1
|
Höglund J, Dias G, Olsen RA, Soares A, Bunikis I, Talla V, Backström N. A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern. Genome Biol Evol 2024; 16:evae031. [PMID: 38368625 PMCID: PMC10901555 DOI: 10.1093/gbe/evae031] [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: 12/15/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/20/2024] Open
Abstract
The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. The development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity, chromosome-level genome assembly of a female clouded apollo butterfly and provide detailed annotations of genes and transposable elements. We find that the large genome (1.5 Gb) of the clouded apollo is extraordinarily repeat rich (73%). Despite that, the combination of sequencing techniques allowed us to assemble all chromosomes (nc = 29) to a high degree of completeness. The annotation resulted in a relatively high number of protein-coding genes (22,854) compared with other Lepidoptera, of which a large proportion (21,635) could be assigned functions based on homology with other species. A comparative analysis indicates that overall genome structure has been largely conserved, both within the genus and compared with the ancestral lepidopteran karyotype. The high-quality genome assembly and detailed annotation presented here will constitute an important tool for forthcoming efforts aimed at understanding the genetic consequences of fragmentation and decline, as well as for assessments of genetic diversity, population structure, inbreeding, and genetic load in the clouded apollo butterfly.
Collapse
Affiliation(s)
- Jacob Höglund
- Animal Ecology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala SE-752 36, Sweden
| | - Guilherme Dias
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala 752 37, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna 17165, Sweden
| | - André Soares
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala 752 37, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure hosted by SciLifeLab, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 752 37, Sweden
| | - Venkat Talla
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala SE-752 36, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala SE-752 36, Sweden
| |
Collapse
|
2
|
Yu B, Dong S, Jiang X, Qiao L, Chen J, Li T, Pan G, Zhou Z, Li C. Cas9-Mediated Gene Editing Using Receptor-Mediated Ovary Transduction of Cargo (ReMOT) Control in Bombyx mori. INSECTS 2023; 14:932. [PMID: 38132605 PMCID: PMC10743513 DOI: 10.3390/insects14120932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Lepidoptera is one of the most speciose insect orders, causing enormous damage to agricultural and forest crops. Although genome editing has been achieved in a few Lepidoptera for insect controls, most techniques are still limited. Here, by injecting female pupae of the Lepidoptera model species, Bombyx mori, gene editing was established using the Receptor-Mediated Ovary Transduction of Cargo (ReMOT) control technique. We identified a B. mori oocytes-targeting peptide ligand (BmOTP, a 29 aa of vitellogenin N-terminal of silkworms) with a highly conserved sequence in lepidopteran insects that could efficiently deliver mCherry into oocytes. When BmOTP was fused to CRISPR-associated protein 9 (Cas9) and the BmOTP-Cas9 ribonucleoprotein complex was injected into female pupae, heritable editing of the offspring was achieved in the silkworms. Compared with embryo microinjection, individual injection is more convenient and eliminates the challenge of injecting extremely small embryos. Our results will significantly facilitate the genetic manipulation of other lepidopteran insects, which is essential for advancing lepidopteran pest control.
Collapse
Affiliation(s)
- Bin Yu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China; (B.Y.); (S.D.); (X.J.); (J.C.); (T.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Sichen Dong
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China; (B.Y.); (S.D.); (X.J.); (J.C.); (T.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Xiaoyu Jiang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China; (B.Y.); (S.D.); (X.J.); (J.C.); (T.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Liang Qiao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China;
| | - Jie Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China; (B.Y.); (S.D.); (X.J.); (J.C.); (T.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Tian Li
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China; (B.Y.); (S.D.); (X.J.); (J.C.); (T.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China; (B.Y.); (S.D.); (X.J.); (J.C.); (T.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Zeyang Zhou
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China; (B.Y.); (S.D.); (X.J.); (J.C.); (T.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China;
| | - Chunfeng Li
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China; (B.Y.); (S.D.); (X.J.); (J.C.); (T.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| |
Collapse
|
3
|
McLellan CF, Montgomery SH. Towards an integrative approach to understanding collective behaviour in caterpillars. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220072. [PMID: 36802788 PMCID: PMC9939266 DOI: 10.1098/rstb.2022.0072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 02/21/2023] Open
Abstract
To evolve, and remain adaptive, collective behaviours must have a positive impact on overall individual fitness. However, these adaptive benefits may not be immediately apparent owing to an array of interactions with other ecological traits, which can depend on a lineage's evolutionary past and the mechanisms controlling group behaviour. A coherent understanding of how these behaviours evolve, are exhibited, and are coordinated across individuals, therefore requires an integrative approach spanning traditional disciplines in behavioural biology. Here, we argue that lepidopteran larvae are well placed to serve as study systems for investigating the integrative biology of collective behaviour. Lepidopteran larvae display a striking diversity in social behaviour, which illustrates critical interactions between ecological, morphological and behavioural traits. While previous, often classic, work has provided an understanding of how and why collective behaviours evolve in Lepidoptera, much less is known about the developmental and mechanistic basis of these traits. Recent advances in the quantification of behaviour, and the availability of genomic resources and manipulative tools, allied with the exploitation of the behavioural diversity of tractable lepidopteran clades, will change this. In doing so, we will be able to address previously intractable questions that can reveal the interplay between levels of biological variation. This article is part of a discussion meeting issue 'Collective behaviour through time'.
Collapse
Affiliation(s)
- Callum F. McLellan
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | | |
Collapse
|
4
|
Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes. Int J Mol Sci 2022; 24:ijms24010649. [PMID: 36614092 PMCID: PMC9820851 DOI: 10.3390/ijms24010649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023] Open
Abstract
Lepidopteran species are mostly pests, causing serious annual economic losses. High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. Long-read sequencing technology and assembly algorithm advances have improved the ability to timeously produce high-quality genomes. Lepidoptera includes a wide variety of insects with high genetic diversity and heterozygosity. Therefore, the selection of an appropriate sequencing and assembly strategy to obtain high-quality genomic information is urgently needed. This research used silkworm as a model to test genome sequencing and assembly through high-coverage datasets by de novo assemblies. We report the first nearly complete telomere-to-telomere reference genome of silkworm Bombyx mori (P50T strain) produced by Pacific Biosciences (PacBio) HiFi sequencing, and highly contiguous and complete genome assemblies of two other silkworm strains by Oxford Nanopore Technologies (ONT) or PacBio continuous long-reads (CLR) that were unrepresented in the public database. Assembly quality was evaluated by use of BUSCO, Inspector, and EagleC. It is necessary to choose an appropriate assembler for draft genome construction, especially for low-depth datasets. For PacBio CLR and ONT sequencing, NextDenovo is superior. For PacBio HiFi sequencing, hifiasm is better. Quality assessment is essential for genome assembly and can provide better and more accurate results. For chromosome-level high-quality genome construction, we recommend using 3D-DNA with EagleC evaluation. Our study references how to obtain and evaluate high-quality genome assemblies, and is a resource for biological control, comparative genomics, and evolutionary studies of Lepidopteran pests and related species.
Collapse
|
5
|
Guo R, Papanicolaou A, Fritz ML. Validation of reference-assisted assembly using existing and novel Heliothine genomes. Genomics 2022; 114:110441. [PMID: 35931274 DOI: 10.1016/j.ygeno.2022.110441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Chloridea subflexa and Chloridea virescens are a pair of closely related noctuid species exhibiting pheromone-based sexual isolation and divergent host plant preferences. We produced a novel Illumina short read C. subflexa genome assembly and an improved C. virescens genome assembly, which offer opportunities to study the genomic basis for evolutionarily important traits in this lepidopteran family with few genomic resources. We then examined the feasibility of reference-assisted assembly, an approach that leverages existing high quality genomic resources for genome improvement in closely related taxa and applied it to our Heliothine genomes. Our work demonstrates that reference-assisted assembly has the potential to enhance contiguity and completeness of existing insect genomic resources with minimal additional laboratory costs. We conclude by discussing both the potential and pitfalls of reference-assisted assembly according to the intended downstream assembly application.
Collapse
Affiliation(s)
- Rong Guo
- Department of Entomology, University of Maryland, College Park, MD 20742, USA; Computational Biology, Bioinformatics and Genomics Program, Department of Biological Sciences, University of Maryland, College Park, MD 20742, USA
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia.
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD 20742, USA; Computational Biology, Bioinformatics and Genomics Program, Department of Biological Sciences, University of Maryland, College Park, MD 20742, USA.
| |
Collapse
|
6
|
Chen X, Zhu W, Wang B, Wang Y, You P. A chromosome-level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21883. [PMID: 35294789 DOI: 10.1002/arch.21883] [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: 12/01/2021] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Paracymoriza distinctalis is a semiaquatic lepidopteran insect, which is of great value for studying the differentiation of the Pyraloidea superfamily. However, the understanding of heredity, evolution, and functional genomics of P. distinctalis are limited by few genome-wide resources. Here, we applied PacBio sequencing and the chromosome capture technique to assemble the first P. distinctalis genome from a single female individual. The genome size is 1.2 Gb with 32 chromosomes and the N50 is 38.91 Mb. Approximately 576.37 Mb, accounting for 48.93% of the genome, was identified as repeats. The genome comprises 39,003 protein-coding genes, 66.56% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of P. distinctalis and Chilo suppressalis lived ~83.5 million years ago. This chromosome-level genome assembly work is not only conducive to the understanding of P. distinctalis, but also may promote the study of the genomes of other lepidopteran species.
Collapse
Affiliation(s)
- Xiaoning Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory for Animal Conservation, Shaanxi Institute of Zoology, Xi'an, Shaanxi, China
| | - Wenbo Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Biao Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Yuqi Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Ping You
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| |
Collapse
|
7
|
Feron R, Waterhouse RM. Exploring new genomic territories with emerging model insects. CURRENT OPINION IN INSECT SCIENCE 2022; 51:100902. [PMID: 35301165 DOI: 10.1016/j.cois.2022.100902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Improvements in reference genome generation for insects and across the tree of life are extending the concept and utility of model organisms beyond traditional laboratory-tractable supermodels. Species or groups of species with comprehensive genome resources can be developed into model systems for studying a large variety of biological phenomena. Advances in sequencing and assembly technologies are supporting these emerging genome-enabled model systems by producing resources that are increasingly accurate and complete. Nevertheless, quality controls including assessing gene content completeness are required to ensure that these data can be included in expanding catalogues of high-quality references that will greatly advance understanding of insect biology and evolution.
Collapse
Affiliation(s)
- Romain Feron
- Department of Ecology and Evolution, University of Lausanne, and the Swiss Institute of Bioinformatics,1015 Lausanne, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and the Swiss Institute of Bioinformatics,1015 Lausanne, Switzerland.
| |
Collapse
|
8
|
Feron R, Waterhouse RM. Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes. Gigascience 2022; 11:6537158. [PMID: 35217859 PMCID: PMC8881204 DOI: 10.1093/gigascience/giac006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/12/2021] [Accepted: 01/13/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. To guide forthcoming genome generation efforts and promote efficient prioritization of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. FINDINGS Here we present an automated analysis workflow that surveys genome assemblies from the United States NCBI, assesses their completeness using the relevant BUSCO datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, examine how key assembly metrics relate to gene content completeness, and compare results from using different BUSCO lineage datasets. CONCLUSIONS These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritizations for ongoing and future sampling, sequencing, and genome generation initiatives.
Collapse
Affiliation(s)
- Romain Feron
- Department of Ecology and Evolution, Le Biophore UNIL-Sorge, University of Lausanne, Lausanne 1015, Switzerland.,Evolutionary-Functional Genomics Group, L'Amphipole UNIL-Sorge, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Le Biophore UNIL-Sorge, University of Lausanne, Lausanne 1015, Switzerland.,Evolutionary-Functional Genomics Group, L'Amphipole UNIL-Sorge, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| |
Collapse
|
9
|
Breeschoten T, van der Linden CFH, Ros VID, Schranz ME, Simon S. Expanding the Menu: Are Polyphagy and Gene Family Expansions Linked across Lepidoptera? Genome Biol Evol 2022; 14:6482744. [PMID: 34951642 PMCID: PMC8725640 DOI: 10.1093/gbe/evab283] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 12/31/2022] Open
Abstract
Evolutionary expansions and contractions of gene families are often correlated with key innovations and/or ecological characteristics. In butterflies and moths (Lepidoptera), expansions of gene families involved in detoxification of plant specialized metabolites are hypothesized to facilitate a polyphagous feeding style. However, analyses supporting this hypothesis are mostly based on a limited number of lepidopteran species. We applied a phylogenomics approach, using 37 lepidopteran genomes, to analyze if gene family evolution (gene gain and loss) is associated with the evolution of polyphagy. Specifically, we compared gene counts and evolutionary gene gain and loss rates of gene families involved in adaptations with plant feeding. We correlated gene evolution to host plant family range (phylogenetic diversity) and specialized metabolite content of plant families (functional metabolite diversity). We found a higher rate for gene loss than gene gain in Lepidoptera, a potential consequence of genomic rearrangements and deletions after (potentially small-scale) duplication events. Gene family expansions and contractions varied across lepidopteran families, and were associated to host plant use and specialization levels. Within the family Noctuidae, a higher expansion rate for gene families involved in detoxification can be related to the large number of polyphagous species. However, gene family expansions are observed in both polyphagous and monophagous lepidopteran species and thus seem to be species-specific in the taxa sampled. Nevertheless, a significant positive correlation of gene counts of the carboxyl- and choline esterase and glutathione-S-transferase detoxification gene families with the level of polyphagy was identified across Lepidoptera.
Collapse
Affiliation(s)
| | | | - Vera I D Ros
- Laboratory of Virology, Wageningen University & Research, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, The Netherlands
| | - Sabrina Simon
- Biosystematics Group, Wageningen University & Research, The Netherlands
| |
Collapse
|
10
|
Zheng YX, Wang Y, Dai BY, Li Z, Huo QR, Cui JX, Liu H, Li XH, Hughes AC, Zhang AB. Flight Mill Experiments and Computer Simulations Indicate Islands Recruit More Capable Flyers of Moths. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.771719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the traits related to species colonization and invasion, is a key question for both pest management and evolution. One of the key components is flight, which has been measured for a number of insect species through radar and tethered flight mill systems, but a general understanding of insect flight at a community level is lacking. In this study, we used flight mill experiments to quantify flight abilities of moth species, and simulation experiments to study which moths in mainland China have the potential for cross-island dispersal. We found that moths from superfamily Geometroidea (family Geometridae) have the weakest flight ability among the seven Lepidoptera superfamilies, which is characterized by the shortest longest single flight (LSF), the shortest time corresponding to the longest single flight (TLSF) (timecorrespondingtothelongestsingleflight), the lowest total distance flown (TDF), and the lowest average speed during the flight (VTDF). Surprisingly, the family Pyralidae (superfamily Pyraloidea) has the highest flight endurance of all 186 species of 12 families in this study, which is unexpected, given its small size and morphological traits yet it shows the longest LSF and TLSF. The comparison between species common to mainland and islands shows that flight distance (LSF) may be more important for species spread than flight speed. The results of mainland-island simulations show that when P(LSF>CD) (the proportion of individuals whose LSF is greater than the closest distance (CD) between mainland and island to the total number of individuals in the population) is less than 0.004, it is difficult for moth species to disperse to across islands without relying on external factors such as airflow. Over extended periods, with the immigration of species with strong flight abilities, islands are more likely to recruit species with stronger flight abilities.
Collapse
|
11
|
Yang M, Li J, Su S, Zhang H, Wang Z, Ding W, Li L. The mitochondrial genomes of Tortricidae: nucleotide composition, gene variation and phylogenetic performance. BMC Genomics 2021; 22:755. [PMID: 34674653 PMCID: PMC8532297 DOI: 10.1186/s12864-021-08041-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Mitochondrial genomes (mitogenomes) have greatly improved our understanding of the backbone phylogeny of Lepidoptera, but few studies on comparative mitogenomics below the family level have been conducted. Here, we generated 13 mitogenomes of eight tortricid species, reannotated 27 previously reported mitogenomes, and systematically performed a comparative analysis of nucleotide composition, gene variation and phylogenetic performance. RESULTS The lengths of completely sequenced mitogenomes ranged from 15,440 bp to 15,778 bp, and the gene content and organization were conserved in Tortricidae and typical for Lepidoptera. Analyses of AT-skew and GC-skew, the effective number of codons and the codon bias index all show a base bias in Tortricidae, with little heterogeneity among the major tortricid groups. Variations in the divergence rates among 13 protein-coding genes of the same tortricid subgroup and of the same PCG among tortricid subgroups were detected. The secondary structures of 22 transfer RNA genes and two ribosomal RNA genes were predicted and comparatively illustrated, showing evolutionary heterogeneity among different RNAs or different regions of the same RNA. The phylogenetic uncertainty of Enarmoniini in Tortricidae was confirmed. The synonymy of Bactrini and Olethreutini was confirmed for the first time, with the representative Bactrini consistently nesting in the Olethreutini clade. Nad6 exhibits the highest phylogenetic informativeness from the root to the tip of the resulting tree, and the combination of the third coding positions of 13 protein-coding genes shows extremely high phylogenetic informativeness. CONCLUSIONS This study presents 13 mitogenomes of eight tortricid species and represents the first detailed comparative mitogenomics study of Tortricidae. The results further our understanding of the evolutionary architectures of tortricid mitogenomes and provide a basis for future studies of population genetics and phylogenetic investigations in this group.
Collapse
Affiliation(s)
- Mingsheng Yang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001 Henan China
| | - Junhao Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001 Henan China
| | - Silin Su
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001 Henan China
| | - Hongfei Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001 Henan China
| | - Zhengbing Wang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001 Henan China
| | - Weili Ding
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001 Henan China
- Finance Office, Zhoukou Normal University, Zhoukou, 466001 Henan China
| | - Lili Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001 Henan China
| |
Collapse
|
12
|
Li X, Ellis E, Plotkin D, Imada Y, Yago M, Heckenhauer J, Cleland TP, Dikow RB, Dikow T, Storer CG, Kawahara AY, Frandsen PB. First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing. Genome Biol Evol 2021; 13:6380144. [PMID: 34599325 PMCID: PMC8557830 DOI: 10.1093/gbe/evab229] [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] [Accepted: 09/27/2021] [Indexed: 11/14/2022] Open
Abstract
We provide a new, annotated genome assembly of Neomicropteryx cornuta, a species of the so-called mandibulate archaic moths (Lepidoptera: Micropterigidae). These moths belong to a lineage that is thought to have split from all other Lepidoptera more than 300 Ma and are consequently vital to understanding the early evolution of superorder Amphiesmenoptera, which contains the order Lepidoptera (butterflies and moths) and its sister order Trichoptera (caddisflies). Using PacBio HiFi sequencing reads, we assembled a highly contiguous genome with a contig N50 of nearly 17 Mb. The assembled genome length of 541,115,538 bp is about half the length of the largest published Amphiesmenoptera genome (Limnephilus lunatus, Trichoptera) and double the length of the smallest (Papilio polytes, Lepidoptera). We find high recovery of universal single copy orthologs with 98.1% of BUSCO genes present and provide a genome annotation of 15,643 genes aided by resolved isoforms from PacBio IsoSeq data. This high-quality genome assembly provides an important resource for studying ecological and evolutionary transitions in the early evolution of Amphiesmenoptera.
Collapse
Affiliation(s)
- Xuankun Li
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, USA
| | - Emily Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, USA
| | - Yume Imada
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Masaya Yago
- The University Museum, The University of Tokyo, Hongo, Bunkyo-ku, Japan
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.,Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA
| | - Torsten Dikow
- Department of Entomology, National Museum of Natural History (USNM), Smithsonian Institution, Washington, District of Columbia, USA
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, USA
| | - Paul B Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA.,Department of Plant and Wildlife Sciences, Brigham Young University, USA
| |
Collapse
|
13
|
Wang M, Zhou Z, Li S, Zhu W, Hu X. Identification and Characterization of Antimicrobial Peptides From Butterflies: An Integrated Bioinformatics and Experimental Study. Front Microbiol 2021; 12:720381. [PMID: 34512599 PMCID: PMC8427292 DOI: 10.3389/fmicb.2021.720381] [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: 06/04/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Butterflies represent one of the largest animal groups on Earth, yet antimicrobial peptides (AMPs) of this group are less studied in comparison with their moth counterparts. This study employed an integrated bioinformatics approach to survey natural AMPs from publicly available genomic datasets. Numerous AMPs, including cecropins, defensins, and moricins, were identified and subsequently used as templates for the design of a series of synthetic AMPs that mimicked the naturally occurring sequences. Despite differing biological effects among the various sequences, the synthetic AMPs exhibited potent antibacterial and antifungal activities in vitro and in vivo, without inducing hemolysis, which implied their therapeutic potential in infectious diseases. Electron and confocal fluorescence microscopies revealed that the AMPs induced distinct morphological and biophysical changes on microbial cell membranes and nuclei, suggesting that the antimicrobial effects were related to a mechanism of membrane penetration and nucleic acid binding by the peptides. In conclusion, this study not only offers insights into butterfly AMPs but also provides a practical strategy for high-throughput natural AMP discoveries that will have implications for future research in this area.
Collapse
Affiliation(s)
- Min Wang
- Beijing Hospital, National Center of Gerontology, Beijing, China.,Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ziyue Zhou
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Simin Li
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Wei Zhu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xianda Hu
- Beijing Tibetan Hospital, China Tibetology Research Center, Beijing, China
| |
Collapse
|
14
|
Sutter A, Price TA, Wedell N. The impact of female mating strategies on the success of insect control technologies. CURRENT OPINION IN INSECT SCIENCE 2021; 45:75-83. [PMID: 33601059 DOI: 10.1016/j.cois.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/11/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Attempts to control insect pests and disease vectors have a long history. Recently, new technology has opened a whole new range of possible methods to suppress or transform natural populations. But it has also become clear that a better understanding of the ecology of targeted populations is needed. One key parameter is mating behaviour. Often modified males are released which need to successfully reproduce with females while competing with wild males. Insect control techniques can be affected by target species' mating ecology, and conversely mating ecology is likely to evolve in response to manipulation attempts. A better understanding of (female) mating behaviour will help anticipate and overcome potential challenges, and thus make desirable outcomes more likely.
Collapse
Affiliation(s)
- Andreas Sutter
- School of Biological Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
| | - Tom Ar Price
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Nina Wedell
- Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK.
| |
Collapse
|
15
|
Tong X, Qiao L, Luo J, Ding X, Wu S. The evolution and genetics of lepidopteran egg and caterpillar coloration. Curr Opin Genet Dev 2021; 69:140-146. [PMID: 34030080 DOI: 10.1016/j.gde.2021.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022]
Abstract
Insect colors and color patterns have fascinated biologists for centuries. While extensive research has focused on the adult colors of Drosophila and butterflies, our understanding of how colors are generated and diversified in embryonic and larval stages remains limited, especially, the genetics behind the protective coloration of the immobile embryonic and larval stages. Lepidoptera, one of the most widespread and species-rich insect orders, are extremely helpful uncovering those mechanisms due to their remarkable diverse colors in eggs and caterpillars within or among species, and these colors usually are variable in different developmental stages or in response to different environments. Here we review the recent progress on coloration of lepidopteran eggs and caterpillars, focusing on the genetic basis, developmental mechanisms, ecology, and evolution underlying the remarkable color diversity.
Collapse
Affiliation(s)
- Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
| | - Liang Qiao
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Jiangwen Luo
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China
| | - Xin Ding
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China
| | - Songyuan Wu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China; College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| |
Collapse
|
16
|
Sparks ME, Hebert FO, Johnston JS, Hamelin R, Cusson M, Levesque R, Gundersen-Rindal DE. Sequencing, Assembly and Annotation of the Whole-Insect Genome of Lymantria dispar dispar, the European Gypsy Moth. G3-GENES GENOMES GENETICS 2021; 11:6261075. [PMID: 33930134 DOI: 10.1093/g3journal/jkab150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/26/2021] [Indexed: 11/14/2022]
Abstract
The European gypsy moth, Lymantria dispar dispar (LDD), is an invasive insect and a threat to urban trees, forests and forest-related industries in North America. For use as a comparator with a previously published genome based on the LD652 pupal ovary-derived cell line, as well as whole-insect genome sequences obtained from the Asian gypsy moth subspecies L. dispar asiatica and L. dispar japonica, the whole-insect LDD genome was sequenced, assembled and annotated. The resulting assembly was 998 Mb in size, with a contig N50 of 662 Kb and GC content of 38.8%. Long interspersed nuclear elements (LINEs) constitute 25.4% of the whole-insect genome, and a total of 11,901 genes predicted by automated gene finding encoded proteins exhibiting homology with reference sequences in the NCBI NR and/or UniProtKB databases at the most stringent similarity cutoff level (i.e., the gold tier). These results will be especially useful in developing a better understanding of the biology and population genetics of L. dispar and the genetic features underlying Lepidoptera in general.
Collapse
Affiliation(s)
- Michael E Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland 20705, USA
| | - Francois Olivier Hebert
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada, G1V 0A6
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Richard Hamelin
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada, G1V 0A6.,Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Michel Cusson
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada, G1V 0A6.,Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Quebec City, Quebec, Canada, G1V 4C7
| | - Roger Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada, G1V 0A6
| | - Dawn E Gundersen-Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland 20705, USA
| |
Collapse
|
17
|
Cabral-de-Mello DC, Marec F. Universal fluorescence in situ hybridization (FISH) protocol for mapping repetitive DNAs in insects and other arthropods. Mol Genet Genomics 2021; 296:513-526. [PMID: 33625598 DOI: 10.1007/s00438-021-01765-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/29/2021] [Indexed: 12/30/2022]
Abstract
Repetitive DNAs comprise large portion of eukaryote genomes. In genome projects, the assembly of repetitive DNAs is challenging due to the similarity between repeats, which generate ambiguities for alignment. Fluorescence in situ hybridization (FISH) is a powerful technique for the physical mapping of various sequences on chromosomes. This technique is thus very helpful in chromosome-based genome assemblies, providing information on the fine architecture of genomes and their evolution. However, various protocols are currently used for FISH mapping, most of which are relatively laborious and expensive, or work properly only with a specific type of probes or sequences, and there is a need for a universal and affordable FISH protocol. Here we tested a FISH protocol for mapping of different DNA repeats, such as multigene families (rDNAs, U snDNAs, histone genes), satellite DNAs, microsatellites, transposable elements, DOP-PCR products, and telomeric motif (TTAGG)n, on the chromosomes of various insects and other arthropods. Different cell types and stages obtained from diverse tissues were used. The FISH procedure proved high quality and reliable results in all experiments performed. We obtained data on the chromosomal distribution of DNA repeats in representatives of insects and other arthropods. Thus, our results allow us to conclude that the protocol is universal and requires only time adjustment for chromosome/DNA denaturation. The use of this FISH protocol will facilitate studies focused on understanding the evolution and role of repetitive DNA in arthropod genomes.
Collapse
Affiliation(s)
- Diogo Cavalcanti Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP- Universidade Estadual Paulista, Rio Claro, São Paulo, CEP 13506-900, Brazil.
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic.
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| |
Collapse
|
18
|
Marco HG, Šimek P, Gäde G. Unique Members of the Adipokinetic Hormone Family in Butterflies and Moths (Insecta, Lepidoptera). Front Physiol 2020; 11:614552. [PMID: 33391031 PMCID: PMC7773649 DOI: 10.3389/fphys.2020.614552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/03/2020] [Indexed: 01/17/2023] Open
Abstract
Lepidoptera is amongst one of the four most speciose insect orders and ecologically very successful because of their ability to fly. Insect flight is always aerobic and exacts a high metabolic demand on the animal. A family of structurally related neuropeptides, generically referred to as adipokinetic hormones (AKHs), play a key role in triggering the release of readily utilizable fuel metabolites into the hemolymph from the storage forms in the fat body. We used mass spectrometry to elucidate AKH sequences from 34 species of Lepidoptera and searched the literature and publicly available databases to compile (in a phylogenetic context) a comprehensive list of all Lepidoptera sequences published/predicted from a total of 76 species. We then used the resulting set of 15 biochemically characterized AKHs in a physiological assay that measures lipid or carbohydrate mobilization in three different lepidopteran species to learn about the functional cross-activity (receptor-ligand interactions) amongst the different butterfly/moth families. Our results include novel peptide structures, demonstrate structural diversity, phylogenetic trends in peptide distribution and order-specificity of Lepidoptera AKHs. There is almost an equal occurrence of octa-, nona-, and decapeptides, with an unparalleled emphasis on nonapeptides than in any insect order. Primitive species make Peram-CAH-II, an octapeptide found also in other orders; the lepidopteran signature peptide is Manse-AKH. Not all of the 15 tested AKHs are active in Pieris brassicae; this provides insight into structure-activity specificity and could be useful for further investigations into possible biorational insecticide development.
Collapse
Affiliation(s)
- Heather G. Marco
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Petr Šimek
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Gerd Gäde
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| |
Collapse
|
19
|
Yadav C, Smith M, Ogunremi D, Yack J. Draft genome assembly and annotation of the masked birch caterpillar, Drepana arcuata (Lepidoptera: Drepanoidea). Data Brief 2020; 33:106531. [PMID: 33299908 PMCID: PMC7704289 DOI: 10.1016/j.dib.2020.106531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/12/2022] Open
Abstract
The masked birch caterpillar, Drepana arcuata Walker (Lepidoptera: Drepanidae), and other Drepanoidea (Lepidoptera) species are excellent organisms for investigating the function and evolution of vibratory communication and sociality in caterpillars. We present a de novo assembled draft genome and functional annotation for D. arcuata, using a combination of short and long sequencing reads generated by Illumina HiSeq X and Oxford Nanopore Technologies (ONT) MinION sequencing platforms, respectively. A total of 460,694,612 150bp paired-end Illumina and 395,890 ONT raw reads were assembled into 11,493 scaffolds spanning a genome size of 270.5Mb. The resulting D. arcuata genome has a GC content of 38.79%, repeat content of 8.26%, is 86.5% complete based on Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment, and comprises 10,398 predicted protein-coding genes. These data represent the first genomic resources for the lepidopteran superfamily Drepanoidea. Although the order Lepidoptera comprises numerous ecologically and economically important species, assembled genomes and annotations are available for < 1% of the total species. These data can be further utilized for research on Lepidoptera genomics as well as on the function and evolution of vibratory communication and sociality in larval insects.
Collapse
Affiliation(s)
- Chanchal Yadav
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Myron Smith
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Dele Ogunremi
- Canadian Food Inspection Agency, Ottawa Laboratory Fallowfield, Ontario K2J 4S1, Canada
| | - Jayne Yack
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| |
Collapse
|
20
|
Gui F, Lan T, Zhao Y, Guo W, Dong Y, Fang D, Liu H, Li H, Wang H, Hao R, Cheng X, Li Y, Yang P, Sahu SK, Chen Y, Cheng L, He S, Liu P, Fan G, Lu H, Hu G, Dong W, Chen B, Jiang Y, Zhang Y, Xu H, Lin F, Slippers B, Postma A, Jackson M, Abate BA, Tesfaye K, Demie AL, Bayeleygne MD, Degefu DT, Chen F, Kuria PK, Kinyua ZM, Liu TX, Yang H, Huang F, Liu X, Sheng J, Kang L. Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda. Protein Cell 2020; 13:513-531. [PMID: 33108584 PMCID: PMC9226219 DOI: 10.1007/s13238-020-00795-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/15/2020] [Indexed: 11/24/2022] Open
Abstract
The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas.
Collapse
Affiliation(s)
- Furong Gui
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Yue Zhao
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Wei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ruoshi Hao
- Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China
| | | | - Yahong Li
- Yunnan Plant Protection and Quarantine Station, Kunming, 650034, China
| | - Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaping Chen
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Le Cheng
- BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, 650106, China
| | - Shuqi He
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Liu
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Haorong Lu
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guohai Hu
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wei Dong
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Bin Chen
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Yuan Jiang
- BGI-Americas, One Broadway, 14th Floor, Cambridge, MA, 02142, USA
| | - Yongwei Zhang
- BGI-Americas, One Broadway, 14th Floor, Cambridge, MA, 02142, USA
| | - Hanhong Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Fei Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Bernard Slippers
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Alisa Postma
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Matthew Jackson
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | | | - Kassahun Tesfaye
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia.,College of Natural Science, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Dawit Tesfaye Degefu
- Melkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Melkassa, Addis Ababa, Ethiopia
| | - Feng Chen
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Paul K Kuria
- Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, Nairobi, 00800, Kenya
| | - Zachary M Kinyua
- Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, Nairobi, 00800, Kenya
| | - Tong-Xian Liu
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huanming Yang
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Fangneng Huang
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China.
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
21
|
Borges dos Santos L, Paulo Gomes Viana J, José Biasotto Francischini F, Victoria Fogliata S, L. Joyce A, Pereira de Souza A, Gabriela Murúa M, J. Clough S, Imaculada Zucchi M. A first draft genome of the Sugarcane borer, Diatraea saccharalis. F1000Res 2020. [DOI: 10.12688/f1000research.26614.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The sugarcane borer (Diatraea saccharalis), a widely distributed moth throughout the Americas, is a pest that affects economically important crops such as sugarcane, sorghum, wheat, maize and rice. Given its significant impact on yield reduction, whole-genome information of the species is needed. Here, we report the first draft assembly of the D. saccharalis genome. Methods: The genomic sequences were obtained using the Illumina HiSeq 2500 whole-genome sequencing of a single adult male specimen. We assembled the short-reads using the SPAdes software and predicted protein-coding genes using MAKER. Genome assembly completeness was assessed through BUSCO and the repetitive content by RepeatMasker. Results: The 453 Mb assembled sequences contain 1,445 BUSCO gene orthologs and 1,161 predicted gene models identified based on homology evidence to the domestic silk moth, Bombyx mori. The repeat content composes 41.18% of the genomic sequences which is in the range of other lepidopteran species. Conclusions: Functional annotation reveals that predicted gene models are involved in important cellular mechanisms such as metabolic pathways and protein synthesis. Thus, the data generated in this study expands our knowledge on the genomic characteristics of this devastating pest and provides essential resources for future genetic studies of the species.
Collapse
|
22
|
Lee J, Nishiyama T, Shigenobu S, Yamaguchi K, Suzuki Y, Shimada T, Katsuma S, Kiuchi T. The genome sequence of Samia ricini, a new model species of lepidopteran insect. Mol Ecol Resour 2020; 21:327-339. [PMID: 32985129 DOI: 10.1111/1755-0998.13259] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 01/15/2023]
Abstract
Samia ricini, a gigantic saturniid moth, has the potential to be a novel lepidopteran model species. Samia ricini is far more resistant to diseases than the current model species Bombyx mori, and therefore can be more easily reared. In addition, genetic resources available for S. ricini rival those for B. mori: at least 26 ecoraces of S. ricini are reported and S. ricini can hybridize with wild Samia species, which are distributed throughout Asian countries, and produce fertile progenies. Physiological traits such as food preference, integument colour and larval spot pattern differ among S. ricini strains and wild Samia species so that those traits can be targeted in forward genetic analyses. To facilitate genetic research in S. ricini, we determined its whole genome sequence. The assembled genome of S. ricini was 458 Mb with 155 scaffolds, and the scaffold N50 length of the assembly was ~ 21 Mb. In total, 16,702 protein coding genes were predicted. While the S. ricini genome was mostly collinear with that of B. mori with some rearrangements and few S. ricini-specific genes were discovered, chorion genes and fibroin genes seemed to have expanded in the S. ricini lineage. As the first step of genetic analyses, causal genes for "Blue," "Yellow," "Spot," and "Red cocoon" phenotypes were mapped to chromosomes.
Collapse
Affiliation(s)
- Jung Lee
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Department of Life Science, Faculty of Science/Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Toru Shimada
- Department of Life Science, Faculty of Science/Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
23
|
Yin NN, Nuo SM, Xiao HY, Zhao YJ, Zhu JY, Liu NY. The ionotropic receptor gene family in Lepidoptera and Trichoptera: Annotation, evolutionary and functional perspectives. Genomics 2020; 113:601-612. [PMID: 33002624 DOI: 10.1016/j.ygeno.2020.09.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/01/2020] [Accepted: 09/24/2020] [Indexed: 10/23/2022]
Abstract
Lepidoptera (moths and butterflies) and Trichoptera (caddisflies), belonging to the superorder Amphiesmenoptera, are the most diverse insect orders as representatives of the terrestrial and aquatic insects, respectively. The insects of the two orders possess different biological and behavioral characteristics, especially their larvae, presumably resulting in the differences of the ionotropic receptor (IR) genes in numbers, sequence characteristics or gene structure. Here, we employed genomics, transcriptomics, bioinformatics, phylogenetics and molecular biology strategies to characterize the IR gene repertoire in Lepidoptera and Trichoptera. Genome and transcriptome analyses with exhaustive homology-based searches and manual efforts, in 32 lepidopterans and five trichopterans, led to the identification of 1449 genes encoding IRs with 1170 full-length sequences, representing the most comprehensive set of chemoreceptor superfamilies across the Amphiesmenoptera. Analysis of gene gains and losses in orthologous groups implied that some IRs were lost in related species, and multiple gene copies occurred mainly in divergent IRs (D-IRs) by gene duplications. Phylogenetic analysis of 2442 IR proteins from 67 species revealed that Lepidoptera and Trichoptera IRs could be classified into three subfamilies, i.e., 14 antennal IRs (A-IRs), five Lepidoptera-specific IRs (LS-IRs) and four D-IRs. Of the three subfamilies, A-IRs and LS-IRs members within orthologous groups exhibited high conservation of gene structure, but D-IRs shared extremely low amino acid identities (below 30%). Expression profiles revealed functional diversities of IRs from Bombyx mori and Papilio xuthus involving smell, taste or reproduction, in which some genes displayed sex-biased expression in antennae associated with specific chemosensory behaviors of female or male adults. Our current study has provided insights into the evolution, conservation and divergence of IRs between/within Lepidoptera and Trichoptera, and allows for further experiments to investigate IR functions.
Collapse
Affiliation(s)
- Ning-Na Yin
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Shu-Mei Nuo
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Hai-Yan Xiao
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Yu-Jie Zhao
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Nai-Yong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
| |
Collapse
|
24
|
Rodriguez-Caro L, Fenner J, Benson C, Van Belleghem SM, Counterman BA. Genome Assembly of the Dogface Butterfly Zerene cesonia. Genome Biol Evol 2020; 12:3580-3585. [PMID: 31755926 PMCID: PMC6944212 DOI: 10.1093/gbe/evz254] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2019] [Indexed: 02/04/2023] Open
Abstract
Comparisons of high-quality, reference butterfly, and moth genomes have been instrumental to advancing our understanding of how hybridization, and natural selection drive genomic change during the origin of new species and novel traits. Here, we present a genome assembly of the Southern Dogface butterfly, Zerene cesonia (Pieridae) whose brilliant wing colorations have been implicated in developmental plasticity, hybridization, sexual selection, and speciation. We assembled 266,407,278 bp of the Z. cesonia genome, which accounts for 98.3% of the estimated 271 Mb genome size. Using a hybrid approach involving Chicago libraries with Hi-Rise assembly and a diploid Meraculous assembly, the final haploid genome was assembled. In the final assembly, nearly all autosomes and the Z chromosome were assembled into single scaffolds. The largest 29 scaffolds accounted for 91.4% of the genome assembly, with the remaining ∼8% distributed among another 247 scaffolds and overall N50 of 9.2 Mb. Tissue-specific RNA-seq informed annotations identified 16,442 protein-coding genes, which included 93.2% of the arthropod Benchmarking Universal Single-Copy Orthologs (BUSCO). The Z. cesonia genome assembly had ∼9% identified as repetitive elements, with a transposable element landscape rich in helitrons. Similar to other Lepidoptera genomes, Z. cesonia showed a high conservation of chromosomal synteny. The Z. cesonia assembly provides a high-quality reference for studies of chromosomal arrangements in the Pierid family, as well as for population, phylo, and functional genomic studies of adaptation and speciation.
Collapse
Affiliation(s)
- Luis Rodriguez-Caro
- Department of Biological Sciences, Mississippi State University.,Division of Biological Sciences, University of Montana, Missoula, MT
| | - Jennifer Fenner
- Department of Biological Sciences, Mississippi State University
| | - Caleb Benson
- Department of Biological Sciences, Mississippi State University
| | | | | |
Collapse
|
25
|
Yen EC, McCarthy SA, Galarza JA, Generalovic TN, Pelan S, Nguyen P, Meier JI, Warren IA, Mappes J, Durbin R, Jiggins CD. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 2020; 9:giaa088. [PMID: 32808665 PMCID: PMC7433188 DOI: 10.1093/gigascience/giaa088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. FINDINGS We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. CONCLUSIONS We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.
Collapse
Affiliation(s)
- Eugenie C Yen
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Downing
Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Juan A Galarza
- Department of Biological and Environmental Science, University of
Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Tomas N Generalovic
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of
Entomology, Branišovská 1160/31, 370 05 České Budějovice, Czech
Republic
- University of South Bohemia, Faculty of Science, Branišovská
1645/31A, 370 05 České Budějovice, Czech Republic
| | - Joana I Meier
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street,
Cambridge CB2 1TP, UK
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Johanna Mappes
- Department of Biological and Environmental Science, University of
Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing
Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street,
Cambridge CB2 1TP, UK
| |
Collapse
|
26
|
Lin Z, Wang JL, Cheng Y, Wang JX, Zou Z. Pattern recognition receptors from lepidopteran insects and their biological functions. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 108:103688. [PMID: 32222357 DOI: 10.1016/j.dci.2020.103688] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 03/03/2020] [Accepted: 03/20/2020] [Indexed: 05/08/2023]
Abstract
Lepidopteran insects have potent innate immunity to fight against the invading pathogens. As the initiation step, pattern recognition receptors (PRRs) recognize and bind microbial surface configurations known as pathogen-associated molecular patterns (PAMPs). Aftermath, they initiate both cellular and humoral immune responses, including phagocytosis, agglutination, nodulation, encapsulation, prophenoloxidase activation, and synthesis of antimicrobial peptides. In this review, we summarize the recent findings concerning PRRs in lepidoptaeran insects, mostly agriculture pests including Helicoverpa armigera, Plutella xylostella, and Spodoptera exigua. We mainly focus on the function and phylogeny of C-type lectins (CTLs), peptidoglycan recognition proteins (PGRPs), β-1,3-glucan recognition proteins (βGRPs), and galectins (GALEs). It enriches our understanding of the immune system of lepidopteran insects and provides directions in the future research.
Collapse
Affiliation(s)
- Zhe Lin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia-Lin Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan, 430079, China
| | - Yang Cheng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Jin-Xing Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, 311300, China.
| |
Collapse
|
27
|
Yadav C, Smith ML, Yack JE. Transcriptome analysis of a social caterpillar, Drepana arcuata: De novo assembly, functional annotation and developmental analysis. PLoS One 2020; 15:e0234903. [PMID: 32569288 PMCID: PMC7307738 DOI: 10.1371/journal.pone.0234903] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
The masked birch caterpillar, Drepana arcuata, provides an excellent opportunity to study mechanisms mediating developmental changes in social behaviour. Larvae transition from being social to solitary during the 3rd instar, concomitant with shifts in their use of acoustic communication. In this study we characterize the transcriptome of D. arcuata to initiate sociogenomic research of this lepidopteran insect. We assembled and annotated the combined larval transcriptome of “social” early and “solitary” late instars using next generation Illumina sequencing, and used this transcriptome to conduct differential gene expression analysis of the two behavioural phenotypes. A total of 211,012,294 reads generated by RNA sequencing were assembled into 231,348 transcripts and 116,079 unigenes for the functional annotation of the transcriptome. Expression analysis revealed 3300 transcripts that were differentially expressed between early and late instars, with a large proportion associated with development and metabolic processes. We independently validated differential expression patterns of selected transcripts using RT-qPCR. The expression profiles of social and solitary larvae revealed differentially expressed transcripts coding for gene products that have been previously reported to influence social behaviour in other insects (e.g. cGMP- and cAMP- dependent kinases, and bioamine receptors). This study provides the first transcriptomic resources for a lepidopteran species belonging to the superfamily Drepanoidea, and gives insight into genetic factors mediating grouping behaviour in insects.
Collapse
Affiliation(s)
- Chanchal Yadav
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Myron L. Smith
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Jayne E. Yack
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
- * E-mail:
| |
Collapse
|
28
|
Caterpillar Venom: A Health Hazard of the 21st Century. Biomedicines 2020; 8:biomedicines8060143. [PMID: 32486237 PMCID: PMC7345192 DOI: 10.3390/biomedicines8060143] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 12/24/2022] Open
Abstract
Caterpillar envenomation is a global health threat in the 21st century. Every direct or indirect contact with the urticating hairs of a caterpillar results in clinical manifestations ranging from local dermatitis symptoms to potentially life-threatening systemic effects. This is mainly due to the action of bioactive components in the venom that interfere with targets in the human body. The problem is that doctors are limited to relieve symptoms, since an effective treatment is still lacking. Only for Lonomia species an effective antivenom does exist. The health and economical damage are an underestimated problem and will be even more of a concern in the future. For some caterpillar species, the venom composition has been the subject of investigation, while for many others it remains unknown. Moreover, the targets involved in the pathophysiology are poorly understood. This review aims to give an overview of the knowledge we have today on the venom composition of different caterpillar species along with their pharmacological targets. Epidemiology, mode of action, clinical time course and treatments are also addressed. Finally, we briefly discuss the future perspectives that may open the doors for future research in the world of caterpillar toxins to find an adequate treatment.
Collapse
|
29
|
Zhang J, Cong Q, Shen J, Brockmann E, Grishin NV. Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae). Proc Biol Sci 2020; 286:20190609. [PMID: 31113329 DOI: 10.1098/rspb.2019.0609] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Biologists marvel at the powers of adaptive convergence, when distantly related animals look alike. While mimetic wing patterns of butterflies have fooled predators for millennia, entomologists inferred that mimics were distant relatives despite similar appearance. However, the obverse question has not been frequently asked. Who are the close relatives of mimetic butterflies and what are their features? As opposed to close convergence, divergence from a non-mimetic relative would also be extreme. When closely related animals look unalike, it is challenging to pair them. Genomic analysis promises to elucidate evolutionary relationships and shed light on molecular mechanisms of divergence. We chose the firetip skipper butterfly as a model due to its phenotypic diversity and abundance of mimicry. We sequenced and analysed whole genomes of nearly 120 representative species. Genomes partitioned this subfamily Pyrrhopyginae into five tribes (1 new), 23 genera and, additionally, 22 subgenera (10 new). The largest tribe Pyrrhopygini is divided into four subtribes (three new). Surprisingly, we found five cases where a uniquely patterned butterfly was formerly placed in a genus of its own and separately from its close relatives. In several cases, extreme and rapid phenotypic divergence involved not only wing patterns but also the structure of the male genitalia. The visually striking wing pattern difference between close relatives frequently involves disappearance or suffusion of spots and colour exchange between orange and blue. These differences (in particular, a transition between unspotted black and striped wings) happen recurrently on a short evolutionary time scale, and are therefore probably achieved by a small number of mutations.
Collapse
Affiliation(s)
- Jing Zhang
- 2 Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center , 5323 Harry Hines Blvd, Dallas, TX 75390-9050 , USA
| | - Qian Cong
- 2 Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center , 5323 Harry Hines Blvd, Dallas, TX 75390-9050 , USA
| | - Jinhui Shen
- 2 Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center , 5323 Harry Hines Blvd, Dallas, TX 75390-9050 , USA
| | | | - Nick V Grishin
- 1 Howard Hughes Medical Institute, University of Texas Southwestern Medical Center , 5323 Harry Hines Blvd, Dallas, TX 75390-9050 , USA.,2 Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center , 5323 Harry Hines Blvd, Dallas, TX 75390-9050 , USA
| |
Collapse
|
30
|
Li F, Zhao X, Li M, He K, Huang C, Zhou Y, Li Z, Walters JR. Insect genomes: progress and challenges. INSECT MOLECULAR BIOLOGY 2019; 28:739-758. [PMID: 31120160 DOI: 10.1111/imb.12599] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/22/2019] [Accepted: 05/14/2019] [Indexed: 05/24/2023]
Abstract
In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data-mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.
Collapse
Affiliation(s)
- F Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - X Zhao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - M Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - K He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - C Huang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Y Zhou
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Z Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - J R Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| |
Collapse
|
31
|
He P, Wang MM, Wang H, Ma YF, Yang S, Li SB, Li XG, Li S, Zhang F, Wang Q, Ran HN, Yang GQ, Dewer Y, He M. Genome-wide identification of chemosensory receptor genes in the small brown planthopper, Laodelphax striatellus. Genomics 2019; 112:2034-2040. [PMID: 31765823 DOI: 10.1016/j.ygeno.2019.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/17/2019] [Accepted: 11/21/2019] [Indexed: 12/29/2022]
Abstract
The small brown planthopper (SBPH), Laodelphax striatellus is one of the major insect pests of rice, but little is known about the molecular-level means by which it locates its hosts. SBPH host-seeking behavior heavily relies on chemosensory receptors (CRs). In this study, we utilized genome analysis of the SBPH to identify 169 CRs, including: 133 odorant receptors (ORs), 13 gustatory receptors (GRs) and 23 ionotropic receptors (IRs). The phylogenetic relationships of OR genes from three rice planthoppers and other insect species revealed that the odorant co-receptor (Orco) clade is the most conserved group. Among the candidate GRs, two sugar receptors and five fructose receptors have been identified but no carbon dioxide receptors investigated. Furthermore, we identified homologs of the three highly conserved IR co-receptors. The obtained results will provide us with precious information needed to better understand the interaction between insect pests and crop plants required for effective crop protection.
Collapse
Affiliation(s)
- Peng He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China.
| | - Mei-Mei Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China
| | - Hong Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China
| | - Yu-Feng Ma
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China
| | - Shao-Bing Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China
| | - Xuan-Gang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China
| | - Shuo Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Fan Zhang
- Key Laboratory of Animal Resistance Research, College of Life Science, Shandong Normal University, 88 East Wenhua Road, Jinan 250014, PR China
| | - Qing Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China
| | - Hui-Nu Ran
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China
| | - Gui-Qing Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China
| | - Youssef Dewer
- Bioassay Research Department, Central Agricultural Pesticide Laboratory, Sabahia Plant Protection Research Station, Agricultural Research Center, Alexandria 21616, Egypt
| | - Ming He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, PR China.
| |
Collapse
|
32
|
Gypsy moth genome provides insights into flight capability and virus-host interactions. Proc Natl Acad Sci U S A 2019; 116:1669-1678. [PMID: 30642971 DOI: 10.1073/pnas.1818283116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Since its accidental introduction to Massachusetts in the late 1800s, the European gypsy moth (EGM; Lymantria dispar dispar) has become a major defoliator in North American forests. However, in part because females are flightless, the spread of the EGM across the United States and Canada has been relatively slow over the past 150 years. In contrast, females of the Asian gypsy moth (AGM; Lymantria dispar asiatica) subspecies have fully developed wings and can fly, thereby posing a serious economic threat if populations are established in North America. To explore the genetic determinants of these phenotypic differences, we sequenced and annotated a draft genome of L. dispar and used it to identify genetic variation between EGM and AGM populations. The 865-Mb gypsy moth genome is the largest Lepidoptera genome sequenced to date and encodes ∼13,300 proteins. Gene ontology analyses of EGM and AGM samples revealed divergence between these populations in genes enriched for several gene ontology categories related to muscle adaptation, chemosensory communication, detoxification of food plant foliage, and immunity. These genetic differences likely contribute to variations in flight ability, chemical sensing, and pathogen interactions among EGM and AGM populations. Finally, we use our new genomic and transcriptomic tools to provide insights into genome-wide gene-expression changes of the gypsy moth after viral infection. Characterizing the immunological response of gypsy moths to virus infection may aid in the improvement of virus-based bioinsecticides currently used to control larval populations.
Collapse
|
33
|
Kawahara AY, Breinholt JW, Espeland M, Storer C, Plotkin D, Dexter KM, Toussaint EFA, St Laurent RA, Brehm G, Vargas S, Forero D, Pierce NE, Lohman DJ. Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set. Mol Phylogenet Evol 2018; 127:600-605. [PMID: 29902572 DOI: 10.1016/j.ympev.2018.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/25/2018] [Accepted: 06/02/2018] [Indexed: 11/28/2022]
Abstract
The Neotropical moth-like butterflies (Hedylidae) are perhaps the most unusual butterfly family. In addition to being species-poor, this family is predominantly nocturnal and has anti-bat ultrasound hearing organs. Evolutionary relationships among the 36 described species are largely unexplored. A new, target capture, anchored hybrid enrichment probe set ('BUTTERFLY2.0') was developed to infer relationships of hedylids and some of their butterfly relatives. The probe set includes 13 genes that have historically been used in butterfly phylogenetics. Our dataset comprised of up to 10,898 aligned base pairs from 22 hedylid species and 19 outgroups. Eleven of the thirteen loci were successfully captured from all samples, and the remaining loci were captured from ≥94% of samples. The inferred phylogeny was consistent with recent molecular studies by placing Hedylidae sister to Hesperiidae, and the tree had robust support for 80% of nodes. Our results are also consistent with morphological studies, with Macrosoma tipulata as the sister species to all remaining hedylids, followed by M. semiermis sister to the remaining species in the genus. We tested the hypothesis that nocturnality evolved once from diurnality in Hedylidae, and demonstrate that the ancestral condition was likely diurnal, with a shift to nocturnality early in the diversification of this family. The BUTTERFLY2.0 probe set includes standard butterfly phylogenetics markers, captures sequences from decades-old museum specimens, and is a cost-effective technique to infer phylogenetic relationships of the butterfly tree of life.
Collapse
Affiliation(s)
- Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; RAPiD Genomics, 747 SW 2nd Avenue, IMB#14, Gainesville, FL 32601, USA
| | - Marianne Espeland
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Arthropoda Department, Zoological Research Museum Alexander Koenig, Adenauer Allee 160, Bonn 53113, Germany
| | - Caroline Storer
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - David Plotkin
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA
| | - Kelly M Dexter
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Ryan A St Laurent
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Gunnar Brehm
- Institute of Zoology and Evolutionary Biology with Phyletic Museum, Friedrich-Schiller-University Jena, Jena 07743, Germany
| | - Sergio Vargas
- Laboratorio de Entomología, Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Dimitri Forero
- Laboratorio de Entomología, Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - David J Lohman
- Biology Department, City College of New York, New York, NY 10031, USA; Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA; Entomology Section, National Museum of the Philippines, Manila 1000, Philippines
| |
Collapse
|
34
|
The silkrose of Bombyx mori effectively prevents vibriosis in penaeid prawns via the activation of innate immunity. Sci Rep 2018; 8:8836. [PMID: 29892000 PMCID: PMC5995915 DOI: 10.1038/s41598-018-27241-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022] Open
Abstract
We previously identified novel bioactive polysaccharides from Bactrocera cucurbitae and Antheraea yamamai that activate innate immunity in RAW264 murine macrophages. However, in terms of potential applications in the cultivation of prawns, there were problems with the availability of these insects. However, we have now identified a polysaccharide from Bombyx mori that activates innate immunity in RAW264 cells and penaeid prawns. This purified polysaccharide, termed silkrose of B. mori (silkrose-BM), has a molecular weight of 1,150,000 and produces a single symmetrical peak on HPLC. Eight of nine constitutive monosaccharides of silkrose-BM are concomitant with dipterose of B. cucurbitae (dipterose-BC) and silkrose of A. yamamai (silkrose-AY). The major differences are found in the molar ratios of the monosaccharides. Silkrose-BM is approximately 500-fold less potent than silkrose-AY (EC50: 2.5 and 0.0043 μg/mL, respectively) in a nitrite oxide (NO) production assay using RAW264 cells. However, the maximum NO production for silkrose-BM and AY were comparable and higher than that of the lipopolysaccharide of Escherichia coli. The survival of penaeid prawns (Litopenaeus vannamei and Marsupenaeus japonicus) after infection with Vibrio penaecida was significantly improved by both dietary silkrose-BM and B. mori pupae. This suggests that silkrose-BM effectively prevents vibriosis in penaeid prawns via the activation of innate immunity.
Collapse
|
35
|
Duplouy A, Hornett EA. Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts. PeerJ 2018; 6:e4629. [PMID: 29761037 PMCID: PMC5947162 DOI: 10.7717/peerj.4629] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 12/18/2022] Open
Abstract
The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host’s body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse. Furthermore, heritable endosymbionts have been repeatedly demonstrated to play an integral role in many aspects of host biology, particularly host reproduction. Here, we review the major findings of research of heritable microbial endosymbionts of butterflies and moths. We promote the Lepidoptera as important models in the study of reproductive manipulations employed by heritable endosymbionts, with the mechanisms underlying male-killing and feminisation currently being elucidated in moths and butterflies. We also reveal that the vast majority of research undertaken of Lepidopteran endosymbionts concerns Wolbachia. While this highly prevalent bacterium is undoubtedly important, studies should move towards investigating the presence of other, and interacting endosymbionts, and we discuss the merits of examining the microbiome of Lepidoptera to this end. We finally consider the importance of understanding the influence of endosymbionts under global environmental change and when planning conservation management of endangered Lepidoptera species.
Collapse
Affiliation(s)
- Anne Duplouy
- Organismal and Evolutionary Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Emily A Hornett
- Department of Zoology, University of Cambridge, Cambridge, UK
| |
Collapse
|
36
|
Barth MB, Buchwalder K, Kawahara AY, Zhou X, Liu S, Krezdorn N, Rotter B, Horres R, Hundsdoerfer AK. Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes. Front Zool 2018; 15:20. [PMID: 29743927 PMCID: PMC5930835 DOI: 10.1186/s12983-018-0252-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/31/2018] [Indexed: 11/10/2022] Open
Abstract
Background The European spurge hawkmoth, Hyles euphorbiae (Lepidoptera, Sphingidae), has been intensively studied as a model organism for insect chemical ecology, cold hardiness and evolution of species delineation. To understand species isolation mechanisms at a molecular level, this study aims at determining genetic factors underlying two adaptive ecological trait candidates, phorbol ester (TPA) detoxification and seasonal cold acclimation. Method A draft transcriptome of H. euphorbiae was generated using Illumina sequencing, providing the first genomic resource for the hawkmoth subfamily Macroglossinae. RNA expression levels in tissues of experimental TPA feeding larvae and cooled pupae was compared to levels in control larvae and pupae using 26 bp RNA sequence tag libraries (DeepSuperSAGE). Differential gene expression was assessed by homology searches of the tags in the transcriptome. Results In total, 389 and 605 differentially expressed transcripts for detoxification and cold hardiness, respectively, could be identified and annotated with proteins. The majority (22 of 28) of differentially expressed detox transcripts of the four 'drug metabolism' enzyme groups (cytochrome P450 (CYP), carboxylesterases (CES), glutathione S-transferases (GST) and lipases) are up-regulated. Triacylglycerol lipase was significantly over proportionally annotated among up-regulated detox transcripts. We record several up-regulated lipases, GSTe2, two CESs, CYP9A21, CYP6BD6 and CYP9A17 as candidate genes for further H. euphorbiae TPA detoxification analyses. Differential gene expression of the cold acclimation treatment is marked by metabolic depression with enriched Gene Ontology terms among down-regulated transcripts almost exclusively comprising metabolism, aerobic respiration and dissimilative functions. Down-regulated transcripts include energy expensive respiratory proteins like NADH dehydrogenase, cytochrome oxidase and ATP synthase. Gene expression patterns show shifts in carbohydrate metabolism towards cryoprotectant production. The Glycolysis enzymes, G1Pase, A1e, Gpi and an Akr isoform are up-regulated. Glycerol, an osmolyte which lowers the body liquid supercooling point, appears to be the predominant polyol cryoprotectant in H. euphorbiae diapause pupae. Several protein candidates involved in glucose, glycerol, myo-inositol and potentially sorbitol and trehalose synthesis were identified. Conclusions A majority of differently expressed transcripts unique for either detoxification or cold hardiness indicates highly specialized functional adaptation which may have evolved from general cell metabolism and stress response.The transcriptome and extracted candidate biomarkers provide a basis for further gene expression studies of physiological processes and adaptive traits in H. euphorbiae.
Collapse
Affiliation(s)
- M Benjamin Barth
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Koenigsbruecker Landstrasse 159, D-01109 Dresden, Germany
| | - Katja Buchwalder
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Koenigsbruecker Landstrasse 159, D-01109 Dresden, Germany
| | - Akito Y Kawahara
- 2Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
| | - Xin Zhou
- 3Department of Entomology, China Agricultural University, Bejing, 100193 China
| | - Shanlin Liu
- 3Department of Entomology, China Agricultural University, Bejing, 100193 China.,4China National Gene Bank, Beijing Genomics Institute, Shenzhen, 518083 China
| | - Nicolas Krezdorn
- 5GenXPro GmbH, Altenhöferallee 3, D-60438 Frankfurt am Main, Germany
| | - Björn Rotter
- 5GenXPro GmbH, Altenhöferallee 3, D-60438 Frankfurt am Main, Germany
| | - Ralf Horres
- 5GenXPro GmbH, Altenhöferallee 3, D-60438 Frankfurt am Main, Germany
| | - Anna K Hundsdoerfer
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Koenigsbruecker Landstrasse 159, D-01109 Dresden, Germany
| |
Collapse
|