Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction
Abstract Background Dung beetles recycle organic matter through the decomposition of feces and support ecological balance. However, these insects are threatened by the indiscriminate use of agrochemicals and habitat destruction. Copris tripartitus Waterhouse (Coleoptera: Scarabaeidae), a dung beetle...
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09122-w |
| _version_ | 1797865465683378176 |
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| author | Hee Ju Hwang Bharat Bhusan Patnaik Snigdha Baliarsingh Hongray Howrelia Patnaik Min Kyu Sang Jie eun Park Hang Chul Cho Dae Kwon Song Jun Yang Jeong Chan Eui Hong Yong Tae Kim Hyeon Jun Sin Liu Ziwei So Young Park Se Won Kang Heon Cheon Jeong Hong Seog Park Yeon Soo Han Yong Seok Lee |
| author_facet | Hee Ju Hwang Bharat Bhusan Patnaik Snigdha Baliarsingh Hongray Howrelia Patnaik Min Kyu Sang Jie eun Park Hang Chul Cho Dae Kwon Song Jun Yang Jeong Chan Eui Hong Yong Tae Kim Hyeon Jun Sin Liu Ziwei So Young Park Se Won Kang Heon Cheon Jeong Hong Seog Park Yeon Soo Han Yong Seok Lee |
| author_sort | Hee Ju Hwang |
| collection | DOAJ |
| description | Abstract Background Dung beetles recycle organic matter through the decomposition of feces and support ecological balance. However, these insects are threatened by the indiscriminate use of agrochemicals and habitat destruction. Copris tripartitus Waterhouse (Coleoptera: Scarabaeidae), a dung beetle, is listed as a class-II Korean endangered species. Although the genetic diversity of C. tripartitus populations has been investigated through analysis of mitochondrial genes, genomic resources for this species remain limited. In this study, we analyzed the transcriptome of C. tripartitus to elucidate functions related to growth, immunity and reproduction for the purpose of informed conservation planning. Results The transcriptome of C. tripartitus was generated using next-generation Illumina sequencing and assembled de novo using a Trinity-based platform. In total, 98.59% of the raw sequence reads were processed as clean reads. These reads were assembled into 151,177 contigs, 101,352 transcripts, and 25,106 unigenes. A total of 23,450 unigenes (93.40%) were annotated to at least one database. The largest proportion of unigenes (92.76%) were annotated to the locally curated PANM-DB. A maximum of 5,512 unigenes had homologous sequences in Tribolium castaneum. Gene Ontology (GO) analysis revealed a maximum of 5,174 unigenes in the Molecular function category. Further, in Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a total of 462 enzymes were associated with established biological pathways. Based on sequence homology to known proteins in PANM-DB, representative immunity, growth, and reproduction-related genes were screened. Potential immunity-related genes were categorized into pattern recognition receptors (PRRs), the Toll-like receptor signaling pathway, the MyD88- dependent pathway, endogenous ligands, immune effectors, antimicrobial peptides, apoptosis, and adaptation-related transcripts. Among PRRs, we conducted detailed in silico characterization of TLR-2, CTL, and PGRP_SC2-like. Repetitive elements such as long terminal repeats, short interspersed nuclear elements, long interspersed nuclear elements and DNA elements were enriched in the unigene sequences. A total of 1,493 SSRs were identified among all unigenes of C. tripartitus. Conclusions This study provides a comprehensive resource for analysis of the genomic topography of the beetle C. tripartitus. The data presented here clarify the fitness phenotypes of this species in the wild and provide insight to support informed conservation planning. |
| first_indexed | 2024-04-09T23:09:00Z |
| format | Article |
| id | doaj.art-44f04da96f974c9581f98a735ff285b4 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-09T23:09:00Z |
| publishDate | 2023-03-01 |
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| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-44f04da96f974c9581f98a735ff285b42023-03-22T10:30:57ZengBMCBMC Genomics1471-21642023-03-0124112210.1186/s12864-023-09122-wTranscriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproductionHee Ju Hwang0Bharat Bhusan Patnaik1Snigdha Baliarsingh2Hongray Howrelia Patnaik3Min Kyu Sang4Jie eun Park5Hang Chul Cho6Dae Kwon Song7Jun Yang Jeong8Chan Eui Hong9Yong Tae Kim10Hyeon Jun Sin11Liu Ziwei12So Young Park13Se Won Kang14Heon Cheon Jeong15Hong Seog Park16Yeon Soo Han17Yong Seok Lee18Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityPG Department of Biosciences and Biotechnology, Fakir Mohan UniversityKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityResearch Support Center (Core-Facility) for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang UniversityKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityiLAB, INSILICOGEN, INC. #2901~2904, Tower-Dong A, HEUNGDEOK IT VALLEYKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityDepartment of Biology, College of Natural Sciences, Soonchunhyang UniversityDepartment of Biology, College of Natural Sciences, Soonchunhyang UniversityBiodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological ResourcesBiological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB)Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityResearch Institute, GnC BIO Co., LTD.College of Agriculture and Life Science, Chonnam National UniversityKorea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang UniversityAbstract Background Dung beetles recycle organic matter through the decomposition of feces and support ecological balance. However, these insects are threatened by the indiscriminate use of agrochemicals and habitat destruction. Copris tripartitus Waterhouse (Coleoptera: Scarabaeidae), a dung beetle, is listed as a class-II Korean endangered species. Although the genetic diversity of C. tripartitus populations has been investigated through analysis of mitochondrial genes, genomic resources for this species remain limited. In this study, we analyzed the transcriptome of C. tripartitus to elucidate functions related to growth, immunity and reproduction for the purpose of informed conservation planning. Results The transcriptome of C. tripartitus was generated using next-generation Illumina sequencing and assembled de novo using a Trinity-based platform. In total, 98.59% of the raw sequence reads were processed as clean reads. These reads were assembled into 151,177 contigs, 101,352 transcripts, and 25,106 unigenes. A total of 23,450 unigenes (93.40%) were annotated to at least one database. The largest proportion of unigenes (92.76%) were annotated to the locally curated PANM-DB. A maximum of 5,512 unigenes had homologous sequences in Tribolium castaneum. Gene Ontology (GO) analysis revealed a maximum of 5,174 unigenes in the Molecular function category. Further, in Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a total of 462 enzymes were associated with established biological pathways. Based on sequence homology to known proteins in PANM-DB, representative immunity, growth, and reproduction-related genes were screened. Potential immunity-related genes were categorized into pattern recognition receptors (PRRs), the Toll-like receptor signaling pathway, the MyD88- dependent pathway, endogenous ligands, immune effectors, antimicrobial peptides, apoptosis, and adaptation-related transcripts. Among PRRs, we conducted detailed in silico characterization of TLR-2, CTL, and PGRP_SC2-like. Repetitive elements such as long terminal repeats, short interspersed nuclear elements, long interspersed nuclear elements and DNA elements were enriched in the unigene sequences. A total of 1,493 SSRs were identified among all unigenes of C. tripartitus. Conclusions This study provides a comprehensive resource for analysis of the genomic topography of the beetle C. tripartitus. The data presented here clarify the fitness phenotypes of this species in the wild and provide insight to support informed conservation planning.https://doi.org/10.1186/s12864-023-09122-wC. tripartitusTranscriptomeIllumina sequencingImmunity-related genesSimple sequence repeatsInformed conservation planning |
| spellingShingle | Hee Ju Hwang Bharat Bhusan Patnaik Snigdha Baliarsingh Hongray Howrelia Patnaik Min Kyu Sang Jie eun Park Hang Chul Cho Dae Kwon Song Jun Yang Jeong Chan Eui Hong Yong Tae Kim Hyeon Jun Sin Liu Ziwei So Young Park Se Won Kang Heon Cheon Jeong Hong Seog Park Yeon Soo Han Yong Seok Lee Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction BMC Genomics C. tripartitus Transcriptome Illumina sequencing Immunity-related genes Simple sequence repeats Informed conservation planning |
| title | Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction |
| title_full | Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction |
| title_fullStr | Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction |
| title_full_unstemmed | Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction |
| title_short | Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction |
| title_sort | transcriptome analysis of the endangered dung beetle copris tripartitus coleoptera scarabaeidae and characterization of genes associated to immunity growth and reproduction |
| topic | C. tripartitus Transcriptome Illumina sequencing Immunity-related genes Simple sequence repeats Informed conservation planning |
| url | https://doi.org/10.1186/s12864-023-09122-w |
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