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Wang Q, Zhang J, Liu C, Ru C, Qian Q, Yang M, Yan S, Liu W, Wang G. Identification of antennal alternative splicing by combining genome and full-length transcriptome analysis in Bactrocera dorsalis. Front Physiol 2024; 15:1384426. [PMID: 38952867 PMCID: PMC11215311 DOI: 10.3389/fphys.2024.1384426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/29/2024] [Indexed: 07/03/2024] Open
Abstract
Alternative splicing is an essential post-transcriptional regulatory mechanism that diversifies gene function by generating multiple protein isoforms from a single gene and act as a crucial role in insect environmental adaptation. Olfaction, a key sense for insect adaptation, relies heavily on the antennae, which are the primary olfactory organs expressing most of the olfactory genes. Despite the extensive annotation of olfactory genes within insect antennal tissues facilitated by high-throughput sequencing technology advancements, systematic analyses of alternative splicing are still relatively less. In this study, we focused on the oriental fruit fly (Bactrocera dorsalis), a significant pest of fruit crops. We performed a detailed analysis of alternative splicing in its antennae by utilizing the full-length transcriptome of its antennal tissue and the insect's genome. The results revealed 8600 non-redundant full-length transcripts identified in the oriental fruit fly antennal full-length transcriptome, spanning 4,145 gene loci. Over 40% of these loci exhibited multiple isoforms. Among these, 161 genes showed sex-biased isoform switching, involving seven different types of alternative splicing. Notably, events involving alternative transcription start sites (ATSS) and alternative transcription termination sites (ATTS) were the most common. Of all the genes undergoing ATSS and ATTS alternative splicing between male and female, 32 genes were alternatively spliced in protein coding regions, potentially affecting protein function. These genes were categorized based on the length of the sex-biased isoforms, with the highest difference in isoform fraction (dIF) associated with the ATSS type, including genes such as BdorABCA13, BdorCAT2, and BdorTSN3. Additionally, transcription factor binding sites for doublesex were identified upstream of both BdorABCA13 and BdorCAT2. Besides being expressed in the antennal tissues, BdorABCA13 and BdorCAT2 are also expressed in the mouthparts, legs, and genitalia of both female and male adults, suggesting their functional diversity. This study reveals alternative splicing events in the antennae of Bactrophora dorsalis from two aspects: odorant receptor genes and other types of genes expressed in the antennae. This study not only provides a research foundation for understanding the regulation of gene function by alternative splicing in the oriental fruit fly but also offers new insights for utilizing olfaction-based behavioral manipulation techniques to manage this pest.
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Affiliation(s)
- Qi Wang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Jie Zhang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Chenhao Liu
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Chuanjian Ru
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Qian Qian
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Minghuan Yang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Shanchun Yan
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Wei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guirong Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Li W, Wang X, Jiang P, Yang M, Li Z, Huang C, He Y. A full-length transcriptome and gene expression analysis of three detoxification gene families in a predatory stink bug, Picromerus lewisi. Front Physiol 2022; 13:1016582. [PMID: 36299261 PMCID: PMC9589283 DOI: 10.3389/fphys.2022.1016582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/16/2022] [Indexed: 12/02/2022] Open
Abstract
The predatory stink bug P. Lewisi shows potential for Integrated Pest Management programs for controlling Lepidoptera pest insects in crops and forests. The importance of this insect for biological control has stimulated several studies into its biology and ecology. However, P. lewisi has little genetic information available. In the present study, PacBio single-molecule real-time (SMRT) sequencing and Illumina RNA-seq sequencing technologies were used to reveal the full-length transcriptome profiling and tissue-specific expression patterns of P. lewisi. A total of 12,997 high-quality transcripts with an average length of 2,292 bp were obtained from different stages of P. lewisi using SMRT sequencing. Among these, 12,101 were successfully annotated in seven public databases. A total of 67 genes of cytochrome P450 monooxygenases, 43 carboxylesterase genes, and 18 glutathione S-transferase genes were identified, most of which were obtained with full-length ORFs. Then, tissue-specific expression patterns of 5th instar nymphs were analyzed using Illumina sequencing. Several candidate genes related to detoxification of insecticides and other xenobiotics as well as the degradation of odors, were identified in the guts and antennae of P. lewisi. The current study offered in-depth knowledge to understand the biology and ecology of this beneficial predator and related species.
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Affiliation(s)
- Wenhong Li
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xinyi Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Po Jiang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mingwei Yang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhimo Li
- Guizhou Provincial Tobacco Company, Zunyi Branch, Zunyi, China
| | - Chunyang Huang
- Guizhou Provincial Tobacco Company, Zunyi Branch, Zunyi, China
- *Correspondence: Chunyang Huang, ; Yueping He,
| | - Yueping He
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Chunyang Huang, ; Yueping He,
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Tan SY, Hong F, Ye C, Wang JJ, Wei D. Functional characterization of four Hsp70 genes involved in high-temperature tolerance in Aphis aurantii (Hemiptera: Aphididae). Int J Biol Macromol 2022; 202:141-149. [PMID: 35038465 DOI: 10.1016/j.ijbiomac.2022.01.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 01/04/2023]
Abstract
The tea aphid, Aphis aurantii (Boyer de Fonscolombe), is a serious pest that can infest many economically important plants. Tea aphids damage plants by directly sucking phloem sap, transmitting viruses, and secreting honeydew to cause sooty mold. At present, tea aphids has become one of the most important pests in tropical and subtropical tea plants. The heat shock protein 70 (Hsp70) is a key protein involved in heat stress tolerance. In this study, we cloned four Hsp70 genes that are highly expressed in tea aphids after heat shock. Bioinformatic analysis of the deduced amino acid sequences showed that these four AaHsp70s had a close genetic relationship to Hsp70 in Hemiptera insects and shared a conserved ATPase domain. After incubation at low (14 °C) or high (36 °C) temperature, the expression of four AaHsp70s was significantly up-regulated compared to the control (25 °C); however, the up-regulation of the AaHsp70s in the low-temperature treatment was far less than that of the high-temperature treatment. The ATPase activity of the four purified recombinant AaHsp70 proteins after high-temperature treatment was significantly increased compared to the control. In addition, these proteins effectively improved the heat tolerance of Escherichia coli in vivo. Our data indicate that AaHsp701, AaHsp702, AaHsp703, AaHsp704 play important roles in response to the high-temperature tolerance in tea aphids.
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Affiliation(s)
- Shan-Yuan Tan
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China; International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Feng Hong
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang 464000, China
| | - Chao Ye
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China; International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jin-Jun Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China; International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Dong Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China; International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
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Cai Z, Xie Z, Huang L, Wang Z, Pan M, Yu X, Xu S, Luo J. Full-length transcriptome analysis of Adiantum flabellulatum gametophyte. PeerJ 2022; 10:e13079. [PMID: 35287343 PMCID: PMC8917799 DOI: 10.7717/peerj.13079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
Ferns are important components of plant communities on earth, but their genomes are generally very large, with many redundant genes, making whole genome sequencing of ferns prohibitively expensive and time-consuming. This means there is a significant lack of fern reference genomes, making molecular biology research difficult. The gametophytes of ferns can survive independently, are responsible for sexual reproduction and the feeding of young sporophytes, and play an important role in the alternation of generations. For this study, we selected Adiantum flabellulatum as it has both ornamental and medicinal value and is also an indicator plant of acidic soil. The full-length transcriptome sequencing of its gametophytes was carried out using PacBio three-generation sequencing technology. A total of 354,228 transcripts were obtained, and 231,705 coding sequences (CDSs) were predicted, including 5,749 transcription factors (TFs), 2,214 transcription regulators (TRs) and 4,950 protein kinases (PKs). The transcripts annotated by non-redundant protein sequence database (NR), Kyoto encyclopedia of genes and genomes (KEGG), eukaryotic ortholog groups (KOG), Swissprot, protein family (Pfma), nucleotide sequence database (NT) and gene ontology (GO) were 251,501, 197,474, 193,630, 194,639, 195,956, 113,069 and 197,883, respectively. In addition, 138,995 simple sequence repeats (SSRs) and 111,793 long non-coding RNAs (lncRNAs) were obtained. We selected nine chlorophyll synthase genes for qRT-PCR, and the results showed that the full-length transcript sequences and the annotation information were reliable. This study can provide a reference gene set for subsequent gene expression quantification.
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Affiliation(s)
- Zeping Cai
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Zhenyu Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Luyao Huang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Zixuan Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Min Pan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Xudong Yu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Shitao Xu
- College of Horticulture, Hainan University, Haikou, Hainan, China
| | - Jiajia Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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Cheng H, Bowler C, Xing X, Bulone V, Shao Z, Duan D. Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes. Mar Drugs 2021; 19:392. [PMID: 34356817 PMCID: PMC8307304 DOI: 10.3390/md19070392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022] Open
Abstract
β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.
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Affiliation(s)
- Haomiao Cheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France;
| | - Xiaohui Xing
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691 Stockholm, Sweden; (X.X.); (V.B.)
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
- Adelaide Glycomics, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691 Stockholm, Sweden; (X.X.); (V.B.)
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
- Adelaide Glycomics, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
| | - Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co., Ltd., Qingdao 266400, China
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Zhou Y, Yang P, Xie S, Shi M, Huang J, Wang Z, Chen X. Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae). Genes (Basel) 2021; 12:genes12060896. [PMID: 34200644 PMCID: PMC8228208 DOI: 10.3390/genes12060896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
The endoparasitic wasp Cotesia vestalis is an important biological agent for controlling the population of Plutella xylostella, a major pest of cruciferous crops worldwide. Though the genome of C. vestalis has recently been reported, molecular mechanisms associated with sexual development have not been comprehensively studied. Here, we combined PacBio Iso-Seq and Illumina RNA-Seq to perform genome-wide profiling of pharate adult and adult development of male and female C. vestalis. Taking advantage of Iso-Seq full-length reads, we identified 14,466 novel transcripts as well as 8770 lncRNAs, with many lncRNAs showing a sex- and stage-specific expression pattern. The differentially expressed gene (DEG) analyses showed 2125 stage-specific and 326 sex-specific expressed genes. We also found that 4819 genes showed 11,856 alternative splicing events through combining the Iso-Seq and RNA-Seq data. The results of comparative analyses showed that most genes were alternatively spliced across developmental stages, and alternative splicing (AS) events were more prevalent in females than in males. Furthermore, we identified six sex-determining genes in this parasitic wasp and verified their sex-specific alternative splicing profiles. Specifically, the characterization of feminizer and doublesex splicing between male and female implies a conserved regulation mechanism of sexual development in parasitic wasps.
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Affiliation(s)
- Yuenan Zhou
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Pei Yang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Shuang Xie
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Min Shi
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Jianhua Huang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Zhizhi Wang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Correspondence: (Z.W.); (X.C.)
| | - Xuexin Chen
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou 310058, China
- Correspondence: (Z.W.); (X.C.)
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