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Hwang HJ, Patnaik BB, Baliarsingh S, Patnaik HH, Sang MK, Park JE, Cho HC, Song DK, Jeong JY, Hong CE, Kim YT, Sin HJ, Ziwei L, Park SY, Kang SW, Jeong HC, Park HS, Han YS, Lee YS. Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction. BMC Genomics 2023; 24:94. [PMID: 36864388 PMCID: PMC9979532 DOI: 10.1186/s12864-023-09122-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/09/2023] [Indexed: 03/04/2023] Open
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.
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Affiliation(s)
- Hee Ju Hwang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,PG Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore-, Odisha, 756089, India.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Snigdha Baliarsingh
- PG Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore-, Odisha, 756089, India
| | - Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Min Kyu Sang
- Research Support Center (Core-Facility) for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hang Chul Cho
- iLAB, INSILICOGEN, INC. #2901~2904, Tower-Dong A, HEUNGDEOK IT VALLEY, 13, Heungdeok 1-Ro, Giheung-Gu, Yongin-Si, 16954, Gyeonggi-do, Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hyeon Jun Sin
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Liu Ziwei
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, South Korea
| | - Heon Cheon Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-Dong, Yuseong-Gu, Daejeon, 34069, Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-Ro, Buk-Gu, Gwangju, 61186, South Korea
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea. .,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea. .,Research Support Center (Core-Facility) for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea.
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Milton A, Muhanguzi D, Male A, Kajubi A, Buah S, Kubiriba J, Tumuhimbise R. Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:637-646. [PMID: 35021224 DOI: 10.1093/jee/toab213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 06/14/2023]
Abstract
The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidus genotyping methods that could be deployed by banana pest control managers to the benefit of C. sordidus control programs in the tropics where such advanced technologies are not readily accessible. We used an in-house C. sordidus transcriptome from the an-ongoing study from which we mined an array of simple sequence repeat (SSR) markers. Of these, six highly polymorphic transcriptome-derived SSR markers were used to successfully genotype within and among banana weevil population genetic diversity of 12 C. sordidus populations collected from four banana-growing agro-ecological zones (AEZs) in Uganda. The developed transcriptome-derived SSR markers can be used by researchers in population genetics for characterization of the C. sordidus and identification of new genes that are linked to traits of particular interest. The significant genetic diversity revealed in C. sordidus provides pertinent information for integrated pest management strategies.
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Affiliation(s)
- Ali Milton
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dennis Muhanguzi
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Allan Male
- International Center for Tropical Agriculture, Kampala, Uganda
| | - Ali Kajubi
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Stephen Buah
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Jerome Kubiriba
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Robooni Tumuhimbise
- Rwebitaba Zonal Agricultural Research and Development Institute, Fort-Portal, Uganda
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Full-Length SMRT Transcriptome Sequencing and SSR Analysis of Bactrocera dorsalis (Hendel). INSECTS 2021; 12:insects12100938. [PMID: 34680707 PMCID: PMC8537375 DOI: 10.3390/insects12100938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022]
Abstract
Simple Summary In this study, a full-length transcriptome was analyzed with single-molecule real-time (SMRT) sequencing, which was first used to discover simple sequence repeat (SSR) genetic markers from B. dorsalis. Moreover, SSR markers from isoforms were screened for the identification of species diversity. These results could provide molecular biology methods for further population research. Abstract Bactrocera dorsalis (Hendel), as one of the most notorious and destructive invasive agricultural pests in the world, causes damage to over 250 different types of fruits and vegetables throughout tropical and subtropical areas. PacBio single-molecule real-time (SMRT) sequencing was used to generate the full-length transcriptome data of B. dorsalis. A total of 40,319,890 subreads (76.6 Gb, clean reads) were generated, including 535,241 circular consensus sequences (CCSs) and 386,916 full-length non-concatemer reads (FLNCs). Transcript cluster analysis of the FLNC reads revealed 22,780 high-quality reads (HQs). In total, 12,274 transcripts were functionally annotated based on four different databases. A total of 1978 SSR loci were distributed throughout 1714 HQ transcripts, of which 1926 were complete SSRs and 52 were complex SSRs. Among the total SSR loci, 2–3 nucleotide repeats were dominant, occupying 83.62%, of which di- and tri- nucleotide repeats were 39.38% and 44.24%, respectively. We detected 105 repeat motifs, of which AT/AT (50.19%), AC/GT (39.15%), CAA/TTG (32.46%), and ACA/TGT (10.86%) were the most common in di- and tri-nucleotide repeats. The repeat SSR motifs were 12–190 bp in length, and 1638 (88.02%) were shorter than 20 bp. According to the randomly selected microsatellite sequence, 80 pairs of primers were designed, and 174 individuals were randomly amplified by PCR using primers. The number of primers that had amplification products with clear bands and showed good polymorphism came to 41, indicating that this was a feasible way to explore SSR markers from the transcriptomic data of B. dorsalis. These results lay a foundation for developing highly polymorphic microsatellites for researching the functional genomics, population genetic structure, and genetic diversity of B. dorsalis.
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Kulanek D, Blank SM, Kramp K. First microsatellite markers for the pine catkin sawfly Xyela concava (Hymenoptera, Xyelidae) and their application in phylogeography and population genetics. PeerJ 2019; 7:e8010. [PMID: 31741792 PMCID: PMC6858820 DOI: 10.7717/peerj.8010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/08/2019] [Indexed: 11/20/2022] Open
Abstract
Microsatellites are widely used as powerful markers in population genetics because of their ability to access recent genetic variation and to resolve subtle population genetic structures. However, their development, especially for non-model organisms with no available genome-wide sequence data has been difficult and time-consuming. Here, a commercial high-throughput sequencing approach (HTS) was used for the very first identification of microsatellite motifs in the genome of Xyela concava and the design of primer pairs flanking those motifs. Sixteen of those primer pairs were selected and implemented successfully to answer questions on the phylogeography and population genetics of X. concava. The markers were characterized in three geographically distinct populations of X. concava and tested for cross-species amplification in two additional Xyela and one Pleroneura species (Xyelidae). All markers showed substantial polymorphism as well as revealing subtle genetic structures among the three genotyped populations. We also analyzed a fragment of the nuclear gene region of sodium/potassium-transporting ATPase subunit alpha (NaK) and a partial mitochondrial gene region coding for cytochrome oxidase subunit I (COI) to demonstrate different genetic resolutions and sex-biased patterns of these markers, and their potential for combined use in future studies on the phylogeography and population genetics of X. concava. Although a limited number of populations was analyzed, we nevertheless obtained new insights on the latter two topics. The microsatellites revealed a generally high gene flow between the populations, but also suggested a deep historical segregation into two genetic lineages. This deep genetic segregation was confirmed by NaK. While the high gene flow was unexpected, because of assumed restricted dispersal ability of X. concava and the discontinuous distribution of the host trees between the populations, the segregation of two lineages is comprehensible and could be explained by different refuge areas of the hosts during glacial times. The COI results showed a discordant strong genetic structure between all populations, which might be explained by the smaller effective population size of the mitochondrial genome. However, given the frequent evidence of a similar nature in recent studies on sawflies, we also consider and discuss mitochondrial introgression on population level as an alternative explanation.
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Affiliation(s)
- Dustin Kulanek
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Stephan M. Blank
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Katja Kramp
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
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Li R, Wang YT, Jiang GF. The transcriptome analysis of the bamboo grasshopper provides insights into hypothermic stress acclimation. Int J Biol Macromol 2019; 134:237-246. [PMID: 31059741 DOI: 10.1016/j.ijbiomac.2019.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 08/28/2018] [Accepted: 05/01/2019] [Indexed: 01/07/2023]
Abstract
The bamboo grasshopper, Ceracris kiangsu Tsai, is a pest of bamboos and widely distributed in China from high temperature plains to low temperature plateaus. In this study, high-throughput sequencing was used to analyze the transcriptome of C. kiangsu. Approximately 129,314,084 reads were generated using an Illumina sequencing. De novo assembly yielded 39,013 unigenes with an average length of 987 bp. Based on sequence similarity searches with known proteins, a total of 19,769 (50.67%) unigenes were identified. Of these annotated unigenes, 2114 and 11,412 unigenes were assigned to clusters of orthologous groups and gene ontology, respectively. Furthermore, 2128 simple sequence repeats (SSRs) were identified in the unigenes Differences were observed in gene expression after hypothermic stress, with the most up-regulated genes including heat shock protein genes (Hsps) and genes involved in ATP-binding. The down-regulation of genes involved in the catalytic activity of metabolic mechanisms was also observed. The obtained transcriptome information revealed the ability of C. kiangsu to build cold-tolerance after exposed to a mild low temperature and the transcriptional responses elicited by hypothermic stress.
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Affiliation(s)
- Ran Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Yi-Ting Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Guo-Fang Jiang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou 362000, People's Republic of China; Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, People's Republic of China.
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Duan X, Wang K, Su S, Tian R, Li Y, Chen M. De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae). PLoS One 2017; 12:e0172513. [PMID: 28212394 PMCID: PMC5315398 DOI: 10.1371/journal.pone.0172513] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/05/2017] [Indexed: 11/21/2022] Open
Abstract
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.
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Affiliation(s)
- Xinle Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China.,College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Sha Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Ruizheng Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yuting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Maohua Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
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