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Shin S, Baker AJ, Enk J, McKenna DD, Foquet B, Vandergast AG, Weissman DB, Song H. Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales. Sci Rep 2024; 14:21377. [PMID: 39271747 PMCID: PMC11399444 DOI: 10.1038/s41598-024-72622-6] [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: 02/01/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024] Open
Abstract
Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.
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Affiliation(s)
- Seunggwan Shin
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Austin J Baker
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
- Entomology Department, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Duane D McKenna
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Bert Foquet
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Amy G Vandergast
- San Diego Field Station, Western Ecological Research Center, U.S. Geological Survey, San Diego, CA, USA
| | - David B Weissman
- Department of Entomology, California Academy of Sciences, Golden Gate Park, San Francisco, CA, USA
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX, USA.
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2
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Sylvester T, Hoover Z, Hjelmen CE, Jonika MM, Blackmon LT, Alfieri JM, Johnston JS, Chien S, Esfandani T, Blackmon H. A reference quality genome assembly for the jewel scarab Chrysina gloriosa. G3 (BETHESDA, MD.) 2024; 14:jkae084. [PMID: 38630623 PMCID: PMC11152064 DOI: 10.1093/g3journal/jkae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 01/23/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
The jewel scarab Chrysina gloriosa is one of the most charismatic beetles in the United States and is found from the mountains of West Texas to the Southeastern Arizona sky islands. This species is highly sought by professional and amateur collectors worldwide due to its gleaming metallic coloration. However, the impact of the large-scale collection of this beetle on its populations is unknown, and there is a limited amount of genetic information available to make informed decisions about its conservation. As a first step, we present the genome of C. gloriosa, which we reconstructed using a single female specimen sampled from our ongoing effort to document population connectivity and the demographic history of this beetle. Using a combination of long-read sequencing and Omni-C data, we reconstructed the C. gloriosa genome at a near-chromosome level. Our genome assembly consisted of 454 scaffolds spanning 642 MB, with the 10 largest scaffolds capturing 98% of the genome. The scaffold N50 was 72 MB, and the BUSCO score was 95.5%. This genome assembly will be an essential tool to accelerate understanding C. gloriosa biology and help make informed decisions for the conservation of Chrysina and other species with similar distributions in this region. This genome assembly will further serve as a community resource for comparative genomic analysis.
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Affiliation(s)
- Terrence Sylvester
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Department of Biology, University of Memphis, Memphis, TN 38111, USA
| | - Zachary Hoover
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Carl E Hjelmen
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Department of Biology, Utah Valley University, Orem, UT 84058, USA
| | - Michelle M Jonika
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, USA
| | - Leslie T Blackmon
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - James M Alfieri
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Sean Chien
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Tahmineh Esfandani
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA
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3
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Le MH, Morgan B, Lu MY, Moctezuma V, Burgos O, Huang JP. The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests. Mol Ecol Resour 2024; 24:e13908. [PMID: 38063363 DOI: 10.1111/1755-0998.13908] [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: 09/24/2022] [Revised: 01/14/2023] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape and body colouration. The four Hercules beetle genomes were assembled to 11 pseudo-chromosomes, where the three genomes assembled using Nanopore data (Dynastes grantii, D. hyllus and D. tityus) were mapped to the genome assembled using PacBio + Hi-C data (D. maya). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the D. maya assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologues of nine and three candidate-gene families that may be associated with the evolution of horn structure and body colouration respectively. Structural variations in Scr and Ebony2 were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts.
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Affiliation(s)
- My-Hanh Le
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Brett Morgan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Mei-Yeh Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Victor Moctezuma
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, Mexico
| | - Oscar Burgos
- Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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4
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Bush J, Webster C, Wegrzyn J, Simon C, Wilcox E, Khan R, Weisz D, Dudchenko O, Aiden EL, Frandsen P. Chromosome-Level Genome Assembly and Annotation of a Periodical Cicada Species: Magicicada septendecula. Genome Biol Evol 2024; 16:evae001. [PMID: 38190231 PMCID: PMC10799293 DOI: 10.1093/gbe/evae001] [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: 11/03/2023] [Revised: 12/16/2023] [Accepted: 12/28/2023] [Indexed: 01/09/2024] Open
Abstract
We present a high-quality assembly and annotation of the periodical cicada species, Magicicada septendecula (Hemiptera: Auchenorrhyncha: Cicadidae). Periodical cicadas have a significant ecological impact, serving as a food source for many mammals, reptiles, and birds. Magicicada are well known for their massive emergences of 1 to 3 species that appear in different locations in the eastern United States nearly every year. These year classes ("broods") emerge dependably every 13 or 17 yr in a given location. Recently, it has become clear that 4-yr early or late emergences of a sizeable portion of a population are an important part of the history of brood formation; however, the biological mechanisms by which they track the passage of time remain a mystery. Using PacBio HiFi reads in conjunction with Hi-C proximity ligation data, we have assembled and annotated the first whole genome for a periodical cicada, an important resource for future phylogenetic and comparative genomic analysis. This also represents the first quality genome assembly and annotation for the Hemipteran superfamily Cicadoidea. With a scaffold N50 of 518.9 Mb and a complete BUSCO score of 96.7%, we are confident that this assembly will serve as a vital resource toward uncovering the genomic basis of periodical cicadas' long, synchronized life cycles and will provide a robust framework for further investigations into these insects.
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Affiliation(s)
- Jonas Bush
- Huck Life Sciences Institute, The Pennsylvania State University, State College, PA, USA
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Cynthia Webster
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Edward Wilcox
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
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5
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Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024; 2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.
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Affiliation(s)
- Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Frankfurt, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Ann Kathrin Huylmans
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Alun R C Jones
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Eckart Stolle
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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6
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Shin NR, Okamura Y, Kirsch R, Pauchet Y. Genome sequencing provides insights into the evolution of gene families encoding plant cell wall-degrading enzymes in longhorned beetles. INSECT MOLECULAR BIOLOGY 2023; 32:469-483. [PMID: 37119017 DOI: 10.1111/imb.12844] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 04/17/2023] [Indexed: 06/19/2023]
Abstract
With more than 36,000 species, the longhorned beetles (family Cerambycidae) are a mega-diverse lineage of mostly xylophagous insects, all of which are represented by the sole sequenced genome of the Asian longhorned beetle (Anoplophora glabripennis; Lamiinae). Their successful radiation has been linked to their ability to degrade plant cell wall components using a range of so-called plant cell wall-degrading enzymes (PCWDEs). Our previous analysis of larval gut transcriptomes demonstrated that cerambycid beetles horizontally acquired genes encoding PCWDEs from various microbial donors; these genes evolved through multiple duplication events to form gene families. To gain further insights into the evolution of these gene families during the Cerambycidae radiation, we assembled draft genomes for four beetle species belonging to three subfamilies using long-read nanopore sequencing. All the PCWDE-encoding genes we annotated from the corresponding larval gut transcriptomes were present in these draft genomes. We confirmed that the newly discovered horizontally acquired glycoside hydrolase family 7 (GH7), subfamily 26 of GH43 (GH43_26), and GH53 (all of which are absent from the A. glabripennis genome) were indeed encoded by these beetles' genome. Most of the PCWDE-encoding genes of bacterial origin gained introns after their transfer into the beetle genome. Altogether, we show that draft genome assemblies generated from nanopore long-reads offer meaningful information to the study of the evolution of gene families in insects. We anticipate that our data will support studies aiming to better understand the biology of the Cerambycidae and other beetles in general.
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Affiliation(s)
- Na Ra Shin
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yu Okamura
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
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7
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Hundsdoerfer AK, Schell T, Patzold F, Wright CJ, Yoshido A, Marec F, Daneck H, Winkler S, Greve C, Podsiadlowski L, Hiller M, Pippel M. High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae). BMC Genomics 2023; 24:443. [PMID: 37550607 PMCID: PMC10405479 DOI: 10.1186/s12864-023-09506-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/05/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Morphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics. RESULTS The genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function. CONCLUSIONS Our two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae).
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Affiliation(s)
- Anna K Hundsdoerfer
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany.
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Franziska Patzold
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany
| | | | - Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Hana Daneck
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - Carola Greve
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
| | - Michael Hiller
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, 751 23, Sweden
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8
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Godfrey RK, Britton SE, Mishra S, Goldberg JK, Kawahara AY. A high-quality, long-read genome assembly of the whitelined sphinx moth (Lepidoptera: Sphingidae: Hyles lineata) shows highly conserved melanin synthesis pathway genes. G3 (BETHESDA, MD.) 2023; 13:jkad090. [PMID: 37119801 PMCID: PMC10234378 DOI: 10.1093/g3journal/jkad090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 03/21/2023] [Accepted: 04/14/2023] [Indexed: 05/01/2023]
Abstract
The sphinx moth genus Hyles comprises 29 described species inhabiting all continents except Antarctica. The genus diverged relatively recently (40-25 MYA), arising in the Americas and rapidly establishing a cosmopolitan distribution. The whitelined sphinx moth, Hyles lineata, represents the oldest extant lineage of this group and is one of the most widespread and abundant sphinx moths in North America. Hyles lineata exhibits the large body size and adept flight control characteristic of the sphinx moth family (Sphingidae), but it is unique in displaying extreme larval color variation and broad host plant use. These traits, in combination with its broad distribution and high relative abundance within its range, have made H. lineata a model organism for studying phenotypic plasticity, plant-herbivore interactions, physiological ecology, and flight control. Despite being one of the most well-studied sphinx moths, little data exist on genetic variation or regulation of gene expression. Here, we report a high-quality genome showing high contiguity (N50 of 14.2 Mb) and completeness (98.2% of Lepidoptera BUSCO genes), an important first characterization to facilitate such studies. We also annotate the core melanin synthesis pathway genes and confirm that they have high sequence conservation with other moths and are most similar to those of another, well-characterized sphinx moth, the tobacco hornworm (Manduca sexta).
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Affiliation(s)
- R Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Rd, Gainesville, FL 32611, USA
| | - Sarah E Britton
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St, Tucson, AZ 85721, USA
| | - Shova Mishra
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Dr., Gainesville, FL 32608, USA
| | - Jay K Goldberg
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St, Tucson, AZ 85721, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Rd, Gainesville, FL 32611, USA
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9
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Zhang Z, Pei P, Zhang M, Li F, Tang G. Chromosome-level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure. PEST MANAGEMENT SCIENCE 2023; 79:1467-1482. [PMID: 36502364 DOI: 10.1002/ps.7319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/26/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Dastarcus helophoroides is an important natural enemy of cerambycids, and is wildly used in biological control of pests. Nevertheless, the absence of complete genomic information limits the investigation of the underlying molecular mechanisms. Here, a chromosome-level of Dastarcus helophoroides genome is assembled using a combination strategy of Illumina, PacBio, 10x™ Genomics, and Hi-C. RESULTS The final assembly is 609.09 Mb with contig N50, scaffold N50 and GC content of 5.46 Mb, 42.56 Mb and 31.50%, respectively, and 95.25% of the contigs anchor into 13 chromosomes. In total 14 890 protein-coding genes and 65.37% repeat sequences are predicted in the assembly genome. The phylogenetic analysis of single-copy gene families shared among 20 insect species indicates that Dastarcus helophoroides is placed as the sister species to clade (Nitidulidae+Curculionoidea+Chrysomeloidea) + Tenebrionoidea, and diverges from the related species ~242.9 Mya. In total 36 expanded gene families are identified in Dastarcus helophoroides genome, and are functionally related to drug metabolism and metabolism of xenobiotics by cytochrome P450. Some members of CYP4 Clade and CYP6 Clade are up-regulated in Dastarcus helophoroides adults upon insecticide exposure, of which expressions of DhCYP4Q, DhCYP6A14X1 and DhCYP4C1 are significantly up-regulated. The silencing of the three genes leads to adults more sensitive to insecticide and increased knocked-down rate, which may indicate their critical roles in stress resistance and detoxication. CONCLUSION Our study systematically integrated the chromosome-level genome, transcriptome and gene expression of Dastarcus helophoroides, which will provide valuable resources for understanding mechanisms of pesticide metabolism, growth and development, and utilization of the natural enemy in integrated control. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Zhengqing Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Pei Pei
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Feifei Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
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10
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Benites P, Zaldívar-Riverón A, Meza-Lázaro RN, Samacá-Sáenz E, Gutiérrez-Rodríguez J, Hernández-López A. Multiple introgression events during the diversification history of the edible mexican grasshopper genus sphenarium (orthoptera: pyrgomorphidae). Mol Phylogenet Evol 2023; 183:107774. [PMID: 36972795 DOI: 10.1016/j.ympev.2023.107774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Speciation with gene flow often leads to ambiguous phylogenetic reconstructions, reticulate patterns of relatedness and conflicting nuclear versus mitochondrial (mt) lineages. Here we employed a fragment of the COI mtDNA gene and nuclear genome-wide data (3RAD) to assess the diversification history of Sphenarium, an orthopteran genus of great economic importance in Mexico that is presumed to have experienced hybridisation events in some of its species. We carried out separate phylogenetic analyses to evaluate the existence of mito-nuclear discordance in the species relationships, and also assessed the genomic diversity and population genomic structure and investigated the existence of interspecific introgression and species limits of the taxa involved based on the nuclear dataset. The species delineation analyses discriminated all the currently recognised species, but also supported the existence of four undescribed species. The mt and nuclear topologies had four discordant species relationships that can be explained by mt introgression, where the mt haplotypes of S. purpurascens appear to have replaced those of S. purpurascens A and B, S. variabile and S. zapotecum. Moreover, our analyses supported the existence of nuclear introgression events between four species pairs that are distributed in the Sierra Madre del Sur province in southeast Mexico, with three of them occurring in the Tehuantepec Isthmus region. Our study highlights the relevance of genomic data to address the relative importance of allopatric isolation versus gene flow in speciation.
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Affiliation(s)
- Pilar Benites
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Rubi N Meza-Lázaro
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Ernesto Samacá-Sáenz
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México; Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Coyoacán, 04510 Ciudad de México, México
| | | | - Antonio Hernández-López
- Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Guanajuato, México
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11
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Coates BS, Walden KKO, Lata D, Vellichirammal NN, Mitchell RF, Andersson MN, McKay R, Lorenzen MD, Grubbs N, Wang YH, Han J, Xuan JL, Willadsen P, Wang H, French BW, Bansal R, Sedky S, Souza D, Bunn D, Meinke LJ, Miller NJ, Siegfried BD, Sappington TW, Robertson HM. A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect. BMC Genomics 2023; 24:19. [PMID: 36639634 PMCID: PMC9840275 DOI: 10.1186/s12864-022-08990-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/04/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Adaptations by arthropod pests to host plant defenses of crops determine their impacts on agricultural production. The larval host range of western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is restricted to maize and a few grasses. Resistance of D. v. virgifera to crop rotation practices and multiple insecticides contributes to its status as the most damaging pest of cultivated maize in North America and Europe. The extent to which adaptations by this pest contributes to host plant specialization remains unknown. RESULTS A 2.42 Gb draft D. v. virgifera genome, Dvir_v2.0, was assembled from short shotgun reads and scaffolded using long-insert mate-pair, transcriptome and linked read data. K-mer analysis predicted a repeat content of ≥ 61.5%. Ortholog assignments for Dvir_2.0 RefSeq models predict a greater number of species-specific gene duplications, including expansions in ATP binding cassette transporter and chemosensory gene families, than in other Coleoptera. A majority of annotated D. v. virgifera cytochrome P450s belong to CYP4, 6, and 9 clades. A total of 5,404 transcripts were differentially-expressed between D. v. virgifera larvae fed maize roots compared to alternative host (Miscanthus), a marginal host (Panicum virgatum), a poor host (Sorghum bicolor) and starvation treatments; Among differentially-expressed transcripts, 1,908 were shared across treatments and the least number were between Miscanthus compared to maize. Differentially-expressed transcripts were enriched for putative spliceosome, proteosome, and intracellular transport functions. General stress pathway functions were unique and enriched among up-regulated transcripts in marginal host, poor host, and starvation responses compared to responses on primary (maize) and alternate hosts. CONCLUSIONS Manual annotation of D. v. virgifera Dvir_2.0 RefSeq models predicted expansion of paralogs with gene families putatively involved in insecticide resistance and chemosensory perception. Our study also suggests that adaptations of D. v. virgifera larvae to feeding on an alternate host plant invoke fewer transcriptional changes compared to marginal or poor hosts. The shared up-regulation of stress response pathways between marginal host and poor host, and starvation treatments may reflect nutrient deprivation. This study provides insight into transcriptomic responses of larval feeding on different host plants and resources for genomic research on this economically significant pest of maize.
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Affiliation(s)
- Brad S. Coates
- grid.508983.fCorn Insects & Crop Genetics Research Unit, USDA-ARS, 2310 Pammel Dr, 532 Science II, Iowa State University, Ames, IA 50011 USA
| | - Kimberly K. O. Walden
- grid.35403.310000 0004 1936 9991Roy J. Carver Biotechnology Center, University of Illinois at Champaign-Urbana, Urbana, IL USA
| | - Dimpal Lata
- grid.62813.3e0000 0004 1936 7806Department of Biology, Illinois Institute of Technology, Chicago, IL USA
| | | | - Robert F. Mitchell
- grid.267474.40000 0001 0674 4543University of Wisconsin Oshkosh, Oshkosh, WI USA
| | - Martin N. Andersson
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
| | - Rachel McKay
- grid.267474.40000 0001 0674 4543University of Wisconsin Oshkosh, Oshkosh, WI USA
| | - Marcé D. Lorenzen
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Nathaniel Grubbs
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Yu-Hui Wang
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Jinlong Han
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Jing Li Xuan
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Peter Willadsen
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Huichun Wang
- grid.24434.350000 0004 1937 0060Department of Entomology, University of Nebraska, Lincoln, NE USA
| | - B. Wade French
- grid.508981.dIntegrated Crop Systems Research Unit, USDA-ARS, Brookings, SD USA
| | - Raman Bansal
- grid.512850.bUSDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA USA
| | - Sammy Sedky
- grid.512850.bUSDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA USA
| | - Dariane Souza
- grid.15276.370000 0004 1936 8091Department of Entomology, University of Florida, Gainesville, FL USA
| | - Dakota Bunn
- grid.62813.3e0000 0004 1936 7806Department of Biology, Illinois Institute of Technology, Chicago, IL USA
| | - Lance J. Meinke
- grid.24434.350000 0004 1937 0060Department of Entomology, University of Nebraska, Lincoln, NE USA
| | - Nicholas J. Miller
- grid.62813.3e0000 0004 1936 7806Department of Biology, Illinois Institute of Technology, Chicago, IL USA
| | - Blair D. Siegfried
- grid.15276.370000 0004 1936 8091Department of Entomology, University of Florida, Gainesville, FL USA
| | - Thomas W. Sappington
- grid.508983.fCorn Insects & Crop Genetics Research Unit, USDA-ARS, 2310 Pammel Dr, 532 Science II, Iowa State University, Ames, IA 50011 USA
| | - Hugh M. Robertson
- grid.35403.310000 0004 1936 9991Department of Entomology, University of Illinois at Champaign-Urbana, Urbana, IL USA
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12
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Trabuco Amaral D, Mitani Y, Aparecida Silva Bonatelli I, Cerri R, Ohmiya Y, Viviani V. Genome analysis of Phrixothrix hirtus (Phengodidae) railroad worm shows the expansion of odorant-binding gene families and positive selection on morphogenesis and sex determination genes. Gene X 2022; 850:146917. [PMID: 36174905 DOI: 10.1016/j.gene.2022.146917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 10/14/2022] Open
Abstract
Among bioluminescent beetles of the Elateroidea superfamily, Phengodidae is the third largest family, with 244 bioluminescent species distributed only in the Americas, but is still the least studied from the phylogenetic and evolutionary points of view. The railroad worm Phrixothrix hirtus is an essential biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing the first source of genomic information and a framework for comparative analyses of the bioluminescent system in Elateroidea. This is the largest genome described in the Elateroidea superfamily, with an estimated size of ∼3.4 Gb, displaying 32 % GC content, and 67 % transposable elements. Comparative genomic analyses showed a positive selection of genes and gene family expansion events of growths and morphogenesis gene products, which could be associated with the atypical anatomical development and morphogenesis found in paedomorphic females and underdeveloped males. We also observed gene family expansion among distinct odorant-binding receptors, which could be associated with the pheromone communication system typical of these beetles, and retrotransposable elements. Common genes putatively regulating bioluminescence production and control, including two luciferase genes corresponding to lateral lanterns green-emitting and head lanterns red-emitting luciferases with 7 exons and 6 introns, and genes potentially involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea.
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Affiliation(s)
- Danilo Trabuco Amaral
- Programa de Pós-Graduação em Biotecnociência, Centro de Ciências Naturais e Humanas. Universidade Federal do ABC (UFABC), Santo André, Brazil
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | | | - Ricardo Cerri
- Department of Computational Science, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, AIST, Ikeda-Osaka, Japan; Osaka Institute of Technology, OIT, Osaka, Japan
| | - Vadim Viviani
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, Brazil; Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Sorocaba, Brazil.
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13
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Abbasi-Karin S, Karimzadeh G, Mohammadi-Bazargani M. Interspecific Chromosomal and Genome Size Variations in <i>In Vitro</i> Propagated Willow Herb (<i>Epilobium</i> spp.) Medicinal Plant. CYTOLOGIA 2022. [DOI: 10.1508/cytologia.87.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Shima Abbasi-Karin
- Department of Plant Genetics and Breeding, College of Agriculture, Tarbiat Modares University
| | - Ghasem Karimzadeh
- Department of Plant Genetics and Breeding, College of Agriculture, Tarbiat Modares University
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14
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Lata D, Coates BS, Walden KKO, Robertson HM, Miller NJ. Genome size evolution in the beetle genus Diabrotica. G3 (BETHESDA, MD.) 2022; 12:jkac052. [PMID: 35234880 PMCID: PMC8982398 DOI: 10.1093/g3journal/jkac052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/22/2022] [Indexed: 11/20/2022]
Abstract
Diabrocite corn rootworms are one of the most economically significant pests of maize in the United States and Europe and an emerging model for insect-plant interactions. Genome sizes of several species in the genus Diabrotica were estimated using flow cytometry along with that of Acalymma vittatum as an outgroup. Genome sizes ranged between 1.56 and 1.64 gigabase pairs and between 2.26 and 2.59 Gb, respectively, for the Diabrotica subgroups fucata and virgifera; the Acalymma vittatum genome size was around 1.65 Gb. This result indicated that a substantial increase in genome size occurred in the ancestor of the virgifera group. Further analysis of the fucata group and the virgifera group genome sequencing reads indicated that the genome size difference between the Diabrotica subgroups could be attributed to a higher content of transposable elements, mostly miniature inverted-transposable elements and gypsy-like long terminal repeat retroelements.
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Affiliation(s)
- Dimpal Lata
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Nicholas J Miller
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
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15
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Monti M, Redi C, Capanna E. Genome size evaluations in cockroaches: new entries. Eur J Histochem 2022; 66. [PMID: 35332752 PMCID: PMC8992379 DOI: 10.4081/ejh.2022.3400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/21/2022] [Indexed: 11/23/2022] Open
Abstract
In this paper, we report genome size (GS) values for nine cockroaches (order Blattodea, families Blattidae, Blaberidae and Ectobiidae, ex Blattelidae), three of which are original additions to the ten already present in the GS database: the death’s head roach (Blaberus craniifer), the Surinam cockroach (Pycnoscelus surinamensis) and the Madeira cockroach (Leucophaea maderae). Regarding the American cockroach (Periplaneta americana), the GS database contains two contrasting values (2.72 vs 3.41 pg); likely, the 2.72 pg value is the correct one as it is strikingly similar to our sperm DNA content evaluation (2.80 ± 0.11 pg). Also, we suggest halving the published GS of the Argentine cockroach Blaptica dubia and the spotted cockroach (the gray cockroach) Nauphoeta cinerea discussing i) the occurrence of a correlation between increasing 2n chromosome number and GS within the order Blattodea; and ii) the possible occurrence of a polyploidization phenomenon doubling a basic GS of 0.58 pg of some termite families (superfamily Blattoidea, epifamily Termitoidae).
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Affiliation(s)
- Manuela Monti
- Department of Public Health, Experimental and Forensic Medicine, Histology and Embryology Unit, University of Pavia.
| | - CarloAlberto Redi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia.
| | - Ernesto Capanna
- Department of Animal Biology "Agostino Bassi", "La Sapienza" University of Rome.
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16
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Bailey E, Field L, Rawlings C, King R, Mohareb F, Pak KH, Hughes D, Williamson M, Ganko E, Buer B, Nauen R. A near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolution. BMC Genomics 2022; 23:198. [PMID: 35279098 PMCID: PMC8917705 DOI: 10.1186/s12864-022-08436-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/11/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Sphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of hemipteran crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs). METHODS AND FINDINGS In this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families across subfamilies between S. rueppellii and some hemipteran crop pests. Additionally, S. rueppellii had larger numbers of detoxification genes than other pollinator species. CONCLUSION AND SIGNIFICANCE This assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.
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Affiliation(s)
- Emma Bailey
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK.
- The Bioinformatics Group, Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK.
| | - Linda Field
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Christopher Rawlings
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Rob King
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Fady Mohareb
- The Bioinformatics Group, Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
| | - Keywan-Hassani Pak
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - David Hughes
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Martin Williamson
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Eric Ganko
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, USA
| | - Benjamin Buer
- Bayer AG, Crop Science Division, R&D, Monheim, Germany
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Monheim, Germany
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17
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Heckenhauer J, Frandsen PB, Sproul JS, Li Z, Paule J, Larracuente AM, Maughan PJ, Barker MS, Schneider JV, Stewart RJ, Pauls SU. Genome size evolution in the diverse insect order Trichoptera. Gigascience 2022; 11:6537159. [PMID: 35217860 PMCID: PMC8881205 DOI: 10.1093/gigascience/giac011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/25/2021] [Accepted: 01/21/2022] [Indexed: 12/30/2022] Open
Abstract
Background Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. Results We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). Conclusion Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.
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Affiliation(s)
- Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.,Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | - Paul B Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.,Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA.,Data Science Lab, Smithsonian Institution, Washington, DC 20560, USA
| | - John S Sproul
- Department of Biology, University of Rochester, Rochester, NY 14620, USA.,Department of Biology, University of Nebraska Omaha, Omaha, NE 68182, USA
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | | | - Peter J Maughan
- Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Julio V Schneider
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | - Russell J Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.,Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany.,Institute for Insect Biotechnology, Justus-Liebig-University, Gießen 35390, Germany
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18
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Kataoka K, Togawa Y, Sanno R, Asahi T, Yura K. Dissecting cricket genomes for the advancement of entomology and entomophagy. Biophys Rev 2022; 14:75-97. [PMID: 35340598 PMCID: PMC8921346 DOI: 10.1007/s12551-021-00924-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Significant advances in biophysical methods such as next-generation sequencing technologies have now opened the way to conduct evolutionary and applied research based on the genomic information of greatly diverse insects. Crickets belonging to Orthoptera (Insecta: Polyneoptera), one of the most flourishing groups of insects, have contributed to the development of multiple scientific fields including developmental biology and neuroscience and have been attractive targets in evolutionary ecology for their diverse ecological niches. In addition, crickets have recently gained recognition as food and feed. However, the genomic information underlying their biological basis and application research toward breeding is currently underrepresented. In this review, we summarize the progress of genomics of crickets. First, we outline the phylogenetic position of crickets in insects and then introduce recent studies on cricket genomics and transcriptomics in a variety of fields. Furthermore, we present findings from our analysis of polyneopteran genomes, with a particular focus on their large genome sizes, chromosome number, and repetitive sequences. Finally, how the cricket genome can be beneficial to the food industry is discussed. This review is expected to enhance greater recognition of how important the cricket genomes are to the multiple biological fields and how basic research based on cricket genome information can contribute to tackling global food security.
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Affiliation(s)
- Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Yuki Togawa
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Ryuto Sanno
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
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19
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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.
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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
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20
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Moqtaderi Z, Brown S, Bender W. Genome-wide oscillations in G + C density and sequence conservation. Genome Res 2021; 31:2050-2057. [PMID: 34649930 PMCID: PMC8559709 DOI: 10.1101/gr.274332.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Eukaryotic genomes typically show a uniform G + C content among chromosomes, but on smaller scales, many species have a G + C density that fluctuates with a characteristic wavelength. This oscillation is evident in many insect species, with wavelengths ranging between 700 bp and 4 kb. Measures of evolutionary conservation oscillate in phase with G + C content, with conserved regions having higher G + C. Loci with large regulatory regions show more regular oscillations; coding sequences and heterochromatic regions show little or no oscillation. There is little oscillation in vertebrate genomes in regions with densely distributed mobile repetitive elements. However, species with few repeats show oscillation in both G + C density and sequence conservation. These oscillations may reflect optimal spacing of cis-regulatory elements.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Susan Brown
- Department of Biology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Welcome Bender
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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Ettinger CL, Byrne FJ, Collin MA, Carter-House D, Walling LL, Atkinson PW, Redak RA, Stajich JE. Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease. G3-GENES GENOMES GENETICS 2021; 11:6324818. [PMID: 34568917 PMCID: PMC8496328 DOI: 10.1093/g3journal/jkab255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022]
Abstract
Homalodisca vitripennis (Hemiptera: Cicadellidae), known as the glassy-winged sharpshooter, is a xylem feeding leafhopper and an important agricultural pest as a vector of Xylella fastidiosa, which causes Pierce’s disease in grapes and a variety of other scorch diseases. The current H. vitripennis reference genome from the Baylor College of Medicine's i5k pilot project is a 1.4-Gb assembly with 110,000 scaffolds, which still has significant gaps making identification of genes difficult. To improve on this effort, we used a combination of Oxford Nanopore long-read sequencing technology combined with Illumina sequencing reads to generate a better assembly and first-pass annotation of the whole genome sequence of a wild-caught Californian (Tulare County) individual of H. vitripennis. The improved reference genome assembly for H. vitripennis is 1.93-Gb in length (21,254 scaffolds, N50 = 650 Mb, BUSCO completeness = 94.3%), with 33.06% of the genome masked as repetitive. In total, 108,762 gene models were predicted including 98,296 protein-coding genes and 10,466 tRNA genes. As an additional community resource, we identified 27 orthologous candidate genes of interest for future experimental work including phenotypic marker genes like white. Furthermore, as part of the assembly process, we generated four endosymbiont metagenome-assembled genomes, including a high-quality near complete 1.7-Mb Wolbachia sp. genome (1 scaffold, CheckM completeness = 99.4%). The improved genome assembly and annotation for H. vitripennis, curated set of candidate genes, and endosymbiont MAGs will be invaluable resources for future research of H. vitripennis.
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Affiliation(s)
- Cassandra L Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Frank J Byrne
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew A Collin
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Derreck Carter-House
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Peter W Atkinson
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Rick A Redak
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
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22
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Bator J, Marshall DC, Hill KBR, Cooley JR, Leston A, Simon C. Phylogeography of the endemic red-tailed cicadas of New Zealand (Hemiptera: Cicadidae: Rhodopsalta), and molecular, morphological and bioacoustical confirmation of the existence of Hudson’s Rhodopsalta microdora. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
Why do some genera radiate, whereas others do not? The genetic structure of present-day populations can provide clues for developing hypotheses. In New Zealand, three Cicadidae genera are depauperate [Amphipsalta (three species), Notopsalta (one species) and Rhodopsalta (three species)], whereas two have speciated extensively [Kikihia (~30 species/subspecies) and Maoricicada (~20 species/subspecies). Here, we examine the evolution of Rhodopsalta, the last New Zealand genus to be studied phylogenetically and phylogeographically. We use Bayesian and maximum-likelihood analyses of mitochondrial cox1 and nuclear EF1α gene sequences. Concatenated and single-gene phylogenies for 70 specimens (58 localities) support its monophyly and three described species: Rhodopsalta cruentata, Rhodopsalta leptomera and Rhodopsalta microdora, the last taxon previously regarded as uncertain. We provide distribution maps, biological notes and the first descriptions of diagnostic songs. We show that both R. cruentata and R. microdora exhibit northern and southern genetic subclades. Subclades of the dry-adapted R. microdora clade show geographical structure, whereas those of the mesic R. cruentata and sand-dune specialist R. leptomera have few discernible patterns. Genetic, bioacoustical and detailed distributional evidence for R. microdora add to the known biodiversity of New Zealand. We designate a lectotype for Tettigonia cruentata Fabricius, 1775, the type species of Rhodopsalta.
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Affiliation(s)
- John Bator
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - David C Marshall
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Kathy B R Hill
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - John R Cooley
- Department of Ecology and Evolutionary Biology, University of Connecticut, 10 South Prospect Street, Hartford, CT 06103, USA
| | - Adam Leston
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
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23
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Cunha MS, Soares FAF, Clarindo WR, Campos LAO, Lopes DM. Robertsonian rearrangements in Neotropical Meliponini karyotype evolution (Hymenoptera: Apidae: Meliponini). INSECT MOLECULAR BIOLOGY 2021; 30:379-389. [PMID: 33797120 DOI: 10.1111/imb.12702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Genome changes, evidenced through karyotype or nuclear genome size data, can result in reproductive isolation, diversification and speciation. The aim of this study was to understand how changes in the karyotype such as chromosome number and nuclear genome size accompanied the evolution of neotropical stingless bees, and to discuss these data in a phylogenetic context focusing on the karyotype evolution of this clade. We sampled 38 species representing the three Neotropical Meliponini groups; 35 for karyotype analyses and 16 for 1C value measurement. The chromosome number varied from 2n = 16 to 2n = 34, with distinct karyotypic formulae and the presence of a few polymorphisms, such as B chromosomes in one species and arm size differences between homologous chromosomes in two species. The mean 1C value varied from 0.31 pg to 0.92 pg. We associated empirical data on chromosome number and mean 1C value to highlight the importance of Robertsonian fusion rearrangements, leading to a decrease in chromosome number during the Neotropical Meliponini evolution. These data also allowed us to infer the independent heterochromatin amplification in several genera. Although less frequent, Melipona species with 2n = 22 represent evidence of Robertsonian fissions. We also pointed out the importance of chromosomal rearrangements that did not alter chromosome number, such as inversions and heterochromatin amplification.
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Affiliation(s)
- M S Cunha
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - F A F Soares
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - W R Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - L A O Campos
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - D M Lopes
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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24
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Oeyen JP, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MJM, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni HV, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SC, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, von Reumont BM, Rosendale AJ, Simao FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biol Evol 2021; 12:1099-1188. [PMID: 32442304 PMCID: PMC7455281 DOI: 10.1093/gbe/evaa106] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
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Affiliation(s)
- Jan Philip Oeyen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Lead Contact
| | | | | | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | | | - Anja Buttstedt
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Germany
| | - Federica Calevro
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Elizabeth I Cash
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University.,Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Hubert Charles
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | | | - Andrew G Cridge
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Peter Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Daniel Dowling
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Elizabeth Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Biology, Georgia Southern University, Statesboro.,Department of Entomology, Purdue University, West Lafayette
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | - Ewald Große-Wilde
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague (CULS), Praha 6-Suchdol, Czech Republic
| | - Cameron Gudobba
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Frank Hauser
- Department of Biology, University of Copenhagen, Denmark
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Emmanuelle Jacquin-Joly
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Versailles, France
| | | | - Jeffery W Jones
- Department of Biological Sciences, Oakland University, Rochester
| | - Steffen Klasberg
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Peter Lesný
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | - Mackenzie Lovegrove
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Sebastian Martin
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | | | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Nicolas Montagné
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Victoria C Moris
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Monica Munoz-Torres
- Berkeley Bioinformatics Open-source Projects (BBOP), Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Shwetha Canchi Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, Kansas
| | - Nicolas Parisot
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Thomas Pauli
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Ralph S Peters
- Arthropoda Department, Center for Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Emma Persyn
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Björn Marcus von Reumont
- Institute for Insect Biotechnology, University of Gießen, Germany.,Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | | | - Felipe A Simao
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - John Skelly
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | | | - Aaron L Stahl
- Department of Biological Sciences, University of Cincinnati.,Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida
| | - Megumi Sumitani
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Owashi, Tsukuba, Japan
| | - Elise M Szuter
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University
| | - Olivia Tidswell
- Biochemistry Department, University of Otago, Dunedin, New Zealand.,Zoology Department, University of Cambridge, United Kingdom
| | | | - Lucia Vedder
- Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Daisuke S Yamamoto
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Yakushiji, Shimotsuke, Japan
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Tanja Ziesmann
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Masatsugu Hatakeyama
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
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25
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Estimation of Genome Size in the Endemic Species Reseda pentagyna and the Locally Rare Species Reseda lutea Using comparative Analyses of Flow Cytometry and K-Mer Approaches. PLANTS 2021; 10:plants10071362. [PMID: 34371565 PMCID: PMC8309327 DOI: 10.3390/plants10071362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022]
Abstract
Genome size is one of the fundamental cytogenetic features of a species, which is critical for the design and initiation of any genome sequencing projects and can provide essential insights in studying taxonomy, cytogenetics, phylogenesis, and evolutionary studies. However, this key cytogenetic information is almost lacking in the endemic species Reseda pentagyna and the locally rare species Reseda lutea in Saudi Arabia. Therefore, genome size was analyzed by propidium iodide PI flow cytometry and compared to k-mer analysis methods. The standard method for genome size measures (flow cytometry) estimated the genome size of R. lutea and R. pentagyna with nuclei isolation MB01 buffer were found to be 1.91 ± 0.02 and 2.09 ± 0.03 pg/2 °C, respectively, which corresponded approximately to a haploid genome size of 934 and 1.022 Mbp, respectively. For validation, K-mer analysis was performed on both species' Illumina paired-end sequencing data from both species. Five k-mer analysis approaches were examined for biocomputational estimation of genome size: A general formula and four well-known programs (CovEST, Kmergenie, FindGSE, and GenomeScope). The parameter preferences had a significant impact on GenomeScope and Kmergenie estimates. While the general formula estimations did not differ considerably, with an average genome size of 867.7 and 896. Mbp. The differences across flow cytometry and biocomputational predictions may be due to the high repeat content, particularly long repetitive regions in both genomes, 71% and 57%, which interfered with k-mer analysis. GenomeScope allowed quantification of high heterozygosity levels (1.04 and 1.37%) of R. lutea and R. pentagyna genomes, respectively. Based on our observations, R. lutea may have a tetraploid genome or higher. Our results revealed fundamental cytogenetic information for R. lutea and R. pentagyna, which should be used in future taxonomic studies and whole-genome sequencing.
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26
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Schramm BW, Labecka AM, Gudowska A, Antoł A, Sikorska A, Szabla N, Bauchinger U, Kozlowski J, Czarnoleski M. Concerted evolution of body mass, cell size and metabolic rate among carabid beetles. JOURNAL OF INSECT PHYSIOLOGY 2021; 132:104272. [PMID: 34186071 DOI: 10.1016/j.jinsphys.2021.104272] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 05/25/2023]
Abstract
Alterations in cell number and size are apparently associated with the body mass differences between species and sexes, but we rarely know which of the two mechanisms underlies the observed variance in body mass. We used phylogenetically informed comparisons of males and females of 19 Carabidae beetle species to compare body mass, resting metabolic rate, and cell size in the ommatidia and Malpighian tubules. We found that the larger species or larger sex (males or females, depending on the species) consistently possessed larger cells in the two tissues, indicating organism-wide coordination of cell size changes in different tissues and the contribution of these changes to the origin of evolutionary and sex differences in body mass. The species or sex with larger cells also exhibited lower mass-specific metabolic rates, and the interspecific mass scaling of metabolism was negatively allometric, indicating that large beetles with larger cells spent relatively less energy on maintenance than small beetles. These outcomes also support existing hypotheses about the fitness consequences of cell size changes, postulating that the low surface-to-volume ratio of large cells helps decrease the energetic demand of maintaining ionic gradients across cell membranes. Analyses with and without phylogenetic information yielded similar results, indicating that the observed patterns were not biased by shared ancestry. Overall, we suggest that natural selection does not operate on each trait independently and that the linkages between concerted cell size changes in different tissues, body mass and metabolic rate should thus be viewed as outcomes of correlational selection.
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Affiliation(s)
- Bartosz W Schramm
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków 30-387, Poland; Sable Systems Europe GmbH, Ostendstraße 25, 12459 Berlin, Germany
| | - Anna Maria Labecka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków 30-387, Poland
| | - Agnieszka Gudowska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków 30-387, Poland
| | - Andrzej Antoł
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków 30-387, Poland; Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - Anna Sikorska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków 30-387, Poland
| | - Natalia Szabla
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków 30-387, Poland
| | - Ulf Bauchinger
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków 30-387, Poland; Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland
| | - Jan Kozlowski
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków 30-387, Poland
| | - Marcin Czarnoleski
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków 30-387, Poland.
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27
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Yuan H, Huang Y, Mao Y, Zhang N, Nie Y, Zhang X, Zhou Y, Mao S. The Evolutionary Patterns of Genome Size in Ensifera (Insecta: Orthoptera). Front Genet 2021; 12:693541. [PMID: 34249107 PMCID: PMC8261143 DOI: 10.3389/fgene.2021.693541] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic size variation has long been a focus for biologists. However, due to the lack of genome size data, the mechanisms behind this variation and the biological significance of insect genome size are rarely studied systematically. The detailed taxonomy and phylogeny of the Ensifera, as well as the extensive documentation concerning their morphological, ecological, behavioral, and distributional characteristics, make them a strong model for studying the important scientific problem of genome size variation. However, data on the genome size of Ensifera are rather sparse. In our study, we used flow cytometry to determine the genome size of 32 species of Ensifera, the smallest one being only 1C = 0.952 pg with the largest species up to 1C = 19.135 pg, representing a 20-fold range. This provides a broader blueprint for the genome size variation of Orthoptera than was previously available. We also completed the assembly of nine mitochondrial genomes and combined mitochondrial genome data from public databases to construct phylogenetic trees containing 32 species of Ensifera and three outgroups. Based on these inferred phylogenetic trees, we detected the phylogenetic signal of genome size variation in Ensifera and found that it was strong in both males and females. Phylogenetic comparative analyses revealed that there were no correlations between genome size and body size or flight ability in Tettigoniidae. Reconstruction of ancestral genome size revealed that the genome size of Ensifera evolved in a complex pattern, in which the genome size of the grylloid clade tended to decrease while that of the non-grylloid clade expanded significantly albeit with fluctuations. However, the evolutionary mechanisms underlying variation of genome size in Ensifera are still unknown.
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Affiliation(s)
- Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Ying Mao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Nan Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yimeng Nie
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xue Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yafu Zhou
- Xi'an Botanical Garden of Shaanxi Province/Institute of Botany of Shaanxi Province, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an, China
| | - Shaoli Mao
- Xi'an Botanical Garden of Shaanxi Province/Institute of Botany of Shaanxi Province, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an, China
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28
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Insights into the genomic evolution of insects from cricket genomes. Commun Biol 2021; 4:733. [PMID: 34127782 PMCID: PMC8203789 DOI: 10.1038/s42003-021-02197-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Most of our knowledge of insect genomes comes from Holometabolous species, which undergo complete metamorphosis and have genomes typically under 2 Gb with little signs of DNA methylation. In contrast, Hemimetabolous insects undergo the presumed ancestral process of incomplete metamorphosis, and have larger genomes with high levels of DNA methylation. Hemimetabolous species from the Orthopteran order (grasshoppers and crickets) have some of the largest known insect genomes. What drives the evolution of these unusual insect genome sizes, remains unknown. Here we report the sequencing, assembly and annotation of the 1.66-Gb genome of the Mediterranean field cricket Gryllus bimaculatus, and the annotation of the 1.60-Gb genome of the Hawaiian cricket Laupala kohalensis. We compare these two cricket genomes with those of 14 additional insects and find evidence that hemimetabolous genomes expanded due to transposable element activity. Based on the ratio of observed to expected CpG sites, we find higher conservation and stronger purifying selection of methylated genes than non-methylated genes. Finally, our analysis suggests an expansion of the pickpocket class V gene family in crickets, which we speculate might play a role in the evolution of cricket courtship, including their characteristic chirping. Ylla, Extavour et al. use genomic data from crickets to investigate the evolution of large genome sizes and DNA methylation events in insects. Their findings indicate that transposable element activity drove genome expansion in hemimetabolous insects, such as crickets and grasshoppers, and that DNA methylation is predominant in conserved genes.
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29
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Lukicheva S, Flot JF, Mardulyn P. Genome Assembly of the Cold-Tolerant Leaf Beetle Gonioctena quinquepunctata, an Important Resource for Studying Its Evolution and Reproductive Barriers between Species. Genome Biol Evol 2021; 13:6296840. [PMID: 34115123 PMCID: PMC8290105 DOI: 10.1093/gbe/evab134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Coleoptera is the most species-rich insect order, yet is currently underrepresented in genomic databases. An assembly was generated for ca. 1.7 Gb genome of the leaf beetle Gonioctena quinquepunctata by first assembling long-sequence reads (Oxford Nanopore; ± 27-fold coverage) and subsequently polishing the resulting assembly with short sequence reads (Illumina; ± 85-fold coverage). The unusually large size (most Coleoptera species are associated with a reported size below 1 Gb) was at least partially attributed to the presence of a large fraction of repeated elements (73.8%). The final assembly was characterized by an N50 length of 432 kb and a BUSCO score of 95.5%. The heterozygosity rate was ± 0.6%. Automated genome annotation informed by RNA-Seq resulted in 40,568 predicted proteins, which is much larger than the typical range 17,000–23,000 predicted for other Coleoptera. However, no evidence of a genome duplication was detected. This new reference genome will contribute to our understanding of genetic variation in the Coleoptera. Among others, it will also allow exploring reproductive barriers between species, investigating introgression in the nuclear genome, and identifying genes involved in resistance to extreme climate conditions.
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Affiliation(s)
- Svitlana Lukicheva
- Evolutionary Biology and Ecology & Interuniversity Institute of Bioinformatics in Brussels - (IB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Jean-François Flot
- Evolutionary Biology and Ecology & Interuniversity Institute of Bioinformatics in Brussels - (IB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology & Interuniversity Institute of Bioinformatics in Brussels - (IB), Université Libre de Bruxelles (ULB), Brussels, Belgium
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30
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Aguirre-Rojas LM, Scully ED, Trick HN, Zhu KY, Smith CM. Comparative analyses of transcriptional responses of Dectes texanus LeConte (Coleoptera: Cerambycidae) larvae fed on three different host plants and artificial diet. Sci Rep 2021; 11:11448. [PMID: 34075134 PMCID: PMC8169664 DOI: 10.1038/s41598-021-90932-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Dectes texanus is an important coleopteran pest of soybeans and cultivated sunflowers in the Midwestern United States that causes yield losses by girdling stems of their host plants. Although sunflower and giant ragweed are primary hosts of D. texanus, they began colonizing soybeans approximately 50 years ago and no reliable management method has been established to prevent or reduce losses by this pest. To identify genes putatively involved when feeding soybean, we compared gene expression of D. texanus third-instar larvae fed soybean to those fed sunflower, giant ragweed, or artificial diet. Dectes texanus larvae differentially expressed 514 unigenes when fed on soybean compared to those fed the other diet treatments. Enrichment analyses of gene ontology terms from up-regulated unigenes in soybean-fed larvae compared to those fed both primary hosts highlighted unigenes involved in oxidoreductase and polygalacturonase activities. Cytochrome P450s, carboxylesterases, major facilitator superfamily transporters, lipocalins, apolipoproteins, glycoside hydrolases 1 and 28, and lytic monooxygenases were among the most commonly up-regulated unigenes in soybean-fed larvae compared to those fed their primary hosts. These results suggest that D. texanus larvae differentially expressed unigenes involved in biotransformation of allelochemicals, digestion of plant cell walls and transport of small solutes and lipids when feeding in soybean.
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Affiliation(s)
- Lina M Aguirre-Rojas
- Deparment of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92506, USA
| | - Erin D Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS-CGAHR, Manhattan, KS, 66502, USA
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Kun Yan Zhu
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - C Michael Smith
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA.
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31
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Genome Size Estimation of Callipogon relictus Semenov (Coleoptera: Cerambycidae), an Endangered Species and a Korea Natural Monument. INSECTS 2021; 12:insects12020111. [PMID: 33513896 PMCID: PMC7910860 DOI: 10.3390/insects12020111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 11/24/2022]
Abstract
Simple Summary The longhorned beetle Calipogon relictus has been considered as a class I endangered species since 2012 in Korea. In an attempt towards beetle conservation, we estimated its genome size at 1.8 ± 0.2 Gb, representing one of the largest cerambycid genomes. This study provides useful insight at the genome level and facilitates the development of an effective conservation strategy. Abstract We estimated the genome size of a relict longhorn beetle, Callipogon relictus Semenov (Cerambycidae: Prioninae)—the Korean natural monument no. 218 and a Class I endangered species—using a combination of flow cytometry and k-mer analysis. The two independent methods enabled accurate estimation of the genome size in Cerambycidae for the first time. The genome size of C. relictus was 1.8 ± 0.2 Gb, representing one of the largest cerambycid genomes studied to date. An accurate estimation of genome size of a critically endangered longhorned beetle is a major milestone in our understanding and characterization of the C. relictus genome. Ultimately, the findings provide useful insight into insect genomics and genome size evolution, particularly among beetles.
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32
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Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Genome size and the position of 18S ribosomal DNA (rDNA) were analysed in two Himacerus, eight Nabis and two Prostemma species from the family Nabidae using flow cytometry and fluorescence in situ hybrization techniques. The karyotypes of Nabis biformis and Nabis maoricus, each with 2n = 16 + XY, and Prostemma aeneicolle, with 2n = 26 + XY, were recorded for the first time. All the species displayed one or two 18S rDNA signals on the X chromosome and up to two signals on the Y chromosome. Several females exhibited two different types of X chromosome breakage, namely within or outside of the 18S rDNA region. Measurements of nuclear DNA content revealed significant differences between all three genera under study. Most notably, the nuclear DNA content of Himacerus species, with 2n = 32/36 + XY (2C = 9–10 pg), was double that of Nabis species, with 2n = 16 + XY (2C = 4–6 pg). Therefore, the previously rejected theory of an autosomal polyploidy event in the evolution of the genus Himacerus is strongly supported by the results of the present study and is now being resurrected.
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33
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Mao Y, Zhang N, Nie Y, Zhang X, Li X, Huang Y. Genome Size of 17 Species From Caelifera (Orthoptera) and Determination of Internal Standards With Very Large Genome Size in Insecta. Front Physiol 2020; 11:567125. [PMID: 33192564 PMCID: PMC7642767 DOI: 10.3389/fphys.2020.567125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
Comparative studies of insect genome size show that Orthoptera is a unique group of Insecta with a significantly enlarged genome. To determine a suitable internal standard for a large genome and to compare the effects of different internal standards on estimates of genome size, we used four internal standards to estimate nuclear DNA content in nine insect species with large genomes. The results showed that the combination of two internal standards, Locusta migratoria (♂1C = 6.20 pg, ♀1C = 6.60 pg) and Periplaneta americana♂ (1C = 3.41 pg), was suitable for estimating large genome of Caelifera by flow cytometry. Using these two internal standards, we estimated the genome sizes of 17 species of Caelifera (12 genera in Acrididae, 2 genera in Pamphagidae, 1 genus in Pyrgomorphidae) using flow cytometry. Genomes ranged from 6.57 pg (Shirakiacris shirakii) to 18.64 pg (Bryodemella holdereri), the largest described in insects to date. These species showed significant genomic dimorphism based on sex: females had a 0.56 pg larger genome than males on average, which might be due to the sex chromosome determinism mechanism of X0(♂)/XX(♀). To test the results obtained by flow cytometry, we used k-mers of Illumina sequencing data to gauge the C-value of Calliptamus abbreviatus and Haplotropis brunneriana. The results of the two methods are slightly different. Genomes were estimated to be about 0.28 and 0.26 pg smaller, respectively, than the flow cytometry values. Furthermore, we also reconstructed the evolutionary relationships of these taxa and discuss the genome size evolution in a phylogenetic framework.
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Affiliation(s)
| | | | | | | | | | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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34
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Marske KA, Thomaz AT, Knowles LL. Dispersal barriers and opportunities drive multiple levels of phylogeographic concordance in the Southern Alps of New Zealand. Mol Ecol 2020; 29:4665-4679. [PMID: 32991032 DOI: 10.1111/mec.15655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 08/23/2020] [Accepted: 09/07/2020] [Indexed: 01/23/2023]
Abstract
Phylogeographic concordance, or the sharing of phylogeographic patterns among codistributed species, suggests similar responses to topography or climatic history. While the orientation and timing of breaks between lineages are routinely compared, spatial dynamics within regions occupied by individual lineages provide a second opportunity for comparing responses to past events. In environments with complex topography and glacial history, such as New Zealand's South Island, geographically nested comparisons can identify the processes leading to phylogeographic concordance between and within regional genomic clusters. Here, we used single nucleotide polymorphisms (obtained via ddRADseq) for two codistributed forest beetle species, Agyrtodes labralis (Leiodidae) and Brachynopus scutellaris (Staphylinidae), to evaluate the role of climate change and topography in shaping phylogeographic concordance at two, nested spatial scales: do species diverge over the same geographic barriers, with similar divergence times? And within regions delimited by these breaks, do species share similar spatial dynamics of directional expansion or isolation-by-distance? We found greater congruence of phylogeographic breaks between regions divided by the strongest dispersal barriers (i.e., the Southern Alps). However, these shared breaks were not indicative of shared spatial dynamics within the regions they delimit, and the most similar spatial dynamics between species occurred within regions with the strongest gradients in historical climatic stability. Our results indicate that lack of concordance as traditionally detected by lineage turnover does not rule out the possibility of shared histories, and variation in the presence and type of concordance may provide insights into the different processes shaping phylogeographic patterns across geologically dynamic regions.
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Affiliation(s)
- Katharine A Marske
- Geographical Ecology Group, Department of Biology, University of Oklahoma, Norman, OK, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Andréa T Thomaz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá DC, Colombia
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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35
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Martinson VG. Rediscovering a Forgotten System of Symbiosis: Historical Perspective and Future Potential. Genes (Basel) 2020; 11:E1063. [PMID: 32916942 PMCID: PMC7563122 DOI: 10.3390/genes11091063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 12/27/2022] Open
Abstract
While the majority of symbiosis research is focused on bacteria, microbial eukaryotes play important roles in the microbiota and as pathogens, especially the incredibly diverse Fungi kingdom. The recent emergence of widespread pathogens in wildlife (bats, amphibians, snakes) and multidrug-resistant opportunists in human populations (Candida auris) has highlighted the importance of better understanding animal-fungus interactions. Regardless of their prominence there are few animal-fungus symbiosis models, but modern technological advances are allowing researchers to utilize novel organisms and systems. Here, I review a forgotten system of animal-fungus interactions: the beetle-fungus symbioses of Drugstore and Cigarette beetles with their symbiont Symbiotaphrina. As pioneering systems for the study of mutualistic symbioses, they were heavily researched between 1920 and 1970, but have received only sporadic attention in the past 40 years. Several features make them unique research organisms, including (1) the symbiont is both extracellular and intracellular during the life cycle of the host, and (2) both beetle and fungus can be cultured in isolation. Specifically, fungal symbionts intracellularly infect cells in the larval and adult beetle gut, while accessory glands in adult females harbor extracellular fungi. In this way, research on the microbiota, pathogenesis/infection, and mutualism can be performed. Furthermore, these beetles are economically important stored-product pests found worldwide. In addition to providing a historical perspective of the research undertaken and an overview of beetle biology and their symbiosis with Symbiotaphrina, I performed two analyses on publicly available genomic data. First, in a preliminary comparative genomic analysis of the fungal symbionts, I found striking differences in the pathways for the biosynthesis of two B vitamins important for the host beetle, thiamine and biotin. Second, I estimated the most recent common ancestor for Drugstore and Cigarette beetles at 8.8-13.5 Mya using sequence divergence (CO1 gene). Together, these analyses demonstrate that modern methods and data (genomics, transcriptomes, etc.) have great potential to transform these beetle-fungus systems into model systems again.
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Affiliation(s)
- Vincent G Martinson
- Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
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36
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Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera). G3-GENES GENOMES GENETICS 2020; 10:3047-3060. [PMID: 32601059 PMCID: PMC7466995 DOI: 10.1534/g3.120.401028] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Measuring genome size across different species can yield important insights into evolution of the genome and allow for more informed decisions when designing next-generation genomic sequencing projects. New techniques for estimating genome size using shallow genomic sequence data have emerged which have the potential to augment our knowledge of genome sizes, yet these methods have only been used in a limited number of empirical studies. In this project, we compare estimation methods using next-generation sequencing (k-mer methods and average read depth of single-copy genes) to measurements from flow cytometry, a standard method for genome size measures, using ground beetles (Carabidae) and other members of the beetle suborder Adephaga as our test system. We also present a new protocol for using read-depth of single-copy genes to estimate genome size. Additionally, we report flow cytometry measurements for five previously unmeasured carabid species, as well as 21 new draft genomes and six new draft transcriptomes across eight species of adephagan beetles. No single sequence-based method performed well on all species, and all tended to underestimate the genome sizes, although only slightly in most samples. For one species, Bembidion sp. nr. transversale, most sequence-based methods yielded estimates half the size suggested by flow cytometry.
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37
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Thapa P, Gu Y, Kil YS, Baek SC, Kim KH, Han AR, Seo EK, Choi H, Chang JH, Nam JW. N-Acetyldopamine derivatives from Periostracum Cicadae and their regulatory activities on Th1 and Th17 cell differentiation. Bioorg Chem 2020; 102:104095. [PMID: 32721777 DOI: 10.1016/j.bioorg.2020.104095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/04/2020] [Accepted: 07/08/2020] [Indexed: 01/07/2023]
Abstract
Bioassay-guided fractionation of a 90% ethanol extract of Periostracum Cicadae led to the isolation of two new N-acetyldopamine dimers (1a/1b) along with six known dimers (2a/2b, 3a/3b, and 4a/4b) and two monomers (5a/5b); compounds 2a/2b, 4a/4b and 5a/5b were newly isolated from this material. All compounds were isolated as enantiomeric mixtures and each enantiomer was successfully separated by chiral-phase HPLC. The structures including absolute configurations were confirmed by high-resolution electrospray ionization mass spectrometry (HR-ESIMS), 1D/2D nuclear magnetic resonance (NMR) spectroscopy, 1H iterative Full Spin Analysis (HiFSA), and electronic circular dichroism (ECD) spectroscopy. Subsequently, the bioactivities of these isolates were evaluated via CD4+ T cell differentiations, which are critical for immune responses and inflammation. The results revealed that compound 5b was observed to enhance the IFN-γ+ Th1 differentiation, which may have a potential for cancer immunotherapy.
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Affiliation(s)
- Punam Thapa
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Ye Gu
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Yun-Seo Kil
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Su Cheol Baek
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ah-Reum Han
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Eun Kyoung Seo
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Jae-Hoon Chang
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea.
| | - Joo-Won Nam
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea; Department of Pharmaceutical Sciences, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States.
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38
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Driscoll TP, Verhoeve VI, Gillespie JJ, Johnston JS, Guillotte ML, Rennoll-Bankert KE, Rahman MS, Hagen D, Elsik CG, Macaluso KR, Azad AF. A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity. BMC Biol 2020; 18:70. [PMID: 32560686 PMCID: PMC7305587 DOI: 10.1186/s12915-020-00802-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/29/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Fleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e., the etiological agents of bubonic plague, endemic and murine typhus). The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea, Ctenocephalides felis, an insect with substantial human health and veterinary importance across the globe. RESULTS By combining Illumina and PacBio sequencing of DNA derived from multiple inbred female fleas with Hi-C scaffolding techniques, we generated a chromosome-level genome assembly for C. felis. Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by ~ 38% of protein-coding genes with two or more copies and over 4000 tRNA genes. A broad range of genome size determinations (433-551 Mb) for individual fleas sampled across different populations supports the widespread presence of fluctuating copy number variation (CNV) in C. felis. Similarly, broad genome sizes were also calculated for individuals of Xenopsylla cheopis (Oriental rat flea), indicating that this remarkable "genome-in-flux" phenomenon could be a siphonapteran-wide trait. Finally, from the C. felis sequence reads, we also generated closed genomes for two novel strains of Wolbachia, one parasitic and one symbiotic, found to co-infect individual fleas. CONCLUSION Rampant CNV in C. felis has dire implications for gene-targeting pest control measures and stands to complicate standard normalization procedures utilized in comparative transcriptomics analysis. Coupled with co-infection by novel Wolbachia endosymbionts-potential tools for blocking pathogen transmission-these oddities highlight a unique and underappreciated disease vector.
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Affiliation(s)
| | - Victoria I Verhoeve
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joseph J Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Mark L Guillotte
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kristen E Rennoll-Bankert
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - M Sayeedur Rahman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Darren Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Christine G Elsik
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- MU Informatics Institute, University of Missouri, Columbia, MO, USA
| | - Kevin R Macaluso
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Abdu F Azad
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D, Dumas Z, Errbii M, Falabella P, Gatti JL, Geuverink E, Gibson JD, Hertaeg C, Hartmann S, Jacquin-Joly E, Lammers M, Lavandero BI, Lindenbaum I, Massardier-Galata L, Meslin C, Montagné N, Pak N, Poirié M, Salvia R, Smith CR, Tagu D, Tares S, Vogel H, Schwander T, Simon JC, Figueroa CC, Vorburger C, Legeai F, Gadau J. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 2020; 21:376. [PMID: 32471448 PMCID: PMC7257214 DOI: 10.1186/s12864-020-6764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. RESULTS We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. CONCLUSIONS These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.
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Affiliation(s)
- Alice B Dennis
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland.
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland.
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Jens Bast
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
- Institute of Zoology, Universität zu Köln, 50674, Köln, Germany
| | - Jan Berghöfer
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Maya Belghazi
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, PINT, PFNT, Marseille, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jan Buellesbach
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Elizabeth Cash
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Zoé Dumas
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Mohammed Errbii
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Jean-Luc Gatti
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA
| | - Corinne Hertaeg
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Department of Environmental Systems Sciences, D-USYS, ETH Zürich, Zürich, Switzerland
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Mark Lammers
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Blas I Lavandero
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ina Lindenbaum
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nina Pak
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Marylène Poirié
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Rosanna Salvia
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Chris R Smith
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
| | - Sophie Tares
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | | | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
| | - Christoph Vorburger
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany.
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40
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Xiong Q, Wan ATY, Tsui SKW. A Mini-review of the Genomes and Allergens of Mites and Ticks. Curr Protein Pept Sci 2020; 21:114-123. [DOI: 10.2174/1389203720666190719150432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 12/20/2022]
Abstract
Mites and ticks are associated with many human diseases including allergic diseases and
scabies. With the recent advances in the high throughput DNA sequencing technology, many mitochondrial
nuclear genomes of these species have been sequenced and the resulting genomic resources
will certainly provide novel insights for the future investigation of the functionally important proteins
and peptides in these species. In this mini-review, the current situation of mite and tick genomes is
described and the future perspectives for the application of the genomic resources are discussed, especially
including the novel identification and structural analysis of allergens.
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Affiliation(s)
- Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Angel Tsz Yau Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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41
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VanKuren NW, Massardo D, Nallu S, Kronforst MR. Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations. Mol Biol Evol 2020; 36:2842-2853. [PMID: 31504750 DOI: 10.1093/molbev/msz194] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptation. However, the causes of gene reuse remain unclear. A small number of large-effect Mendelian loci control a huge diversity of mimetic butterfly wing color patterns, but reasons for their reuse are difficult to identify because the genetic basis of mimicry has primarily been studied in two systems with correlated factors: female-limited Batesian mimicry in Papilio swallowtails (Papilionidae) and non-sex-limited Müllerian mimicry in Heliconius longwings (Nymphalidae). Here, we break the correlation between phylogenetic relationship and sex-limited mimicry by identifying loci controlling female-limited mimicry polymorphism Hypolimnas misippus (Nymphalidae) and non-sex-limited mimicry polymorphism in Papilio clytia (Papilionidae). The Papilio clytia polymorphism is controlled by the genome region containing the gene cortex, the classic P supergene in Heliconius numata, and loci controlling color pattern variation across Lepidoptera. In contrast, female-limited mimicry polymorphism in Hypolimnas misippus is associated with a locus not previously implicated in color patterning. Thus, although many species repeatedly converged on cortex and its neighboring genes over 120 My of evolution of diverse color patterns, female-limited mimicry polymorphisms each evolved using a different gene. Our results support conclusions that gene reuse occurs mainly within ∼10 My and highlight the puzzling diversity of genes controlling seemingly complex female-limited mimicry polymorphisms.
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Affiliation(s)
| | - Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
| | - Sumitha Nallu
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
| | - Marcus R Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
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42
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Simon C, Gordon ERL, Moulds MS, Cole JA, Haji D, Lemmon AR, Lemmon EM, Kortyna M, Nazario K, Wade EJ, Meister RC, Goemans G, Chiswell SM, Pessacq P, Veloso C, McCutcheon JP, Łukasik P. Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Phylogenetic asymmetry is common throughout the tree of life and results from contrasting patterns of speciation and extinction in the paired descendant lineages of ancestral nodes. On the depauperate side of a node, we find extant ‘relict’ taxa that sit atop long, unbranched lineages. Here, we show that a tiny, pale green, inconspicuous and poorly known cicada in the genus Derotettix, endemic to degraded salt-plain habitats in arid regions of central Argentina, is a relict lineage that is sister to all other modern cicadas. Nuclear and mitochondrial phylogenies of cicadas inferred from probe-based genomic hybrid capture data of both target and non-target loci and a morphological cladogram support this hypothesis. We strengthen this conclusion with genomic data from one of the cicada nutritional bacterial endosymbionts, Sulcia, an ancient and obligate endosymbiont of the larger plant-sucking bugs (Auchenorrhyncha) and an important source of maternally inherited phylogenetic data. We establish Derotettiginae subfam. nov. as a new, monogeneric, fifth cicada subfamily, and compile existing and new data on the distribution, ecology and diet of Derotettix. Our consideration of the palaeoenvironmental literature and host-plant phylogenetics allows us to predict what might have led to the relict status of Derotettix over 100 Myr of habitat change in South America.
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Affiliation(s)
- Chris Simon
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Eric R L Gordon
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - M S Moulds
- Australian Museum Research Institute, Sydney, NSW, Australia
| | - Jeffrey A Cole
- Natural Sciences Division, Pasadena City College, Pasadena, CA, USA
| | - Diler Haji
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | | | - Michelle Kortyna
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Katherine Nazario
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Elizabeth J Wade
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Department of Natural Sciences and Mathematics, Curry College, Milton, MA, USA
| | - Russell C Meister
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Geert Goemans
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | | | - Pablo Pessacq
- Centro de Investigaciones Esquel de Montaña y Estepa Patagónicas, Esquel, Chubut, Argentina
| | - Claudio Veloso
- Department of Ecological Sciences, Science Faculty, University of Chile, Santiago, Chile
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Piotr Łukasik
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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43
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Sadílek D, Urfus T, Vilímová J. Genome Size and Sex Chromosome Variability of Bed Bugs Feeding on Animal Hosts Compared to Cimex lectularius Parasitizing Human (Heteroptera: Cimicidae). Cytometry A 2019; 95:1158-1166. [PMID: 31603621 DOI: 10.1002/cyto.a.23905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/08/2019] [Accepted: 09/16/2019] [Indexed: 11/11/2022]
Abstract
Genome size and chromosome number of five Cimicidae species were compared with the similar data recently received from Cimex lectularius parasitizing human. The average nuclear DNA content (males) was 2C = 1.47 pg in C. hemipterus, 2C = 1.61 pg in C. hirundinis, 2C = 1.80 pg in C. lectularius from bats, 2C = 1.68 pg in C. pipistrelli, and 2C = 1.22 pg in Paracimex cf. chaeturus. In the genomes of all cimicid species analyzed, the average GC content ranged from 32.74% in C. pipistrelli to 35.87% in P. cf. chaeturus. Chromosome variability with two male cytotypes, 2n = 28 + X1 X2 Y and 28 + X1 X2 X3 Y, was confirmed in C. pipistrelli. In addition, intraspecific variability in chromosome number was revealed in C. lectularius from bats with 2n = 26 + X1 X2 Y and 26 + X1 X2 X3 Y. We suggest that the origin of intraspecific variability in chromosome number of C. lectularius from bats and C. pipistrelli is not only the result of simple fragmentation, but additive rearrangements like duplications are probably also involved. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- David Sadílek
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, CZ-12844, Praha, Czech Republic
| | - Tomáš Urfus
- Faculty of Science, Department of Botany, Charles University, Benátská 2, CZ-12844, Praha, Czech Republic
| | - Jitka Vilímová
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, CZ-12844, Praha, Czech Republic
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44
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019. [PMID: 30935422 DOI: 10.1101/201731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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45
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019; 20:64. [PMID: 30935422 PMCID: PMC6444547 DOI: 10.1186/s13059-019-1660-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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46
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Hjelmen CE, Garrett MA, Holmes VR, Mynes M, Piron E, Johnston JS. Genome Size Evolution within and between the Sexes. J Hered 2019; 110:219-228. [PMID: 30476187 DOI: 10.1093/jhered/esy063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 11/21/2018] [Indexed: 02/02/2023] Open
Abstract
Genome sizes are known to vary between closely related species, but the patterns behind this variation have yet to be fully understood. Although this variation has been evaluated between species and within sexes, unknown is the extent to which this variation is driven by differentiation in sex chromosomes. To address this longstanding question, we examine the mode and tempo of genome size evolution for a total of 87 species of Drosophilidae, estimating and updating male genome size values for 44 of these species. We compare the evolution of genome size within each sex to the evolution of the differences between the sexes. Utilizing comparative phylogenetic methods, we find that male and female genome size evolution is largely a neutral process, reflective of phylogenetic relatedness between species, which supports the newly proposed accordion model for genome size change. When similarly analyzed, the difference between the sexes due to heteromorphic sex chromosomes is a dynamic process; the male-female genome size difference increases with time with or without known neo-Y events or complete loss of the Y. Observed instances of rapid change match theoretical expectations and known neo-Y and Y loss events in individual species.
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Affiliation(s)
- Carl E Hjelmen
- Department of Entomology, Texas A&M University, College Station, TX
| | - Margaret A Garrett
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
| | - V Renee Holmes
- Department of Entomology, Texas A&M University, College Station, TX
| | - Melissa Mynes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
| | - Elizabeth Piron
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
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Král J, Forman M, Kořínková T, Lerma ACR, Haddad CR, Musilová J, Řezáč M, Herrera IMÁ, Thakur S, Dippenaar-Schoeman AS, Marec F, Horová L, Bureš P. Insights into the karyotype and genome evolution of haplogyne spiders indicate a polyploid origin of lineage with holokinetic chromosomes. Sci Rep 2019; 9:3001. [PMID: 30816146 PMCID: PMC6395618 DOI: 10.1038/s41598-019-39034-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/07/2019] [Indexed: 12/17/2022] Open
Abstract
Spiders are an ancient and extremely diverse animal order. They show a considerable diversity of genome sizes, karyotypes and sex chromosomes, which makes them promising models to analyse the evolution of these traits. Our study is focused on the evolution of the genome and chromosomes in haplogyne spiders with holokinetic chromosomes. Although holokinetic chromosomes in spiders were discovered a long time ago, information on their distribution and evolution in these arthropods is very limited. Here we show that holokinetic chromosomes are an autapomorphy of the superfamily Dysderoidea. According to our hypothesis, the karyotype of ancestral Dysderoidea comprised three autosome pairs and a single X chromosome. The subsequent evolution has frequently included inverted meiosis of the sex chromosome and an increase of 2n. We demonstrate that caponiids, a sister clade to Dysderoidea, have enormous genomes and high diploid and sex chromosome numbers. This pattern suggests a polyploid event in the ancestors of caponiids. Holokinetic chromosomes could have arisen by subsequent multiple chromosome fusions and a considerable reduction of the genome size. We propose that spider sex chromosomes probably do not pose a major barrier to polyploidy due to specific mechanisms that promote the integration of sex chromosome copies into the genome.
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Affiliation(s)
- Jiří Král
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic.
| | - Martin Forman
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Tereza Kořínková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Azucena C Reyes Lerma
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Charles R Haddad
- Department of Zoology and Entomology, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Jana Musilová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
- Crop Research Institute, Drnovská 73, 161 06, Prague 6, Ruzyně, Czech Republic
| | - Milan Řezáč
- Crop Research Institute, Drnovská 73, 161 06, Prague 6, Ruzyně, Czech Republic
| | - Ivalú M Ávila Herrera
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Shefali Thakur
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Ansie S Dippenaar-Schoeman
- Department of Zoology and Centre for Invasion Biology, University of Venda, Thohoyandou, 0950, South Africa
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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48
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Sadílek D, Urfus T, Vilímová J, Hadrava J, Suda J. Nuclear Genome Size in Contrast to Sex Chromosome Number Variability in the Human Bed Bug, Cimex lectularius (Heteroptera: Cimicidae). Cytometry A 2019; 95:746-756. [PMID: 30729668 DOI: 10.1002/cyto.a.23729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/02/2019] [Accepted: 01/21/2019] [Indexed: 11/12/2022]
Abstract
The human bed bug Cimex lectularius is one of the most prevalent human ectoparasites in temperate climate zones. The cytogenetic features of this resilient pest include holokinetic chromosomes, special chromosome behavior in meiosis, and numerical variation of chromosomes, where the diploid number ranges from 26 + X1 X2 Y to 26 + X1-20 Y. It is desirable to assess the nuclear DNA content of various cytotypes for a further detailed study of the C. lectularius genome. Detailed knowledge of the DNA content of this parasite could also clarify the origin of additional chromosomes. The average nuclear genome size C. lectularius with 2n = 26 + X1 X2 Y is 2C = 1.94 pg for males and 1.95 pg for females. There is a significant correlation between genome size and the number of chromosomes, but in some specimens with additional chromosomes, nuclear genome size decreases or remains average. Several species used as the internal reference standard were tested for further investigations of genome size in C. lectularius, and the plant Solanum pseudocaspicum turned out to be the most suitable. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- David Sadílek
- Faculty of Science, Department of Zoology, Charles University, Praha, Czech Republic
| | - Tomáš Urfus
- Faculty of Science, Department of Botany, Charles University, Praha, Czech Republic
| | - Jitka Vilímová
- Faculty of Science, Department of Zoology, Charles University, Praha, Czech Republic
| | - Jiří Hadrava
- Faculty of Science, Department of Zoology, Charles University, Praha, Czech Republic.,Institute of Entomology, Biological Centre, Czech Academy of Science, České Budějovice, Czech Republic
| | - Jan Suda
- Faculty of Science, Department of Botany, Charles University, Praha, Czech Republic
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49
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Zhang S, Gu S, Ni X, Li X. Genome Size Reversely Correlates With Host Plant Range in Helicoverpa Species. Front Physiol 2019; 10:29. [PMID: 30761014 PMCID: PMC6363812 DOI: 10.3389/fphys.2019.00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 01/11/2019] [Indexed: 12/02/2022] Open
Abstract
In organisms with very low percentages of transposable elements (TEs), genome size may positively or negatively correlate with host range, depending on whether host adaptation or host modification is the main route to host generalism. To test if this holds true for insect herbivores with greater percentages of TEs, we conducted flow cytometry to measure the endopolyploidy levels and C-values of the host modification (salivary gland and mandibular gland in head), host adaptation (midgut), and host use-independent tissues (male gonad, hemolymph, and Malpighian tubules) of the generalist Helicoverpa armigera and the head of its older specialist sister H. assulta. Larval salivary gland displayed a consecutive chain of endopolyploidy particles from 8Cx to higher than 32Cx and larval head and midgut had endopolyploidy nuclei clusters of 16Cx and 32Cx, whereas larval male gonad, hemolymph, and Malpighian tubules possessed no endopolyploidy nuclei of higher than 8Cx. The estimated genome size of the Solanaceae plant specialist H. assulta is 430 Mb, significantly larger than that of its older generalist sister Heliothis virescens (408 Mb) and those of its two generalist descendants H. armigera (394 Mb) and H. zea (363 Mb). These data not only reveal a negative correlation between host plant range and genome size in this terminal lineage, but also imply that Helicoverpa species appear to depend more on host modification than on host adaptation to achieve polyphagy.
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Affiliation(s)
- Shen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaohua Gu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinzhi Ni
- USDA-ARS Crop Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Xianchun Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, United States
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50
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Johnston JS, Bernardini A, Hjelmen CE. Genome Size Estimation and Quantitative Cytogenetics in Insects. Methods Mol Biol 2019; 1858:15-26. [PMID: 30414107 DOI: 10.1007/978-1-4939-8775-7_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
With care, it is possible using flow cytometry to create a precise and accurate estimate of the genome size of an insect that is useful for genomics, genetics, molecular/cell biology, or systematics. Genome size estimation is a useful first step in a complete genome sequencing project. The number of sequencing reads required to produce a given level of coverage depends directly upon the 1C amount of DNA per cell, while an even more critical need is an accurate 1C genome size estimate to compare against the final assembly. Here we present a detailed protocol to estimate genome size using flow cytometry. Published genome size estimates should be submitted to genomesize.com so that they are available to all.
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Affiliation(s)
- J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Angelina Bernardini
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, USA
| | - Carl E Hjelmen
- Department of Entomology, Texas A&M University, College Station, TX, USA.
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