring. We used PacBio Iso-Seq technology to sequence the full-length transcriptome of P. striolata. After isoform sequence clustering and removal of redundant transcripts, a total of 41,293 transcripts were obtained, and 35,640 of these were annotated in the database of gene products. Structure analysis uncovered 4,307 alternative splicing events, and 3,836 sequences were recognized as lncRNAs. Transcripts with the complete coding region of important detoxification enzymes were further classified. There were 57 transcripts of P450s distributed in CYP2, CYP3, CYP4, and Mito CYP clades, 29 transcripts of ESTs from 4 functional groups, 17 transcripts of GSTs classified into 5 families, 51 transcripts of ABCs distributed in 6 families, and 19 transcripts of UGTs. Twenty-five lncRNAs were predicted to be regulators of these detoxification genes. Full-length transcriptome sequencing is an efficient method for molecular study of P. striolata and it is also useful for gene function analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Coleoptera / genetics*
Gene Expression Profiling / methods
Insecticide Resistance / genetics*
Transcriptome / genetics*

Grants and funding

This study was funded in part by the National Key R&D Program of China (2017YFD0200900) to GM.S., Fundamental Research Funds for the Central Universities (SWU115073) to GM.S., Chongqing Postgraduate Research and Innovation Project (CYS19105) to L.H., and National Student’s Program for Innovation and Entrepreneurship Training Program (X202010635501) to C.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.