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Chen Z, Ren L, Li J, Fu N, Yun Q, Luo Y. Chromosomal-level genome assembly of Hylurgus ligniperda: insights into host adaptation and environmental tolerance. BMC Genomics 2024; 25:792. [PMID: 39164658 PMCID: PMC11337627 DOI: 10.1186/s12864-024-10711-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 08/14/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Hylurgus ligniperda (Coleoptera: Curculionidae) is a worldwide forest quarantine pest. It is widely distributed, has many host tree species, and possesses strong adaptability. To explore its environmental adaptability and the related molecular mechanisms, we conducted chromosome-level genome sequencing and analyzed the transcriptome under different environmental factors, identifying key expressed genes. RESULTS We employed PacBio, Illumina, and Hi-C sequencing techniques to assemble a 520 Mb chromosomal-level genome of H. ligniperda, obtaining an N50 of 39.97 Mb across 138 scaffolds. A total of 10,765 protein-coding genes were annotated after repeat masking. Fourteen chromosomes were identified, among which Hyli14 was determined to be the sex chromosome. Survival statistics were tested over various growth periods under high temperature and low humidity conditions. The maximum survival period of adults reached 292 days at 25 °C, 65% relative humidity. In comparison, the maximum survival period was 14 days under 35 °C, 65% relative humidity, and 106 days under 25°C, 40% relative humidity. This indicated that environmental stress conditions significantly reduced adults' survival period. We further conducted transcriptome analysis to screen for potentially influential differentially expressed genes, such as CYP450 and Histone. Subsequently, we performed gene family analysis to gain insights into their functions and interactions, such as CYP450 and Histone. CYP450 genes affected the detoxification metabolism of enzymes in the Cytochrome P450 pathway to adapt to different environments. Histone genes are involved in insect hormone biosynthesis and longevity-regulating pathways in H. ligniperda to adapt to environmental stress. CONCLUSIONS The genome at the chromosome level of H. ligniperda was assembled for the first time. The mortality of H. ligniperda increased significantly at 35 ℃, 65% RH, and 25 ℃, 40% RH. CYP450 and Histone genes played an important role in response to environmental stress. This genome offers a substantial genetic resource for investigating the molecular mechanisms behind beetle invasion and spread.
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Affiliation(s)
- Zhiqian Chen
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, 100083, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, 100083, China.
| | - Jiaxing Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, 100083, China
| | - Ningning Fu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, 100083, China
- Department of Forest Protection, College of Forestry, Hebei Agricultural University, Baoding, 071033, China
| | | | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, 100083, China.
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Biswas T, Vogel H, Biedermann PHW, Lehenberger M, Yuvaraj JK, Andersson MN. Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology. BMC Genomics 2024; 25:764. [PMID: 39107741 PMCID: PMC11302349 DOI: 10.1186/s12864-024-10678-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Chemoreception is crucial for insect fitness, underlying for instance food-, host-, and mate finding. Chemicals in the environment are detected by receptors from three divergent gene families: odorant receptors (ORs), gustatory receptors (GRs), and ionotropic receptors (IRs). However, how the chemoreceptor gene families evolve in parallel with ecological specializations remains poorly understood, especially in the order Coleoptera. Hence, we sequenced the genome and annotated the chemoreceptor genes of the specialised ambrosia beetle Trypodendron lineatum (Coleoptera, Curculionidae, Scolytinae) and compared its chemoreceptor gene repertoires with those of other scolytines with different ecological adaptations, as well as a polyphagous cerambycid species. RESULTS We identified 67 ORs, 38 GRs, and 44 IRs in T. lineatum ('Tlin'). Across gene families, T. lineatum has fewer chemoreceptors compared to related scolytines, the coffee berry borer Hypothenemus hampei and the mountain pine beetle Dendroctonus ponderosae, and clearly fewer receptors than the polyphagous cerambycid Anoplophora glabripennis. The comparatively low number of chemoreceptors is largely explained by the scarcity of large receptor lineage radiations, especially among the bitter taste GRs and the 'divergent' IRs, and the absence of alternatively spliced GR genes. Only one non-fructose sugar receptor was found, suggesting several sugar receptors have been lost. Also, we found no orthologue in the 'GR215 clade', which is widely conserved across Coleoptera. Two TlinORs are orthologous to ORs that are functionally conserved across curculionids, responding to 2-phenylethanol (2-PE) and green leaf volatiles (GLVs), respectively. CONCLUSIONS Trypodendron lineatum reproduces inside the xylem of decaying conifers where it feeds on its obligate fungal mutualist Phialophoropsis ferruginea. Like previous studies, our results suggest that stenophagy correlates with small chemoreceptor numbers in wood-boring beetles; indeed, the few GRs may be due to its restricted fungal diet. The presence of TlinORs orthologous to those detecting 2-PE and GLVs in other species suggests these compounds are important for T. lineatum. Future functional studies should test this prediction, and chemoreceptor annotations should be conducted on additional ambrosia beetle species to investigate whether few chemoreceptors is a general trait in this specialized group of beetles.
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Affiliation(s)
- Twinkle Biswas
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden
| | - Heiko Vogel
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Peter H W Biedermann
- Chair of Forest Entomology and Protection, University of Freiburg, Stegen-Wittental, Germany
| | | | | | - Martin N Andersson
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden.
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Xie M, Yao Y, Feng Y, Xie L, Mao C, He J, Li X, Ni Q. Chromosome-Level Genome Assembly of Apoderus dimidiatus Voss (Coleoptera: Attelabidae): Insights into Evolution and Behavior. INSECTS 2024; 15:431. [PMID: 38921146 PMCID: PMC11204265 DOI: 10.3390/insects15060431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/27/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Attelabidae insects have attracted much attention due to their unique leaf rolling behavior before oviposition. However, the lack of genomic data makes it difficult to understand the molecular mechanism behind their behavior and their evolutionary relationship with other species. To address this gap, we utilized Illumina and Nanopore sequencing platforms along with Hi-C technology to establish a highly accurate whole genome of A. dimidiatus at the chromosome level. The resulting genome size was determined to be 619.26 Mb, with a contig N50 of 50.89 Mb and GC content of 33.89%. Moreover, a total of 12,572 genes were identified, with 82.59% being functionally annotated, and 64.78% designated as repeat sequences. Our subsequent phylogenetic tree analysis revealed that Attelabidae's divergence from Curculionidae occurred approximately 161.52 million years ago. Furthermore, the genome of A. dimidiatus contained 334 expanded gene families and 1718 contracted gene families. In addition, using Phylogenetic Analysis by Maximum Likelihood (PAML), we identified 106 rapidly evolved genes exhibiting significant signals and 540 positively selected genes. Our research endeavors to serve as an invaluable genomic data resource for the study of Attelabidae, offering fresh perspectives for the exploration of its leaf rolling behavior.
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Affiliation(s)
- Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China; (M.X.); (Y.Y.)
| | - Yuhao Yao
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China; (M.X.); (Y.Y.)
| | - Yuling Feng
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.F.); (L.X.)
| | - Lei Xie
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.F.); (L.X.)
| | - Chuyang Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming 650223, China; (C.M.); (J.H.)
| | - Jinwu He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming 650223, China; (C.M.); (J.H.)
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming 650223, China; (C.M.); (J.H.)
| | - Qingyong Ni
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.F.); (L.X.)
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Copeland M, Landa S, Owoyemi A, Jonika MM, Alfieri J, Sylvester T, Hoover Z, Hjelmen CE, Spencer Johnston J, Kyre BR, Rieske LK, Blackmon H, Casola C. Genome assembly of the southern pine beetle ( Dendroctonus frontalis Zimmerman) reveals the origins of gene content reduction in Dendroctonus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.592785. [PMID: 38766115 PMCID: PMC11100688 DOI: 10.1101/2024.05.08.592785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Dendroctonus frontalis, also known as southern pine beetle (SPB), represents the most damaging forest pest in the southeastern United States. Strategies to predict, monitor and suppress SPB outbreaks have had limited success. Genomic data are critical to inform on pest biology and to identify molecular targets to develop improved management approaches. Here, we produced a chromosome-level genome assembly of SPB using long-read sequencing data. Synteny analyses confirmed the conservation of the core coleopteran Stevens elements and validated the bona fide SPB X chromosome. Transcriptomic data were used to obtain 39,588 transcripts corresponding to 13,354 putative protein-coding loci. Comparative analyses of gene content across 14 beetle and 3 other insects revealed several losses of conserved genes in the Dendroctonus clade and gene gains in SPB and Dendroctonus that were enriched for loci encoding membrane proteins and extracellular matrix proteins. While lineage-specific gene losses contributed to the gene content reduction observed in Dendroctonus, we also showed that widespread misannotation of transposable elements represents a major cause of the apparent gene expansion in several non-Dendroctonus species. Our findings uncovered distinctive features of the SPB gene complement and disentangled the role of biological and annotation-related factors contributing to gene content variation across beetles.
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Affiliation(s)
- Megan Copeland
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Shelby Landa
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Adekola Owoyemi
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | | | - Jamie Alfieri
- Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Terrence Sylvester
- Department of Biological Sciences, The University of Memphis, Memphis, TN, USA
| | - Zachary Hoover
- Department of Biochemistry, Texas A&M University, College Station, TX, USA
| | - Carl E. Hjelmen
- Department of Biology, Utah Valley University, Orem, UT, USA
| | | | - Bethany R. Kyre
- USDA Forest Service, Forest Health Protection, San Bernardino, CA, USA
| | - Lynne K. Rieske
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, USA
- Interdisciplinary Doctoral Degree Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, USA
- Interdisciplinary Doctoral Degree Program in Genetics and Genomics, Texas A&M University, College Station, USA
| | - Claudio Casola
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
- Interdisciplinary Doctoral Degree Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, USA
- Interdisciplinary Doctoral Degree Program in Genetics and Genomics, Texas A&M University, College Station, USA
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Lu TT, Yin NN, Yang AJ, Yao YJ, Li ZQ, Liu NY. Comparative transcriptomics reveals the conservation and divergence of reproductive genes across three sympatric Tomicus bark beetles. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101168. [PMID: 38061252 DOI: 10.1016/j.cbd.2023.101168] [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: 08/31/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 02/15/2024]
Abstract
Three tree-killing bark beetles belonging to the genus Tomicus, Tomicus yunnanensis, Tomicus brevipilosus and Tomicus minor (Coleoptera; Curculionidae, Scolytinae), are serious wood-borers with larvae feeding on the phloem tissues of Pinus yunnanensis. The three Tomicus beetles, in some cases, coexist in a same habitat, providing a best system for exploring the conservation and divergence of reproductive genes. Here, we applied comparative transcriptomics and molecular biology approaches to characterize reproductive-related genes in three sympatric Tomicus species. Illumina sequencing of female and male reproductive systems and residual bodies generated a large number of clean reads, representing 185,920,232 sequences in T. yunnanensis, 169,153,404 in T. brevipilosus and 178,493,176 in T. minor that were assembled into 32,802, 56,912 and 33,670 unigenes, respectively. The majority of the genes had detectable expression in reproductive tissues (FPKM >1), particularly those genes in T. brevipilosus accounting for 76.61 % of the total genes. From the transcriptomes, totally 838 genes encoding 463 detoxification enzymes, 339 chemosensory membrane proteins and 36 ionotropic glutamate receptors (iGluRs) were identified, including 622 reproductive tissue-expressed genes. Of these, members of carboxylesterases (COEs), ionotropic receptors (IRs), sensory neuron membrane proteins (SNMPs) and iGluRs were highly conserved in gene numbers and sequence identities across three Tomicus species. Further, expression profiling analyses revealed a number of genes expressed in reproductive tissues and the diverse expression characteristics in these beetles. The results provide evidence for the conservation and differences of reproductive genes among three sympatric closely related beetles, helping understand their different reproductive strategies and the maximization of the reproductive success.
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Affiliation(s)
- Ting-Ting Lu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Ning-Na Yin
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - An-Jing Yang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Yu-Juan Yao
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Zhao-Qun Li
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou 310008, China.
| | - Nai-Yong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
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Sylvester T, Adams R, Hunter WB, Li X, Rivera-Marchand B, Shen R, Shin NR, McKenna DD. The genome of the invasive and broadly polyphagous Diaprepes root weevil, Diaprepes abbreviatus (Coleoptera), reveals an arsenal of putative polysaccharide-degrading enzymes. J Hered 2024; 115:94-102. [PMID: 37878740 DOI: 10.1093/jhered/esad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/14/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
The Diaprepes root weevil (DRW), Diaprepes abbreviatus, is a broadly polyphagous invasive pest of agriculture in the southern United States and the Caribbean. Its genome was sequenced, assembled, and annotated to study genomic correlates of specialized plant-feeding and invasiveness and to facilitate the development of new methods for DRW control. The 1.69 Gb D. abbreviatus genome assembly was distributed across 653 contigs, with an N50 of 7.8 Mb and the largest contig of 62 Mb. Most of the genome was comprised of repetitive sequences, with 66.17% in transposable elements, 5.75% in macrosatellites, and 2.06% in microsatellites. Most expected orthologous genes were present and fully assembled, with 99.5% of BUSCO genes present and 1.5% duplicated. One hundred and nine contigs (27.19 Mb) were identified as putative fragments of the X and Y sex chromosomes, and homology assessment with other beetle X chromosomes indicated a possible sex chromosome turnover event. Genome annotation identified 18,412 genes, including 43 putative horizontally transferred (HT) loci. Notably, 258 genes were identified from gene families known to encode plant cell wall degrading enzymes and invertases, including carbohydrate esterases, polysaccharide lyases, and glycoside hydrolases (GH). GH genes were unusually numerous, with 239 putative genes representing 19 GH families. Interestingly, several other beetle species with large numbers of GH genes are (like D. abbreviatus) successful invasive pests of agriculture or forestry.
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Affiliation(s)
- Terrence Sylvester
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
| | - Richard Adams
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, United States
- Agricultural Statistics Laboratory, University of Arkansas, Fayetteville, AR, United States
| | - Wayne B Hunter
- USDA, ARS, U. S. Horticultural Research Laboratory, Fort Pierce, FL 34945, United States
| | - Xuankun Li
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Bert Rivera-Marchand
- Office of Academic Affairs, Polk State College, Lakeland Campus, Lakeland, FL, 33803, United States
| | - Rongrong Shen
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
| | - Na Ra Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
| | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
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Herbette M, Ross L. Paternal genome elimination: patterns and mechanisms of drive and silencing. Curr Opin Genet Dev 2023; 81:102065. [PMID: 37413739 DOI: 10.1016/j.gde.2023.102065] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 07/08/2023]
Abstract
In thousands of arthropod species, males inherit, but subsequently eliminate the entire haploid genome of their father. However, why this peculiar reproductive strategy evolved repeatedly across diverse species and what mechanisms are involved in paternal genome elimination (PGE) remains largely unknown. In this review, we summarize what we know about the patterns of paternal chromosome elimination during various stages of development in the diverse taxa that have been studied. We also discuss some other unusual features often associated with PGE, such as the transcriptional silencing of paternally derived chromosomes in males and sex determination through the early embryonic elimination of X chromosomes. Little is known about the molecular mechanisms underlying the parent-of-origin-dependent chromosome elimination and silencing under PGE, but we discuss the insight of several studies that are pioneering this work and highlight directions for future research.
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Affiliation(s)
- Marion Herbette
- School of Biological Sciences, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Laura Ross
- School of Biological Sciences, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK.
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Abstract
Food production depends on biodiversity and ecosystem services (ES) such as pest control and pollination. Our knowledge about biodiversity benefits to crop production has increased in recent decades, but most studies treat ES separately and then add up their values. Ignoring that these services, being part of the same system, likely interact is blinding us to potential synergies and trade-offs. Our field experiment shows, at realistic field scales, that pest control and pollination can interact positively. This synergy translates directly to improved yields and income for coffee farmers, who produce a global commodity worth $24 billion per year. Our findings highlight the need to study interactions to understand the linkages between biodiversity, ES, and farmers’ livelihoods. Biodiversity-mediated ecosystem services (ES) support human well-being, but their values are typically estimated individually. Although ES are part of complex socioecological systems, we know surprisingly little about how multiple ES interact ecologically and economically. Interactions could be positive (synergy), negative (trade-offs), or absent (additive effects), with strong implications for management and valuation. Here, we evaluate the interactions of two ES, pollination and pest control, via a factorial field experiment in 30 Costa Rican coffee farms. We found synergistic interactions between these two critical ES to crop production. The combined positive effects of birds and bees on fruit set, fruit weight, and fruit weight uniformity were greater than their individual effects. This represents experimental evidence at realistic farm scales of positive interactions among ES in agricultural systems. These synergies suggest that assessments of individual ES may underestimate the benefits biodiversity provides to agriculture and human well-being. Using our experimental results, we demonstrate that bird pest control and bee pollination services translate directly into monetary benefits to coffee farmers. Excluding both birds and bees resulted in an average yield reduction of 24.7% (equivalent to losing US$1,066.00/ha). These findings highlight that habitat enhancements to support native biodiversity can have multiple benefits for coffee, a valuable crop that supports rural livelihoods worldwide. Accounting for potential interactions among ES is essential to quantifying their combined ecological and economic value.
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