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Li X, Jayaprasad S, Einarsdottir E, Cooper SJB, Suh A, Kawakami T, Palacios-Gimenez OM. Chromosome-level genome assembly of the morabine grasshopper Vandiemenella viatica19. Sci Data 2024; 11:997. [PMID: 39266578 PMCID: PMC11393057 DOI: 10.1038/s41597-024-03858-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 09/04/2024] [Indexed: 09/14/2024] Open
Abstract
Morabine grasshoppers in the Vandiemenella viatica species group, which show karyotype diversity, have been studied for their ecological distribution and speciation in relation to their genetic and chromosomal diversity. They are good models for studying sex chromosome evolution as "old" and newly emerged sex chromosomes co-exist within the group. Here we present a reference genome for the viatica19 chromosomal race, that possesses the ancestral karyotype within the group. Using PacBio HiFi and Hi-C sequencing, we generated a chromosome-level assembly of 4.09 Gb in span, scaffold N50 of 429 Mb, and complete BUSCO score of 98.1%, containing 10 pseudo-chromosomes. We provide Illumina datasets of males and females, used to identify the X chromosome. The assembly contains 19,034 predicted protein-coding genes, and a total of 75.21% of repetitive DNA sequences. By leveraging HiFi reads, we mapped the genome-wide distribution of methylated bases (5mC and 6 mA). This comprehensive assembly offers a robust reference for morabine grasshoppers and supports further research into speciation and sex chromosome diversification within the group and its related species.
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Affiliation(s)
- Xuan Li
- Department of Organismal Biology-Systematic Biology, Science for Life Laboratory, Evolutionary Biology Centre, Uppsala University, 75236, Uppsala, Sweden.
| | - Suvratha Jayaprasad
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Elisabet Einarsdottir
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute Technology, SE-17121, Solna, Sweden
| | - Steven J B Cooper
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences and Environment Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Alexander Suh
- Department of Organismal Biology-Systematic Biology, Science for Life Laboratory, Evolutionary Biology Centre, Uppsala University, 75236, Uppsala, Sweden
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121, Bonn, Germany
| | | | - Octavio Manuel Palacios-Gimenez
- Department of Organismal Biology-Systematic Biology, Science for Life Laboratory, Evolutionary Biology Centre, Uppsala University, 75236, Uppsala, Sweden.
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, 07743, Jena, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
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2
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Leader DP, Naseem MT, Halberg KV. BeetleAtlas: An Ontogenetic and Tissue-specific Transcriptomic Atlas of the Red Flour Beetle Tribolium castaneum. J Mol Biol 2024; 436:168520. [PMID: 39237197 DOI: 10.1016/j.jmb.2024.168520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 09/07/2024]
Abstract
The red flour beetle Tribolium castaneum has emerged as a powerful model in insect functional genomics. However, a major limitation in the field is the lack of a detailed spatio-temporal view of the genetic signatures underpinning the function of distinct tissues and life stages. Here, we present an ontogenetic and tissue-specific web-based resource for Tribolium transcriptomics: BeetleAtlas (https://www.beetleatlas.org). This web application provides access to a database populated with quantitative expression data for nine adult and seven larval tissues, as well as for four embryonic stages of Tribolium. BeetleAtlas allows one to search for individual Tribolium genes to obtain values of both total gene expression and enrichment in different tissues, together with data for individual isoforms. To facilitate cross-species studies, one can also use Drosophila melanogaster gene identifiers to search for related Tribolium genes. For retrieved genes there are options to identify and display the tissue expression of related Tribolium genes or homologous Drosophila genes. Five additional search modes are available to find genes conforming to any of the following criteria: exhibiting high expression in a particular tissue; showing significant differences in expression between larva and adult; having a peak of expression at a specific stage of embryonic development; belonging to a particular functional category; and displaying a pattern of tissue expression similar to that of a query gene. We illustrate how the different feaures of BeetleAtlas can be used to illuminate our understanding of the genetic mechanisms underpinning the biology of what is the largest animal group on earth.
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Affiliation(s)
- David P Leader
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Muhammad T Naseem
- Department of Biology, Section for Cell and Neurobiology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Kenneth V Halberg
- Department of Biology, Section for Cell and Neurobiology, University of Copenhagen, Copenhagen DK-2100, Denmark.
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3
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Schulz NK, Asgari D, Liu S, Birnbaum SS, Williams AM, Prakash A, Tate AT. Resources modulate developmental shifts but not infection tolerance upon coinfection in an insect system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.01.606236. [PMID: 39149267 PMCID: PMC11326177 DOI: 10.1101/2024.08.01.606236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Energetic resources fuel immune responses and parasite growth within organisms, but it is unclear whether energy allocation is sufficient to explain changes in infection outcomes under the threat of multiple parasites. We manipulated diet in flour beetles (Tribolium confusum) infected with two natural parasites to investigate the role of resources in shifting metabolic and immune responses after single and co-infection. Our results suggest that gregarine parasites alter the within-host energetic environment, and by extension juvenile development time, in a diet-dependent manner. Gregarines do not affect host resistance to acute bacterial infection but do stimulate the expression of an alternative set of immune genes and promote damage to the gut, ultimately contributing to reduced survival regardless of diet. Thus, energy allocation is not sufficient to explain the immunological contribution to coinfection outcomes, emphasizing the importance of mechanistic insight for predicting the impact of coinfection across levels of biological organization.
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Affiliation(s)
- Nora K.E. Schulz
- Department of Biological Sciences, Vanderbilt University, Nashville TN 37232
| | - Danial Asgari
- Department of Biological Sciences, Vanderbilt University, Nashville TN 37232
| | - Siqin Liu
- Department of Biological Sciences, Vanderbilt University, Nashville TN 37232
| | | | - Alissa M. Williams
- Department of Biological Sciences, Vanderbilt University, Nashville TN 37232
| | - Arun Prakash
- Department of Biological Sciences, Vanderbilt University, Nashville TN 37232
| | - Ann T. Tate
- Department of Biological Sciences, Vanderbilt University, Nashville TN 37232
- Evolutionary Studies Initiative, Vanderbilt University, Nashville TN 37232
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4
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Pang B, Zhan Z, Wang Y. A chromosome-level genome assembly of Prosopocoilus inquinatus Westwood, 1848 (Coleoptera: Lucanidae). Sci Data 2024; 11:808. [PMID: 39033188 PMCID: PMC11271282 DOI: 10.1038/s41597-024-03647-9] [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: 01/26/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024] Open
Abstract
Lucanidae (Coleoptera: Scarabaeidae) are fascinating beetles exhibiting significant dimorphism and are widely used as beetle evolutionary study models. However, lacking high-quality genomes prohibits our understanding of Lucanidae. Herein, we proposed a chromosome-level genome assembly of a widespread species, Prosopocoilus inquinatus, combining PacBio HiFi, Illumina, and Hi-C data. The genome size reaches 649.73 Mb, having the scaffold N50 size of 59.50 Mb, and 99.6% (647.13 Mb) of the assembly successfully anchored on 12 chromosomes. The BUSCO analysis of the genome exhibits a completeness of 99.6% (n = 1,367), including 1,362 (98.5%) single-copy BUSCOs and 15 (1.1%) duplicated BUSCOs. The genome annotation identifies that the genome contains 61.41% repeat elements and 13,452 predicted protein-coding genes. This high-quality Lucanidae genome provides treasured genomic information to our knowledge of stag beetles.
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Affiliation(s)
- Bo Pang
- Plant Protection Department, College of Agriculture and Animal Husbandry of Xizang Autonomous Region, Lhasa, 850000, China.
| | - Zhihong Zhan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunchao Wang
- College of Biology and Agriculture, Zunyi Normal University, Zunyi, 563006, China
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5
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Mann KE, Panfilio KA. Tissue-Level Integration Overrides Gradations of Differentiating Cell Identity in Beetle Extraembryonic Tissue. Cells 2024; 13:1211. [PMID: 39056793 PMCID: PMC11274815 DOI: 10.3390/cells13141211] [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: 04/12/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
During animal embryogenesis, one of the earliest specification events distinguishes extraembryonic (EE) from embryonic tissue fates: the serosa in the case of the insects. While it is well established that the homeodomain transcription factor Zen1 is the critical determinant of the serosa, the subsequent realization of this tissue's identity has not been investigated. Here, we examine serosal differentiation in the beetle Tribolium castaneum based on the quantification of morphological and morphogenetic features, comparing embryos from a Tc-zen1 RNAi dilution series, where complete knockdown results in amnion-only EE tissue identity. We assess features including cell density, tissue boundary morphology, and nuclear size as dynamic readouts for progressive tissue maturation. While some features exhibit an all-or-nothing outcome, other key features show dose-dependent phenotypic responses with trait-specific thresholds. Collectively, these findings provide nuance beyond the known status of Tc-Zen1 as a selector gene for serosal tissue patterning. Overall, our approach illustrates how the analysis of tissue maturation dynamics from live imaging extends but also challenges interpretations based on gene expression data, refining our understanding of tissue identity and when it is achieved.
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Affiliation(s)
- Katie E. Mann
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Kristen A. Panfilio
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Department of Molecular Genetics, Institute of Biology, University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany
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6
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Huang YH, Sun YF, Li H, Li HS, Pang H. PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era. Mol Biol Evol 2024; 41:msae150. [PMID: 39041199 PMCID: PMC11287380 DOI: 10.1093/molbev/msae150] [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: 02/14/2024] [Revised: 05/15/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024] Open
Abstract
The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, prior to core analyses, traditional methods typically involve intricate and time-consuming procedures, including assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple sequence alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive data sets. In this study, we develop PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as a reference for phylogenetic and evolutionary analyses. Through testing with simulated data sets of species spanning the tree of life, PhyloAln demonstrates consistently robust performance compared with other reference-based tools across different data types, sequencing technologies, coverages, and species, with percent completeness and identity at least 50 percentage points higher in the alignments. Additionally, we validate the efficacy of PhyloAln in removing a minimum of 90% foreign and 70% cross-contamination issues, which are prevalent in sequencing data but often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments (completeness mostly larger than 80%, identity larger than 90%) and reconstructing robust phylogenies using real data sets of transcriptomes of ladybird beetles, plastid genes of peppers, or ultraconserved elements of turtles. With these advantages, PhyloAln is expected to facilitate phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.
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Affiliation(s)
- Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Yi-Fei Sun
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
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7
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Jackson DJ, Cerveau N, Posnien N. De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide. Front Zool 2024; 21:17. [PMID: 38902827 PMCID: PMC11188175 DOI: 10.1186/s12983-024-00538-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the 'scientific status' of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
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Affiliation(s)
- Daniel J Jackson
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany.
| | - Nicolas Cerveau
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany
| | - Nico Posnien
- University of Göttingen, Department of Developmental Biology, GZMB, Justus-Von-Liebig-Weg 11, Göttingen, 37077, Germany.
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8
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Volarić M, Despot-Slade E, Veseljak D, Pavlek M, Vojvoda Zeljko T, Mravinac B, Meštrović N. The Genome Organization of 5S rRNA Genes in the Model Organism Tribolium castaneum and Its Sibling Species Tribolium freemani. Genes (Basel) 2024; 15:776. [PMID: 38927712 PMCID: PMC11202950 DOI: 10.3390/genes15060776] [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: 04/11/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
5S ribosomal DNAs (rDNAs) are arranged in tandem and are often under-represented in genome assemblies. In the present study, we performed a global and in-depth analysis of the 5S rDNAs in the model insect Tribolium castaneum and its closely related species Tribolium freemani. To accomplish this goal, we used our recently published genome assemblies based on Nanopore and PacBio long-read sequencing. Although these closely related species share the 5S rRNA gene sequence with high homology, they show a different organization of the 5S rDNA locus. Analysis of 5S rDNA arrays in T. castaneum revealed a typical tandemly repeated organization characterized by repeat units consisting of the 121 bp long 5S rRNA gene and the 71 bp long nontranscribed spacer (NTS). In contrast, T. freemani showed a much more complex organization of 5S rDNA arrays characterized by two patterns. The first is based on the association of 5S rRNA gene with arrays of a satellite DNA, representing the NTS sequence of the 5S rDNA genes in T. freemani. The second, more complex type is characterized by a somewhat less frequent occurrence of the 5S rRNA gene and its association with longer satellite DNA arrays that are regularly interrupted by Jockey-like retrotransposons. This organization, in which the ribosomal gene is associated with two completely different repetitive elements such as satellite DNAs and retrotransposons, suggests that the 5S rRNA gene, regardless of its crucial function in the genome, could be a subject of extremely dynamic genomic rearrangements.
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Affiliation(s)
| | | | | | | | | | | | - Nevenka Meštrović
- Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.V.); (E.D.-S.); (D.V.); (M.P.); (T.V.Z.); (B.M.)
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9
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Xing L, Liu B, Yu D, Tang X, Sun J, Zhang B. A near-complete genome assembly of Monochamus alternatus a major vector beetle of pinewood nematode. Sci Data 2024; 11:312. [PMID: 38531927 DOI: 10.1038/s41597-024-03150-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
The Japanese sawyer beetle, Monochamus alternatus, is not only one of the most important wood boring pest itself, but also a major vector of the invasive pinewood nematode (PWN), which is the causal agent of the devastative pine wilt disease (PWD) and threats the global pine forest. Here, we present a near-complete genome of M. alternatus at the chromosome level. The assembled genome was 792.05 Mb with contig N50 length of 55.99 Mb, which is the largest N50 size among the sequenced Coleoptera insects currently. 99.57% of sequence was anchored onto ten pseudochromosomes (one X-chromosome and nine autosomes), and the final genome harbored only 13 gaps. BUSCO evaluation revealed the presence of 99.0% of complete core genes. Thus, our genome assembly represented the highest-contiguity genome assembly as well as high completeness in insects so far. We identified 20,471 protein-coding genes, of which 20,070 (98.04%) were functionally annotated. The genome assembly of M. alternatus provides a valuable resource for exploring the evolution of the symbiosis between PWN and the vector insects.
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Affiliation(s)
- Longsheng Xing
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Bo Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dunyang Yu
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Xuan Tang
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Jianghua Sun
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
| | - Bin Zhang
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
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10
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Jin J, Zhan Z, Wei X, Pan Z, Zhao Y, Yu D, Zhang F. Genomic insights into the chromosomal elongation in a family of Collembola. Proc Biol Sci 2024; 291:20232937. [PMID: 38471545 DOI: 10.1098/rspb.2023.2937] [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: 01/02/2024] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Collembola is a highly diverse and abundant group of soil arthropods with chromosome numbers ranging from 5 to 11. Previous karyotype studies indicated that the Tomoceridae family possesses an exceptionally long chromosome. To better understand chromosome size evolution in Collembola, we obtained a chromosome-level genome of Yoshiicerus persimilis with a size of 334.44 Mb and BUSCO completeness of 97.0% (n = 1013). Both genomes of Y. persimilis and Tomocerus qinae (recently published) have an exceptionally large chromosome (ElChr greater than 100 Mb), accounting for nearly one-third of the genome. Comparative genomic analyses suggest that chromosomal elongation occurred independently in the two species approximately 10 million years ago, rather than in the ancestor of the Tomoceridae family. The ElChr elongation was caused by large tandem and segmental duplications, as well as transposon proliferation, with genes in these regions experiencing weaker purifying selection (higher dN/dS) than conserved regions. Moreover, inter-genomic synteny analyses indicated that chromosomal fission/fusion events played a crucial role in the evolution of chromosome numbers (ranging from 5 to 7) within Entomobryomorpha. This study provides a valuable resource for investigating the chromosome evolution of Collembola.
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Affiliation(s)
- Jianfeng Jin
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhihong Zhan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiping Wei
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhixiang Pan
- School of Life Sciences, Taizhou University, Taizhou 318000, People's Republic of China
| | - Yuxin Zhao
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Daoyuan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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11
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Robben M, Ramesh B, Pau S, Meletis D, Luber J, Demuth J. scRNA-seq Reveals Novel Genetic Pathways and Sex Chromosome Regulation in Tribolium Spermatogenesis. Genome Biol Evol 2024; 16:evae059. [PMID: 38513111 PMCID: PMC10980526 DOI: 10.1093/gbe/evae059] [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] [Received: 12/30/2023] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Spermatogenesis is critical to sexual reproduction yet evolves rapidly in many organisms. High-throughput single-cell transcriptomics promises unparalleled insight into this important process but understanding can be impeded in nonmodel systems by a lack of known genes that can reliably demarcate biologically meaningful cell populations. Tribolium castaneum, the red flour beetle, lacks known markers for spermatogenesis found in insect species like Drosophila melanogaster. Using single-cell sequencing data collected from adult beetle testes, we implement a strategy for elucidating biologically meaningful cell populations by using transient expression stage identification markers, weighted principal component clustering, and SNP-based haploid/diploid phasing. We identify populations that correspond to observable points in sperm differentiation and find species specific markers for each stage. Our results indicate that molecular pathways underlying spermatogenesis in Coleoptera are substantially diverged from those in Diptera. We also show that most genes on the X chromosome experience meiotic sex chromosome inactivation. Temporal expression of Drosophila MSL complex homologs coupled with spatial analysis of potential chromatin entry sites further suggests that the dosage compensation machinery may mediate escape from meiotic sex chromosome inactivation and postmeiotic reactivation of the X chromosome.
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Affiliation(s)
- Michael Robben
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Balan Ramesh
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Shana Pau
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Demetra Meletis
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Jacob Luber
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Jeffery Demuth
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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12
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Davidson PL, Moczek AP. Genome evolution and divergence in cis-regulatory architecture is associated with condition-responsive development in horned dung beetles. PLoS Genet 2024; 20:e1011165. [PMID: 38442113 PMCID: PMC10942260 DOI: 10.1371/journal.pgen.1011165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/15/2024] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
Phenotypic plasticity is thought to be an important driver of diversification and adaptation to environmental variation, yet the genomic mechanisms mediating plastic trait development and evolution remain poorly understood. The Scarabaeinae, or true dung beetles, are a species-rich clade of insects recognized for their highly diversified nutrition-responsive development including that of cephalic horns-evolutionarily novel, secondary sexual weapons that exhibit remarkable intra- and interspecific variation. Here, we investigate the evolutionary basis for horns as well as other key dung beetle traits via comparative genomic and developmental assays. We begin by presenting chromosome-level genome assemblies of three dung beetle species in the tribe Onthophagini (> 2500 extant species) including Onthophagus taurus, O. sagittarius, and Digitonthophagus gazella. Comparing these assemblies to those of seven other species across the order Coleoptera identifies evolutionary changes in coding sequence associated with metabolic regulation of plasticity and metamorphosis. We then contrast chromatin accessibility in developing head horn tissues of high- and low-nutrition O. taurus males and females and identify distinct cis-regulatory architectures underlying nutrition- compared to sex-responsive development, including a large proportion of recently evolved regulatory elements sensitive to horn morph determination. Binding motifs of known and new candidate transcription factors are enriched in these nutrition-responsive open chromatin regions. Our work highlights the importance of chromatin state regulation in mediating the development and evolution of plastic traits, demonstrates gene networks are highly evolvable transducers of environmental and genetic signals, and provides new reference-quality genomes for three species that will bolster future developmental, ecological, and evolutionary studies of this insect group.
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Affiliation(s)
- Phillip L Davidson
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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Arnqvist G, Westerberg I, Galbraith J, Sayadi A, Scofield DG, Olsen RA, Immonen E, Bonath F, Ewels P, Suh A. A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements. G3 (BETHESDA, MD.) 2024; 14:jkad266. [PMID: 38092066 PMCID: PMC10849321 DOI: 10.1093/g3journal/jkad266] [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: 06/16/2023] [Accepted: 10/30/2023] [Indexed: 02/09/2024]
Abstract
Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala SE75236, Sweden
| | - Ivar Westerberg
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala SE75236, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm SE10691, Sweden
| | - James Galbraith
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK
| | - Ahmed Sayadi
- Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala SE75236, Sweden
| | - Douglas G Scofield
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala SE75236, Sweden
- Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala SE75236, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE10691, Sweden
| | - Elina Immonen
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala SE75236, Sweden
| | - Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm SE10691, Sweden
| | | | - Alexander Suh
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala SE75236, Sweden
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14
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Critchlow JT, Prakash A, Zhong KY, Tate AT. Mapping the functional form of the trade-off between infection resistance and reproductive fitness under dysregulated immune signaling. PLoS Pathog 2024; 20:e1012049. [PMID: 38408106 PMCID: PMC10919860 DOI: 10.1371/journal.ppat.1012049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 03/07/2024] [Accepted: 02/15/2024] [Indexed: 02/28/2024] Open
Abstract
Immune responses benefit organismal fitness by clearing parasites but also exact costs associated with immunopathology and energetic investment. Hosts manage these costs by tightly regulating the induction of immune signaling to curtail excessive responses and restore homeostasis. Despite the theoretical importance of turning off the immune response to mitigate these costs, experimentally connecting variation in the negative regulation of immune responses to organismal fitness remains a frontier in evolutionary immunology. In this study, we used a dose-response approach to manipulate the RNAi-mediated knockdown efficiency of cactus (IκBα), a central regulator of Toll pathway signal transduction in flour beetles (Tribolium castaneum). By titrating cactus activity across four distinct levels, we derived the shape of the relationship between immune response investment and traits associated with host fitness, including infection susceptibility, lifespan, fecundity, body mass, and gut homeostasis. Cactus knock-down increased the overall magnitude of inducible immune responses and delayed their resolution in a dsRNA dose-dependent manner, promoting survival and resistance following bacterial infection. However, these benefits were counterbalanced by dsRNA dose-dependent costs to lifespan, fecundity, body mass, and gut integrity. Our results allowed us to move beyond the qualitative identification of a trade-off between immune investment and fitness to actually derive its functional form. This approach paves the way to quantitatively compare the evolution and impact of distinct regulatory elements on life-history trade-offs and fitness, filling a crucial gap in our conceptual and theoretical models of immune signaling network evolution and the maintenance of natural variation in immune systems.
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Affiliation(s)
- Justin T Critchlow
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Arun Prakash
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Katherine Y Zhong
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Institute, Vanderbilt University, Nashville, Tennessee, United States of America
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15
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He J, Li J, Zhang R, Dong Z, Liu G, Chang Z, Bi W, Ruan Y, Yang Y, Liu H, Qiu L, Zhao R, Wan W, Li Z, Chen L, Li Y, Li X. Multiple Origins of Bioluminescence in Beetles and Evolution of Luciferase Function. Mol Biol Evol 2024; 41:msad287. [PMID: 38174583 PMCID: PMC10798137 DOI: 10.1093/molbev/msad287] [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] [Received: 03/10/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
Bioluminescence in beetles has long fascinated biologists, with diverse applications in biotechnology. To date, however, our understanding of its evolutionary origin and functional variation mechanisms remains poor. To address these questions, we obtained high-quality reference genomes of luminous and nonluminous beetles in 6 Elateroidea families. We then reconstructed a robust phylogenetic relationship for all luminous families and related nonluminous families. Comparative genomic analyses and biochemical functional experiments suggested that gene evolution within Elateroidea played a crucial role in the origin of bioluminescence, with multiple parallel origins observed in the luminous beetle families. While most luciferase-like proteins exhibited a conserved nonluminous amino acid pattern (TLA346 to 348) in the luciferin-binding sites, luciferases in the different luminous beetle families showed divergent luminous patterns at these sites (TSA/CCA/CSA/LVA). Comparisons of the structural and enzymatic properties of ancestral, extant, and site-directed mutant luciferases further reinforced the important role of these sites in the trade-off between acyl-CoA synthetase and luciferase activities. Furthermore, the evolution of bioluminescent color demonstrated a tendency toward hypsochromic shifts and variations among the luminous families. Taken together, our results revealed multiple parallel origins of bioluminescence and functional divergence within the beetle bioluminescent system.
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Affiliation(s)
- Jinwu He
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Jun Li
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ru Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Zhiwei Dong
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guichun Liu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zhou Chang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wenxuan Bi
- Room 401, No. 2, Lane 155, Lianhua South Road, Shanghai 201100, China
| | - Yongying Ruan
- Plant Protection Research Center, Shenzhen Polytechnic University, Shenzhen 518055, China
| | - Yuxia Yang
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Haoyu Liu
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Lu Qiu
- Engineering Research Center for Forest and Grassland Disaster Prevention and Reduction, Mianyang Normal University, 621000 Mianyang, China
| | - Ruoping Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wenting Wan
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zihe Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Xueyan Li
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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16
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Cheng S, Jacobs CGC, Mogollón Pérez EA, Chen D, van de Sanden JT, Bretscher KM, Verweij F, Bosman JS, Hackmann A, Merks RMH, van den Heuvel J, van der Zee M. A life-history allele of large effect shortens developmental time in a wild insect population. Nat Ecol Evol 2024; 8:70-82. [PMID: 37957313 DOI: 10.1038/s41559-023-02246-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023]
Abstract
Developmental time is a key life-history trait with large effects on Darwinian fitness. In many insects, developmental time is currently under strong selection to minimize ecological mismatches in seasonal timing induced by climate change. The genetic basis of responses to such selection, however, is poorly understood. To address this problem, we set up a long-term evolve-and-resequence experiment in the beetle Tribolium castaneum and selected replicate, outbred populations for fast or slow embryonic development. The response to this selection was substantial and embryonic developmental timing of the selection lines started to diverge during dorsal closure. Pooled whole-genome resequencing, gene expression analysis and an RNAi screen pinpoint a 222 bp deletion containing binding sites for Broad and Tramtrack upstream of the ecdysone degrading enzyme Cyp18a1 as a main target of selection. Using CRISPR/Cas9 to reconstruct this allele in the homogenous genetic background of a laboratory strain, we unravel how this single deletion advances the embryonic ecdysone peak inducing dorsal closure and show that this allele accelerates larval development but causes a trade-off with fecundity. Our study uncovers a life-history allele of large effect and reveals the evolvability of developmental time in a natural insect population.
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Affiliation(s)
- Shixiong Cheng
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Elisa A Mogollón Pérez
- Institute of Biology, Leiden University, Leiden, the Netherlands
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Daipeng Chen
- Mathematical Institute, Leiden University, Leiden, the Netherlands
| | - Joep T van de Sanden
- Institute of Biology, Leiden University, Leiden, the Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | | | - Femke Verweij
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Jelle S Bosman
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Amke Hackmann
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Roeland M H Merks
- Institute of Biology, Leiden University, Leiden, the Netherlands
- Mathematical Institute, Leiden University, Leiden, the Netherlands
| | - Joost van den Heuvel
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
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17
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Aase-Remedios ME, Janssen R, Leite DJ, Sumner-Rooney L, McGregor AP. Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication. Mol Biol Evol 2023; 40:msad239. [PMID: 37935059 PMCID: PMC10726417 DOI: 10.1093/molbev/msad239] [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] [Received: 05/26/2023] [Revised: 10/02/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalization to partition ancestral functions and/or neofunctionalization to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is a key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterized the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organization while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalization between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.
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Affiliation(s)
| | - Ralf Janssen
- Department of Earth Sciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Daniel J Leite
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom
| | - Lauren Sumner-Rooney
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, 10115, Germany
| | - Alistair P McGregor
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom
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18
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Cheatle Jarvela AM, Wexler JR. Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution. Dev Genes Evol 2023; 233:59-76. [PMID: 37982820 DOI: 10.1007/s00427-023-00712-y] [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] [Received: 06/16/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023]
Abstract
Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.
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Affiliation(s)
- Alys M Cheatle Jarvela
- Department of Entomology, University of Maryland, College Park, MD, USA.
- HHMI Janelia Research Campus, Ashburn, VA, USA.
| | - Judith R Wexler
- Department of Ecology, Evolution, and Behavior, The Hebrew University in Jerusalem, Jerusalem, Israel.
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19
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Strobl F, Ratke J, Krämer F, Utta A, Becker S, Stelzer EHK. Next generation marker-based vector concepts for rapid and unambiguous identification of single and double homozygous transgenic organisms. Biol Open 2023; 12:bio060015. [PMID: 37855381 PMCID: PMC10602009 DOI: 10.1242/bio.060015] [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: 05/17/2023] [Accepted: 08/15/2023] [Indexed: 10/20/2023] Open
Abstract
For diploid model organisms, the actual transgenesis processes require subsequent periods of transgene management, which are challenging in emerging model organisms due to the lack of suitable methodology. We used the red flour beetle Tribolium castaneum, a stored-grain pest, to perform a comprehensive functional evaluation of our AClashOfStrings (ACOS) and the combined AGameOfClones/AClashOfStrings (AGOC/ACOS) vector concepts, which use four clearly distinguishable markers to provide full visual control over up to two independent transgenes. We achieved comprehensive statistical validation of our approach by systematically creating seventeen novel single and double homozygous sublines intended for fluorescence live imaging, including several sublines in which the microtubule cytoskeleton is labeled. During the mating procedures, we genotyped more than 20,000 individuals in less than 80 working hours, which corresponds to about 10 to 15 s per individual. We also confirm the functionality of our combined concept in two double transgene special cases, i.e. integration of both transgenes in close proximity on the same chromosome and integration of one transgene on the X allosome. Finally, we discuss our vector concepts regarding performance, genotyping accuracy, throughput, resource saving potential, fluorescent protein choice, modularity, adaptation to other diploid model organisms and expansion capability.
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Affiliation(s)
- Frederic Strobl
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Julia Ratke
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Franziska Krämer
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Ana Utta
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Sigrun Becker
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Ernst H. K. Stelzer
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
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20
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Critchlow JT, Prakash A, Zhong KY, Tate AT. Mapping the functional form of the trade-off between infection resistance and reproductive fitness under dysregulated immune signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552815. [PMID: 37645726 PMCID: PMC10461925 DOI: 10.1101/2023.08.10.552815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Immune responses benefit organismal fitness by clearing parasites but also exact costs associated with immunopathology and energetic investment. Hosts manage these costs by tightly regulating the induction of immune signaling to curtail excessive responses and restore homeostasis. Despite the theoretical importance of turning off the immune response to mitigate these costs, experimentally connecting variation in the negative regulation of immune responses to organismal fitness remains a frontier in evolutionary immunology. In this study, we used a dose-response approach to manipulate the RNAi-mediated knockdown efficiency of cactus (IκBα), a central regulator of Toll pathway signal transduction in flour beetles (Tribolium castaneum). By titrating cactus activity along a continuous gradient, we derived the shape of the relationship between immune response investment and traits associated with host fitness, including infection susceptibility, lifespan, fecundity, body mass, and gut homeostasis. Cactus knock-down increased the overall magintude of inducible immune responses and delayed their resolution in a dsRNA dose-dependent manner, promoting survival and resistance following bacterial infection. However, these benefits were counterbalanced by dsRNA dose-dependent costs to lifespan, fecundity, body mass, and gut integrity. Our results allowed us to move beyond the qualitative identification of a trade-off between immune investment and fitness to actually derive its functional form. This approach paves the way to quantitatively compare the evolution and impact of distinct regulatory elements on life-history trade-offs and fitness, filling a crucial gap in our conceptual and theoretical models of immune signaling network evolution and the maintenance of natural variation in immune systems.
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Affiliation(s)
- Justin T. Critchlow
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Arun Prakash
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Katherine Y. Zhong
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ann T. Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Institute, Vanderbilt University, Nashville, Tennessee, United States of America
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21
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Bracewell RR, Stillman JH, Dahlhoff EP, Smeds E, Chatla K, Bachtrog D, Williams C, Rank NE. A chromosome-scale genome assembly and evaluation of mtDNA variation in the willow leaf beetle Chrysomela aeneicollis. G3 (BETHESDA, MD.) 2023; 13:jkad106. [PMID: 37178174 PMCID: PMC10320752 DOI: 10.1093/g3journal/jkad106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/08/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
The leaf beetle Chrysomela aeneicollis has a broad geographic range across Western North America but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2,700-3,500 m) where they are limited by reduced oxygen supply and recent drought conditions that are associated with climate change. Here, we report a chromosome-scale genome assembly alongside a complete mitochondrial genome and characterize differences among mitochondrial genomes along a latitudinal gradient over which beetles show substantial population structure and adaptation to fluctuating temperatures. Our scaffolded genome assembly consists of 21 linkage groups; one of which we identified as the X chromosome based on female/male whole genome sequencing coverage and orthology with Tribolium castaneum. We identified repetitive sequences in the genome and found them to be broadly distributed across all linkage groups. Using a reference transcriptome, we annotated a total of 12,586 protein-coding genes. We also describe differences in putative secondary structures of mitochondrial RNA molecules, which may generate functional differences important in adaptation to harsh abiotic conditions. We document substitutions at mitochondrial tRNA molecules and substitutions and insertions in the 16S rRNA region that could affect intermolecular interactions with products from the nuclear genome. This first chromosome-level reference genome will enable genomic research in this important model organism for understanding the biological impacts of climate change on montane insects.
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Affiliation(s)
- Ryan R Bracewell
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathon H Stillman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | | | - Elliott Smeds
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Caroline Williams
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nathan E Rank
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
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22
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Catto MA, Labadie PE, Jacobson AL, Kennedy GG, Srinivasan R, Hunt BG. Pest status, molecular evolution, and epigenetic factors derived from the genome assembly of Frankliniella fusca, a thysanopteran phytovirus vector. BMC Genomics 2023; 24:343. [PMID: 37344773 DOI: 10.1186/s12864-023-09375-5] [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: 11/30/2022] [Accepted: 05/13/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND The tobacco thrips (Frankliniella fusca Hinds; family Thripidae; order Thysanoptera) is an important pest that can transmit viruses such as the tomato spotted wilt orthotospovirus to numerous economically important agricultural row crops and vegetables. The structural and functional genomics within the order Thysanoptera has only begun to be explored. Within the > 7000 known thysanopteran species, the melon thrips (Thrips palmi Karny) and the western flower thrips (Frankliniella occidentalis Pergrande) are the only two thysanopteran species with assembled genomes. RESULTS A genome of F. fusca was assembled by long-read sequencing of DNA from an inbred line. The final assembly size was 370 Mb with a single copy ortholog completeness of ~ 99% with respect to Insecta. The annotated genome of F. fusca was compared with the genome of its congener, F. occidentalis. Results revealed many instances of lineage-specific differences in gene content. Analyses of sequence divergence between the two Frankliniella species' genomes revealed substitution patterns consistent with positive selection in ~ 5% of the protein-coding genes with 1:1 orthologs. Further, gene content related to its pest status, such as xenobiotic detoxification and response to an ambisense-tripartite RNA virus (orthotospovirus) infection was compared with F. occidentalis. Several F. fusca genes related to virus infection possessed signatures of positive selection. Estimation of CpG depletion, a mutational consequence of DNA methylation, revealed that F. fusca genes that were downregulated and alternatively spliced in response to virus infection were preferentially targeted by DNA methylation. As in many other insects, DNA methylation was enriched in exons in Frankliniella, but gene copies with homology to DNA methyltransferase 3 were numerous and fragmented. This phenomenon seems to be relatively unique to thrips among other insect groups. CONCLUSIONS The F. fusca genome assembly provides an important resource for comparative genomic analyses of thysanopterans. This genomic foundation allows for insights into molecular evolution, gene regulation, and loci important to agricultural pest status.
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Affiliation(s)
- Michael A Catto
- Department of Entomology, University of Georgia, Athens, GA, 30602, USA
| | - Paul E Labadie
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alana L Jacobson
- Department of Entomology and Plant Pathology, Auburn University College of Agriculture, Auburn, AL, 36849, USA
| | - George G Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, GA, 30223, USA.
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23
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Kaur S, Stinson SA, diCenzo GC. Whole genome assemblies of Zophobas morio and Tenebrio molitor. G3 (BETHESDA, MD.) 2023; 13:jkad079. [PMID: 37002914 PMCID: PMC10234394 DOI: 10.1093/g3journal/jkad079] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/29/2023] [Indexed: 01/12/2024]
Abstract
Zophobas morio (=Zophobas atratus) and Tenebrio molitor are darkling beetles with industrial importance due to their use as feeder insects and their apparent ability to biodegrade plastics. High quality genome assemblies were recently reported for both species. Here, we report additional independent Z. morio and T. molitor genome assemblies generated from Nanopore and Illumina data. Following scaffolding against the published genomes, haploid assemblies of 462 Mb (scaffold N90 of 16.8 Mb) and 258 Mb (scaffold N90 of 5.9 Mb) were produced for Z. morio and T. molitor, respectively. Gene prediction led to the prediction of 28,544 and 19,830 genes for Z. morio and T. molitor, respectively. Benchmarking Universal Single Copy Orthologs (BUSCO) analyses suggested that both assemblies have a high level of completeness; 91.5 and 89.0% of the BUSCO endopterygota marker genes were complete in the Z. morio assembly and proteome, respectively, while 99.1 and 92.8% were complete in the T. molitor assembly and proteome, respectively. Phylogenomic analyses of four genera from the family Tenebrionidae yielded phylogenies consistent with those previously constructed based on mitochondrial genomes. Synteny analyses revealed large stretches of macrosynteny across the family Tenebrionidae, as well as numerous within-chromosome rearrangements. Finally, orthogroup analysis identified ∼28,000 gene families across the family Tenebrionidae, of which 8,185 were identified in all five of the analyzed species, and 10,837 were conserved between Z. morio and T. molitor. We expect that the availability of multiple whole genome sequences for Z. morio and T. molitor will facilitate population genetics studies to identify genetic variation associated with industrially relevant phenotypes.
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Affiliation(s)
- Sabhjeet Kaur
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada
| | - Sydnie A Stinson
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada
| | - George C diCenzo
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada
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24
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Morita S, Shibata TF, Nishiyama T, Kobayashi Y, Yamaguchi K, Toga K, Ohde T, Gotoh H, Kojima T, Weber JN, Salvemini M, Bino T, Mase M, Nakata M, Mori T, Mori S, Cornette R, Sakura K, Lavine LC, Emlen DJ, Niimi T, Shigenobu S. The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation. Sci Rep 2023; 13:8735. [PMID: 37253792 DOI: 10.1038/s41598-023-35246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 05/15/2023] [Indexed: 06/01/2023] Open
Abstract
The Japanese rhinoceros beetle Trypoxylus dichotomus is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as a research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10 × Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. We focused on the genes related to horn formation and obtained new insights into the evolution of the gene repertoire and sexual dimorphism as exemplified by the sex-specific splicing pattern of the doublesex gene. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.
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Grants
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- IOS-1456133 National Science Foundation
- IOS-1456133 National Science Foundation
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Affiliation(s)
- Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
| | - Tomoko F Shibata
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Tomoaki Nishiyama
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Yuuki Kobayashi
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki, Japan
| | - Katsushi Yamaguchi
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Kouhei Toga
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- URA Division, Office of Research and Academia-Government-Community Collaboration, Hiroshima University, Hiroshima, Japan
| | - Takahiro Ohde
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroki Gotoh
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Agrobiological Resources, Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Jesse N Weber
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Takahiro Bino
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Mutsuki Mase
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Moe Nakata
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tomoko Mori
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Shogo Mori
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Richard Cornette
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kazuki Sakura
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Laura C Lavine
- Department of Entomology, Washington State University, Pullman, WA, USA
| | - Douglas J Emlen
- Division of Biological Sciences, The University of Montana, Missoula, MT, USA
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan.
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan.
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
| | - Shuji Shigenobu
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan.
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki, Japan.
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan.
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25
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Gržan T, Dombi M, Despot-Slade E, Veseljak D, Volarić M, Meštrović N, Plohl M, Mravinac B. The Low-Copy-Number Satellite DNAs of the Model Beetle Tribolium castaneum. Genes (Basel) 2023; 14:genes14050999. [PMID: 37239359 DOI: 10.3390/genes14050999] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The red flour beetle Tribolium castaneum is an important pest of stored agricultural products and the first beetle whose genome was sequenced. So far, one high-copy-number and ten moderate-copy-number satellite DNAs (satDNAs) have been described in the assembled part of its genome. In this work, we aimed to catalog the entire collection of T. castaneum satDNAs. We resequenced the genome using Illumina technology and predicted potential satDNAs via graph-based sequence clustering. In this way, we discovered 46 novel satDNAs that occupied a total of 2.1% of the genome and were, therefore, considered low-copy-number satellites. Their repeat units, preferentially 140-180 bp and 300-340 bp long, showed a high A + T composition ranging from 59.2 to 80.1%. In the current assembly, we annotated the majority of the low-copy-number satDNAs on one or a few chromosomes, discovering mainly transposable elements in their vicinity. The current assembly also revealed that many of the in silico predicted satDNAs were organized into short arrays not much longer than five consecutive repeats, and some of them also had numerous repeat units scattered throughout the genome. Although 20% of the unassembled genome sequence masked the genuine state, the predominance of scattered repeats for some low-copy satDNAs raises the question of whether these are essentially interspersed repeats that occur in tandem only sporadically, with the potential to be satDNA "seeds".
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Affiliation(s)
- Tena Gržan
- Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
- University Hospital Centre Zagreb, HR-10000 Zagreb, Croatia
| | - Mira Dombi
- Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Damira Veseljak
- Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
| | - Marin Volarić
- Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
| | - Nevenka Meštrović
- Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
| | - Miroslav Plohl
- Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
| | - Brankica Mravinac
- Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
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26
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Analysis of the Toll and Spaetzle Genes Involved in Toll Pathway-Dependent Antimicrobial Gene Induction in the Red Flour Beetle, Tribolium castaneum (Coleoptera; Tenebrionidae). Int J Mol Sci 2023; 24:ijms24021523. [PMID: 36675034 PMCID: PMC9861120 DOI: 10.3390/ijms24021523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
Insects rely only on their innate immune system to protect themselves from pathogens. Antimicrobial peptide (AMP) production is the main immune reaction in insects. In Drosophila melanogaster, the reaction is regulated mainly by the Toll and immune deficiency (IMD) pathways. Spaetzle proteins, activated by immune signals from upstream components, bind to Toll proteins, thus, activating the Toll pathway, which in turn, induces AMP genes. Previous studies have shown the difference in immune systems related to Toll and IMD pathways between D. melanogaster and Tribolium castaneum. In T. castaneum, nine Toll and seven spaetzle (spz) genes were identified. To extend our understanding of AMP production by T. castaneum, we conducted functional assays of Toll and spaetzle genes related to Toll-pathway-dependent AMP gene expression in T. castaneum under challenge with bacteria or budding yeast. The results revealed that Toll3 and Toll4 double-knockdown and spz7 knockdown strongly and moderately reduced the Toll-pathway-dependent expression of AMP genes, respectively. Moreover, Toll3 and Toll4 double-knockdown pupae more rapidly succumbed to entomopathogenic bacteria than the control pupae, but spz7 knockdown pupae did not. The results suggest that Toll3 and Toll4 play a large role in Toll-pathway-dependent immune reactions, whereas spz7 plays a small part.
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27
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Chen Q, Sasikala-Appukuttan AK, Husain Z, Shrivastava A, Spain M, Sendler ED, Daines B, Fischer S, Chen R, Cook TA, Friedrich M. Global Gene Expression Analysis Reveals Complex Cuticle Organization of the Tribolium Compound Eye. Genome Biol Evol 2023; 15:evac181. [PMID: 36575057 PMCID: PMC9866248 DOI: 10.1093/gbe/evac181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
The red flour beetle Tribolium castaneum is a resource-rich model for genomic and developmental studies. To extend previous studies on Tribolium eye development, we produced transcriptomes for normal-eyed and eye-depleted heads of pupae and adults to identify differentially transcript-enriched (DE) genes in the visual system. Unexpectedly, cuticle-related genes were the largest functional class in the pupal compound eye DE gene population, indicating differential enrichment in three distinct cuticle components: clear lens facet cuticle, highly melanized cuticle of the ocular diaphragm, which surrounds the Tribolium compound eye for internal fortification, and newly identified facet margins of the tanned cuticle, possibly enhancing external fortification. Phylogenetic, linkage, and high-throughput gene knockdown data suggest that most cuticle proteins (CPs) expressed in the Tribolium compound eye stem from the deployment of ancient CP genes. Consistent with this, TcasCPR15, which we identified as the major lens CP gene in Tribolium, is a beetle-specific but pleiotropic paralog of the ancient CPR RR-2 CP gene family. The less abundant yet most likely even more lens-specific TcasCP63 is a member of a sprawling family of noncanonical CP genes, documenting a role of local gene family expansions in the emergence of the Tribolium compound eye CP repertoire. Comparisons with Drosophila and the mosquito Anopheles gambiae reveal a steady turnover of lens-enriched CP genes during insect evolution.
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Affiliation(s)
- Qing Chen
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | | | - Zahabiya Husain
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Anura Shrivastava
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Marla Spain
- Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Edward D Sendler
- Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Bryce Daines
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Stefan Fischer
- Evolutionary Biology of Invertebrates, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Rui Chen
- Evolutionary Biology of Invertebrates, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Tiffany A Cook
- Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
- Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, USA
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28
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Zhu Y, Kuang W, Leng J, Wang X, Qiu L, Kong X, Wang Y, Zhao Q. The apple 14-3-3 gene MdGRF6 negatively regulates salt tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1161539. [PMID: 37077638 PMCID: PMC10106762 DOI: 10.3389/fpls.2023.1161539] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
The 14-3-3 (GRF, general regulatory factor) regulatory proteins are highly conserved and are widely distributed throughout the eukaryotes. They are involved in the growth and development of organisms via target protein interactions. Although many plant 14-3-3 proteins were identified in response to stresses, little is known about their involvement in salt tolerance in apples. In our study, nineteen apple 14-3-3 proteins were cloned and identified. The transcript levels of Md14-3-3 genes were either up or down-regulated in response to salinity treatments. Specifically, the transcript level of MdGRF6 (a member of the Md14-3-3 genes family) decreased due to salt stress treatment. The phenotypes of transgenic tobacco lines and wild-type (WT) did not affect plant growth under normal conditions. However, the germination rate and salt tolerance of transgenic tobacco was lower compared to the WT. Transgenic tobacco demonstrated decreased salt tolerance. The transgenic apple calli overexpressing MdGRF6 exhibited greater sensitivity to salt stress compared to the WT plants, whereas the MdGRF6-RNAi transgenic apple calli improved salt stress tolerance. Moreover, the salt stress-related genes (MdSOS2, MdSOS3, MdNHX1, MdATK2/3, MdCBL-1, MdMYB46, MdWRKY30, and MdHB-7) were more strongly down-regulated in MdGRF6-OE transgenic apple calli lines than in the WT when subjected to salt stress treatment. Taken together, these results provide new insights into the roles of 14-3-3 protein MdGRF6 in modulating salt responses in plants.
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Affiliation(s)
- Yuqing Zhu
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
- Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao Agricultural University, Qingdao, Shandong, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wei Kuang
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
- Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao Agricultural University, Qingdao, Shandong, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Jun Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
- Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao Agricultural University, Qingdao, Shandong, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xue Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
- Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao Agricultural University, Qingdao, Shandong, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Linlin Qiu
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
- Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao Agricultural University, Qingdao, Shandong, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xiangyue Kong
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
- Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao Agricultural University, Qingdao, Shandong, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yongzhang Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
- Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao Agricultural University, Qingdao, Shandong, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
- *Correspondence: Qiang Zhao, ; Yongzhang Wang,
| | - Qiang Zhao
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong, China
- Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao Agricultural University, Qingdao, Shandong, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
- *Correspondence: Qiang Zhao, ; Yongzhang Wang,
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Eleftheriou E, Aury JM, Vacherie B, Istace B, Belser C, Noel B, Moret Y, Rigaud T, Berro F, Gasparian S, Labadie-Bretheau K, Lefebvre T, Madoui MA. Chromosome-scale assembly of the yellow mealworm genome. OPEN RESEARCH EUROPE 2022; 1:94. [PMID: 37645128 PMCID: PMC10445852 DOI: 10.12688/openreseurope.13987.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 03/12/2024]
Abstract
Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.
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Affiliation(s)
- Evangelia Eleftheriou
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benoît Vacherie
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Yannick Moret
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Thierry Rigaud
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | | | | | - Karine Labadie-Bretheau
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | | | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
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30
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Horn T, Narov KD, Panfilio KA. Persistent Parental RNAi in the Beetle Tribolium castaneum Involves Maternal Transmission of Long Double-Stranded RNA. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100064. [PMID: 36620196 PMCID: PMC9744488 DOI: 10.1002/ggn2.202100064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Indexed: 01/11/2023]
Abstract
Parental RNA interference (pRNAi) is a powerful and widely used method for gene-specific knockdown. Yet in insects its efficacy varies between species, and how the systemic response is transmitted from mother to offspring remains elusive. Using the beetle Tribolium castaneum, an RT-qPCR strategy to distinguish the presence of double-stranded RNA (dsRNA) from endogenous mRNA is reported. It is found that injected dsRNA is directly transmitted into the egg and persists throughout embryogenesis. Despite this depletion of dsRNA from the mother, it is shown that strong pRNAi can persist for months before waning at strain-specific rates. In seeking the receptor proteins for cellular uptake of long dsRNA into the egg, a phylogenomics profiling approach of candidate proteins is also presented. A visualization strategy based on taxonomically hierarchical assessment of orthology clustering data to rapidly assess gene age and copy number changes, refined by sequence-based evidence, is demonstrated. Repeated losses of SID-1-like channel proteins in the arthropods, including wholesale loss in the Heteroptera (true bugs), which are nonetheless highly sensitive to pRNAi, are thereby documented. Overall, practical considerations for insect pRNAi against a backdrop of outstanding questions on the molecular mechanism of dsRNA transmission for long-term, systemic knockdown are elucidated.
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Affiliation(s)
- Thorsten Horn
- Institute for Zoology: Developmental BiologyUniversity of CologneZülpicher Straße 47b50674CologneGermany
| | - Kalin D. Narov
- School of Life SciencesUniversity of WarwickGibbet Hill CampusCoventryCV4 7ALUK
| | - Kristen A. Panfilio
- Institute for Zoology: Developmental BiologyUniversity of CologneZülpicher Straße 47b50674CologneGermany
- School of Life SciencesUniversity of WarwickGibbet Hill CampusCoventryCV4 7ALUK
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Liu Z, Xing L, Huang W, Liu B, Wan F, Raffa KF, Hofstetter RW, Qian W, Sun J. Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens. BMC Biol 2022; 20:190. [PMID: 36002826 PMCID: PMC9400205 DOI: 10.1186/s12915-022-01388-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that has caused substantial tree mortality in China. The lack of a high-quality reference genome seriously limits deciphering the extent to which genetic adaptions resulted in a secondary pest becoming so destructive in its invaded area. RESULTS Here, we present a 322.41 Mb chromosome-scale reference genome of RTB, of which 98% of assembled sequences are anchored onto fourteen linkage groups including the X chromosome with a N50 size of 24.36 Mb, which is significantly greater than other Coleoptera species. Repetitive sequences make up 45.22% of the genome, which is higher than four other Coleoptera species, i.e., Mountain pine beetle Dendroctonus ponderosae, red flour beetle Tribolium castaneum, blister beetle Hycleus cichorii, and Colorado potato beetle Leptinotarsa decemlineata. We identify rapidly expanded gene families and positively selected genes in RTB, which may be responsible for its rapid environmental adaptation. Population genetic structure of RTB was revealed by genome resequencing of geographic populations in native and invaded regions, suggesting substantial divergence of the North American population and illustrates the possible invasion and spread route in China. Selective sweep analysis highlighted the enhanced ability of Chinese populations in environmental adaptation. CONCLUSIONS Overall, our high-quality reference genome represents an important resource for genomics study of invasive bark beetles, which will facilitate the functional study and decipher mechanism underlying invasion success of RTB by integrating the Pinus tabuliformis genome.
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Affiliation(s)
- Zhudong Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 1000101, China
| | - Longsheng Xing
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | | | - Bo Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Fanghao Wan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kenneth F Raffa
- Department of Entomology, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Wanqiang Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Jianghua Sun
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 1000101, China.
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Lehmann S, Atika B, Grossmann D, Schmitt-Engel C, Strohlein N, Majumdar U, Richter T, Weißkopf M, Ansari S, Teuscher M, Hakeemi MS, Li J, Weißbecker B, Klingler M, Bucher G, Wimmer EA. Phenotypic screen and transcriptomics approach complement each other in functional genomics of defensive stink gland physiology. BMC Genomics 2022; 23:608. [PMID: 35987630 PMCID: PMC9392906 DOI: 10.1186/s12864-022-08822-z] [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: 11/26/2021] [Accepted: 08/03/2022] [Indexed: 11/27/2022] Open
Abstract
Background Functional genomics uses unbiased systematic genome-wide gene disruption or analyzes natural variations such as gene expression profiles of different tissues from multicellular organisms to link gene functions to particular phenotypes. Functional genomics approaches are of particular importance to identify large sets of genes that are specifically important for a particular biological process beyond known candidate genes, or when the process has not been studied with genetic methods before. Results Here, we present a large set of genes whose disruption interferes with the function of the odoriferous defensive stink glands of the red flour beetle Tribolium castaneum. This gene set is the result of a large-scale systematic phenotypic screen using RNA interference applied in a genome-wide forward genetics manner. In this first-pass screen, 130 genes were identified, of which 69 genes could be confirmed to cause phenotypic changes in the glands upon knock-down, which vary from necrotic tissue and irregular reservoir size to irregular color or separation of the secreted gland compounds. Gene ontology analysis revealed that many of those genes are encoding enzymes (peptidases and cytochromes P450) as well as proteins involved in membrane trafficking with an enrichment in lysosome and mineral absorption pathways. The knock-down of 13 genes caused specifically a strong reduction of para-benzoquinones in the gland reservoirs, suggesting a specific function in the synthesis of these toxic compounds. Only 14 of the 69 confirmed gland genes are differentially overexpressed in stink gland tissue and thus could have been detected in a transcriptome-based analysis. However, only one out of eight genes identified by a transcriptomics approach known to cause phenotypic changes of the glands upon knock-down was recognized by this phenotypic screen, indicating the limitation of such a non-redundant first-pass screen. Conclusion Our results indicate the importance of combining diverse and independent methodologies to identify genes necessary for the function of a certain biological tissue, as the different approaches do not deliver redundant results but rather complement each other. The presented phenotypic screen together with a transcriptomics approach are now providing a set of close to hundred genes important for odoriferous defensive stink gland physiology in beetles. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08822-z.
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A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects. Genomics 2022; 114:110437. [PMID: 35902070 DOI: 10.1016/j.ygeno.2022.110437] [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: 05/08/2022] [Revised: 07/03/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
Abstract
Neoneuromus ignobilis is an archaic holometabolous aquatic predatory insect. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for adaptive evolution. Here, we provided a high-contiguity, chromosome-level genome assembly of N. ignobilis using high coverage Nanopore and PacBio reads with the Hi-C technique. The final assembly is 480.67 MB in size, containing 12 telomere-ended pseudochromosomes with only 17 gaps. We compared 42 hexapod species genomes including six independent lineages comprising 11 aquatic insects, and found convergent expansions of long wavelength-sensitive and blue-sensitive opsins, thermal stress response TRP channels, and sulfotransferases in aquatic insects, which may be related to their aquatic adaptation. We also detected strong nonrandom signals of convergent amino acid substitutions in aquatic insects. Collectively, our comparative genomic analysis revealed the evidence of molecular convergences in aquatic insects during both gene family evolution and convergent amino acid substitutions.
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Klingler M, Bucher G. The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution. EvoDevo 2022; 13:14. [PMID: 35854352 PMCID: PMC9295526 DOI: 10.1186/s13227-022-00201-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
The red flour beetle Tribolium castaneum has emerged as an important insect model system for a variety of topics. With respect to studying gene function, it is second only to the vinegar fly D. melanogaster. The RNAi response in T. castaneum is exceptionally strong and systemic, and it appears to target all cell types and processes. Uniquely for emerging model organisms, T. castaneum offers the opportunity of performing time- and cost-efficient large-scale RNAi screening, based on commercially available dsRNAs targeting all genes, which are simply injected into the body cavity. Well established transgenic and genome editing approaches are met by ease of husbandry and a relatively short generation time. Consequently, a number of transgenic tools like UAS/Gal4, Cre/Lox, imaging lines and enhancer trap lines are already available. T. castaneum has been a genetic experimental system for decades and now has become a workhorse for molecular and reverse genetics as well as in vivo imaging. Many aspects of development and general biology are more insect-typical in this beetle compared to D. melanogaster. Thus, studying beetle orthologs of well-described fly genes has allowed macro-evolutionary comparisons in developmental processes such as axis formation, body segmentation, and appendage, head and brain development. Transgenic approaches have opened new ways for in vivo imaging. Moreover, this emerging model system is the first choice for research on processes that are not represented in the fly, or are difficult to study there, e.g. extraembryonic tissues, cryptonephridial organs, stink gland function, or dsRNA-based pesticides.
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Affiliation(s)
- Martin Klingler
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Staudtstr. 5, 91058, Erlangen, Germany.
| | - Gregor Bucher
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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Filipović I, Rašić G, Hereward J, Gharuka M, Devine GJ, Furlong MJ, Etebari K. A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros). BMC Genomics 2022; 23:426. [PMID: 35672676 PMCID: PMC9172067 DOI: 10.1186/s12864-022-08628-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in insects. Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetle's mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). As an invasive pest of palm trees, O. rhinoceros is undergoing an expansion in its range across the Pacific Islands, requiring new approaches to management that may include strategies facilitated by genome assembly and annotation. RESULTS High-quality DNA isolated from an adult female was used to create four ONT libraries that were sequenced using four MinION flow cells, producing a total of 27.2 Gb of high-quality long-read sequences. We employed an iterative assembly process and polishing with one lane of high-accuracy Illumina reads, obtaining a final size of the assembly of 377.36 Mb that had high contiguity (fragment N50 length = 12 Mb) and accuracy, as evidenced by the exceptionally high completeness of the benchmarked set of conserved single-copy orthologous genes (BUSCO completeness = 99.1%). These quality metrics place our assembly ahead of the published Coleopteran genomes, including that of an insect model, the red flour beetle (Tribolium castaneum). The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes, with only 2.8% missing BUSCOs, and the expected number of non-coding RNAs. The number and structure of paralogous genes in a gene family like Sigma GST is lower than in another scarab beetle (Onthophagus taurus), but higher than in the red flour beetle (Tribolium castaneum), which suggests expansion of this GST class in Scarabaeidae. The quality of our gene models was also confirmed with the correct placement of O. rhinoceros among other members of the rhinoceros beetles (subfamily Dynastinae) in a phylogeny based on the sequences of 95 protein-coding genes in 373 beetle species from all major lineages of Coleoptera. Finally, we provide a list of 30 candidate dsRNA targets whose orthologs have been experimentally validated as highly effective targets for RNAi-based control of several beetles. CONCLUSIONS The genomic resources produced in this study form a foundation for further functional genetic research and management programs that may inform the control and surveillance of O. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect.
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Affiliation(s)
- Igor Filipović
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia.
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - James Hereward
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Maria Gharuka
- Research Division, Ministry of Agriculture and Livestock, Honiara, Solomon Islands
| | - Gregor J Devine
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Kayvan Etebari
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
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Feron R, Waterhouse RM. Exploring new genomic territories with emerging model insects. CURRENT OPINION IN INSECT SCIENCE 2022; 51:100902. [PMID: 35301165 DOI: 10.1016/j.cois.2022.100902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Improvements in reference genome generation for insects and across the tree of life are extending the concept and utility of model organisms beyond traditional laboratory-tractable supermodels. Species or groups of species with comprehensive genome resources can be developed into model systems for studying a large variety of biological phenomena. Advances in sequencing and assembly technologies are supporting these emerging genome-enabled model systems by producing resources that are increasingly accurate and complete. Nevertheless, quality controls including assessing gene content completeness are required to ensure that these data can be included in expanding catalogues of high-quality references that will greatly advance understanding of insect biology and evolution.
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Affiliation(s)
- Romain Feron
- Department of Ecology and Evolution, University of Lausanne, and the Swiss Institute of Bioinformatics,1015 Lausanne, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and the Swiss Institute of Bioinformatics,1015 Lausanne, Switzerland.
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Volarić M, Despot-Slade E, Veseljak D, Meštrović N, Mravinac B. Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani. Int J Mol Sci 2022; 23:5869. [PMID: 35682551 PMCID: PMC9180572 DOI: 10.3390/ijms23115869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/06/2023] Open
Abstract
The flour beetle Tribolium freemani is a sibling species of the model organism and important pest Tribolium castaneum. The two species are so closely related that they can produce hybrid progeny, but the genetic basis of their differences has not been revealed. In this work, we sequenced the T. freemani genome by applying PacBio HiFi technology. Using the well-assembled T. castaneum genome as a reference, we assembled 262 Mb of the T. freemani genomic sequence and anchored it in 10 linkage groups corresponding to nine autosomes and sex chromosome X. The assembly showed 99.8% completeness of conserved insect genes, indicating a high-quality reference genome. Comparison with the T. castaneum assembly revealed that the main differences in genomic sequence between the two sibling species come from repetitive DNA, including interspersed and tandem repeats. In this work, we also provided the complete assembled mitochondrial genome of T. freemani. Although the genome assembly needs to be ameliorated in tandemly repeated regions, the first version of the T. freemani reference genome and the complete mitogenome presented here represent useful resources for comparative evolutionary studies of related species and for further basic and applied research on different biological aspects of economically important pests.
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Affiliation(s)
| | | | | | | | - Brankica Mravinac
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.V.); (E.D.-S.); (D.V.); (N.M.)
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Nishiko M, Sakamoto T, Mun S, Noh MY, Arakane Y, Kanost MR, Arai K, Tabunoki H. Superoxide dismutase 6 is required during metamorphosis for the development of properly movable legs in Tribolium castaneum. Sci Rep 2022; 12:6900. [PMID: 35477951 PMCID: PMC9046187 DOI: 10.1038/s41598-022-10166-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/04/2022] [Indexed: 11/09/2022] Open
Abstract
The body form of holometabolous insects dramatically transforms from larval to adult stages during metamorphosis that occurs in the pupal stage. The larval disorganization and then new adult tissues are built up at this time. In motoneuron, larval neuronal cells degenerate, and new adult neurons are remodeled. Finally, adult neurons reconnect to new adult muscles. However, the factors that control metamorphosis have not yet been fully elucidated. Here, we show that an antioxidant enzyme, Tribolium castaneum superoxide dismutase 6 (TcSOD6), is secreted into the haemolymph and is required for proper movable legs during metamorphosis. TcSOD6 has a unique domain architecture and is mainly expressed in the pupal stage. The depletion of TcSOD6 expression in the pupa inhibits normal axon development and results in adults that display dysfunctional leg motions, suggesting that SOD6 expression is required for the development of properly movable legs. Therefore, we speculate that TcSOD6 might participate in some of the processes for larval neurons to be remodelled to new adult functions in the legs during metamorphosis, providing new insight into the evolution of SOD functions.
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Affiliation(s)
- Maaya Nishiko
- Department of United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takuma Sakamoto
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Seulgi Mun
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea
| | - Mi Young Noh
- Department of Forest Resources, AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju, 61186, South Korea
| | - Yasuyuki Arakane
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea
| | - Michael R Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141Chalmers Hall, Manhattan, KS, 66506-3702, USA
| | - Katsuhiko Arai
- Department of Tissue Physiology, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Hiroko Tabunoki
- Department of United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
- Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and System Engineering, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
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Hakeemi MS, Ansari S, Teuscher M, Weißkopf M, Großmann D, Kessel T, Dönitz J, Siemanowski J, Wan X, Schultheis D, Frasch M, Roth S, Schoppmeier M, Klingler M, Bucher G. Screens in fly and beetle reveal vastly divergent gene sets required for developmental processes. BMC Biol 2022; 20:38. [PMID: 35135533 PMCID: PMC8827203 DOI: 10.1186/s12915-022-01231-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/12/2022] [Indexed: 12/05/2022] Open
Abstract
Background Most of the known genes required for developmental processes have been identified by genetic screens in a few well-studied model organisms, which have been considered representative of related species, and informative—to some degree—for human biology. The fruit fly Drosophila melanogaster is a prime model for insect genetics, and while conservation of many gene functions has been observed among bilaterian animals, a plethora of data show evolutionary divergence of gene function among more closely-related groups, such as within the insects. A quantification of conservation versus divergence of gene functions has been missing, without which it is unclear how representative data from model systems actually are. Results Here, we systematically compare the gene sets required for a number of homologous but divergent developmental processes between fly and beetle in order to quantify the difference of the gene sets. To that end, we expanded our RNAi screen in the red flour beetle Tribolium castaneum to cover more than half of the protein-coding genes. Then we compared the gene sets required for four different developmental processes between beetle and fly. We found that around 50% of the gene functions were identified in the screens of both species while for the rest, phenotypes were revealed only in fly (~ 10%) or beetle (~ 40%) reflecting both technical and biological differences. Accordingly, we were able to annotate novel developmental GO terms for 96 genes studied in this work. With this work, we publish the final dataset for the pupal injection screen of the iBeetle screen reaching a coverage of 87% (13,020 genes). Conclusions We conclude that the gene sets required for a homologous process diverge more than widely believed. Hence, the insights gained in flies may be less representative for insects or protostomes than previously thought, and work in complementary model systems is required to gain a comprehensive picture. The RNAi screening resources developed in this project, the expanding transgenic toolkit, and our large-scale functional data make T. castaneum an excellent model system in that endeavor. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01231-4.
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Affiliation(s)
- Muhammad Salim Hakeemi
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Salim Ansari
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Current address: Institute of Clinical Pharmacology, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Matthias Teuscher
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Matthias Weißkopf
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Daniela Großmann
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Current address: Department of Medical Bioinformatics, University Medical Center Göttingen, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Tobias Kessel
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.,Current address: Department of Insect Biotechnology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Gießen, Germany
| | - Jürgen Dönitz
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Janna Siemanowski
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Current address: Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50924, Cologne, Germany
| | - Xuebin Wan
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Dorothea Schultheis
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.,Current address: Institute of Neuropathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Manfred Frasch
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Siegfried Roth
- Institute for Zoology/Developmental Biology, University of Cologne, Biocenter, Zülpicher Straße 47b, D-50674, Köln, Germany
| | - Michael Schoppmeier
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Martin Klingler
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Gregor Bucher
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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Simakov O, Bredeson J, Berkoff K, Marletaz F, Mitros T, Schultz DT, O’Connell BL, Dear P, Martinez DE, Steele RE, Green RE, David CN, Rokhsar DS. Deeply conserved synteny and the evolution of metazoan chromosomes. SCIENCE ADVANCES 2022; 8:eabi5884. [PMID: 35108053 PMCID: PMC8809688 DOI: 10.1126/sciadv.abi5884] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 12/10/2021] [Indexed: 05/04/2023]
Abstract
Animal genomes show networks of deeply conserved gene linkages whose phylogenetic scope and chromosomal context remain unclear. Here, we report chromosome-scale conservation of synteny among bilaterians, cnidarians, and sponges and use comparative analysis to reconstruct ancestral chromosomes across major animal groups. Comparisons among diverse metazoans reveal the processes of chromosome evolution that produced contemporary karyotypes from their Precambrian progenitors. On the basis of these findings, we introduce a simple algebraic representation of chromosomal change and use it to establish a unified systematic framework for metazoan chromosome evolution. We find that fusion-with-mixing, a previously unappreciated mode of chromosome change, has played a central role. We find that relicts of several metazoan chromosomal units are preserved in unicellular eukaryotes. These conserved pre-metazoan linkages include the chromosomal unit that encodes the most diverse set of metazoan homeobox genes, suggesting a candidate genomic context for the early diversification of this key gene family.
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Affiliation(s)
- Oleg Simakov
- Department for Neurosciences and Developmental
Biology, University of Vienna, Vienna 1010, Austria
| | - Jessen Bredeson
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Kodiak Berkoff
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Ferdinand Marletaz
- Molecular Genetics Unit, Okinawa Institute of Science
and Technology Graduate University, 1919-1, Tancha, Onna, Okinawa 904-0495,
Japan
- Division of Biosciences, University College London,
Gower St., London WC1E 6BT, UK
| | - Therese Mitros
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Darrin T. Schultz
- Department of Biomolecular Engineering, University of
California, Santa Cruz, Santa Cruz, CA 95064, USA
- Monterey Bay Aquarium Research Institute, Moss
Landing, CA 95039, USA
| | - Brendan L. O’Connell
- Department of Biomolecular Engineering, University of
California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Paul Dear
- Mote Research Ltd, Babraham Hall, Babraham, Cambridge
CB2 4AT, UK
| | | | - Robert E. Steele
- Department of Biological Chemistry, University of
California, Irvine, Irvine, CA 92697-1700, USA
| | - Richard E. Green
- Department of Biomolecular Engineering, University of
California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Charles N. David
- Faculty of Biology, Ludwig Maximilian University of
Munich, Munich 80539, Germany
| | - Daniel S. Rokhsar
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
- Molecular Genetics Unit, Okinawa Institute of Science
and Technology Graduate University, 1919-1, Tancha, Onna, Okinawa 904-0495,
Japan
- Chan Zuckerberg Biohub, 499 Illinois St., San
Francisco, CA 94158, USA
- U.S. Department of Energy Joint Genome Institute,
Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720,
USA
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41
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Campbell JF, Athanassiou CG, Hagstrum DW, Zhu KY. Tribolium castaneum: A Model Insect for Fundamental and Applied Research. ANNUAL REVIEW OF ENTOMOLOGY 2022; 67:347-365. [PMID: 34614365 DOI: 10.1146/annurev-ento-080921-075157] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Tribolium castaneum has a long history as a model species in many distinct subject areas, but improved connections among the genetics, genomics, behavioral, ecological, and pest management fields are needed to fully realize this species' potential as a model. Tribolium castaneum was the first beetle whose genome was sequenced, and a new genome assembly and enhanced annotation, combined with readily available genomic research tools, have facilitated its increased use in a wide range of functional genomics research. Research into T. castaneum's sensory systems, response to pheromones and kairomones, and patterns of movement and landscape utilization has improved our understanding of behavioral and ecological processes. Tribolium castaneum has also been a model in the development of pest monitoring and management tactics, including evaluation of insecticide resistance mechanisms. Application of functional genomics approaches to behavioral, ecological, and pest management research is in its infancy but offers a powerful tool that can link mechanism with function and facilitate exploitation of these relationships to better manage this important food pest.
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Affiliation(s)
- James F Campbell
- Center for Grain and Animal Health Research, Agricultural Research Service, United States Department of Agriculture, Manhattan, Kansas 66502, USA;
| | - Christos G Athanassiou
- Laboratory of Entomology and Agricultural Zoology, Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Volos 382 21, Greece;
| | - David W Hagstrum
- Department of Entomology, Kansas State University, Manhattan, Kansas 66506, USA; ,
| | - Kun Yan Zhu
- Department of Entomology, Kansas State University, Manhattan, Kansas 66506, USA; ,
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Manni M, Berkeley MR, Seppey M, Zdobnov EM. BUSCO: Assessing Genomic Data Quality and Beyond. Curr Protoc 2021; 1:e323. [PMID: 34936221 DOI: 10.1002/cpz1.323] [Citation(s) in RCA: 304] [Impact Index Per Article: 101.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evaluation of the quality of genomic "data products" such as genome assemblies or gene sets is of critical importance in order to recognize possible issues and correct them during the generation of new data. It is equally essential to guide subsequent or comparative analyses with existing data, as the correct interpretation of the results necessarily requires knowledge about the quality level and reliability of the inputs. Using datasets of near universal single-copy orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy of genomic data by providing biologically meaningful metrics based on expected gene content. These can complement technical metrics such as contiguity measures (e.g., number of contigs/scaffolds, and N50 values). Here, we describe the use of the BUSCO tool suite to assess different data types that can range from genome assemblies of single isolates and assembled transcriptomes and annotated gene sets to metagenome-assembled genomes where the taxonomic origin of the species is unknown. BUSCO is the only tool capable of assessing all these types of sequences from both eukaryotic and prokaryotic species. The protocols detail the various BUSCO running modes and the novel workflows introduced in versions 4 and 5, including the batch analysis on multiple inputs, the auto-lineage workflow to run assessments without specifying a dataset, and a workflow for the evaluation of (large) eukaryotic genomes. The protocols further cover the BUSCO setup, guidelines to interpret the results, and BUSCO "plugin" workflows for performing common operations in genomics using BUSCO results, such as building phylogenomic trees and visualizing syntenies. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Assessing an input sequence with a BUSCO dataset specified manually Basic Protocol 2: Assessing an input sequence with a dataset automatically selected by BUSCO Basic Protocol 3: Assessing multiple inputs Alternate Protocol: Decreasing analysis runtime when assessing a large number of small genomes with BUSCO auto-lineage workflow and Snakemake Support Protocol 1: BUSCO setup Support Protocol 2: Visualizing BUSCO results Support Protocol 3: Building phylogenomic trees.
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Affiliation(s)
- Mosè Manni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Matthew R Berkeley
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Mathieu Seppey
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
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43
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Pechmann M, Prpic NM. The T-box gene optomotor-blind organizes proximodistal leg patterning in the beetle Tribolium castaneum by repressing dorsal Dpp pathway activity. Dev Biol 2021; 482:124-134. [PMID: 34942194 DOI: 10.1016/j.ydbio.2021.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/26/2021] [Accepted: 12/16/2021] [Indexed: 11/03/2022]
Abstract
Leg axis formation in Drosophila is organized by Wingless (Wg) and Decapentaplegic (Dpp) that control a number of downstream factors to pattern the dorsoventral (DV) and proximodistal (PD) axis. The T-box genes are important downstream factors mainly involved in dorsoventral leg axis formation. The ventral side is specified by H15 and midline, whereas optomotor-blind (omb) and Dorsocross (Doc1) are factors to specify dorsal cell fates. We show here that omb also organizes PD leg axis patterning in the beetle Tribolium castaneum. In the legs, Tc-omb is expressed along the dorsal side and represses ventral factors like wg and H15. Intriguingly, removing Tc-omb function leads to the activation of the Dpp pathway along the dorsal side of the legs, thus mimicking normal dpp expression in Drosophila. Dpp activity along the dorsal side leads to altered expression of proximal-distal patterning genes such as Distal-less (Dll) and dachshund (dac). Our results indicate a cell-autonomous activation of Dll and repression of dac by dpp. These findings are compatible with the cross-regulatory "cascade model" of proximal-distal leg imaginal disc patterning of Drosophila.
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Affiliation(s)
- Matthias Pechmann
- Universität zu Köln, Biozentrum Köln, Institut für Zoologie, Zülpicher Straße 47b, 50674, Köln, Germany.
| | - Nikola-Michael Prpic
- Justus-Liebig-Universität Gießen, Institut für Allgemeine Zoologie und Entwicklungsbiologie, AG Zoologie mit dem Schwerpunkt Molekulare Entwicklungsbiologie, Heinrich-Buff-Ring 38, 35392, Gießen, Germany.
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44
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Parisot N, Vargas-Chávez C, Goubert C, Baa-Puyoulet P, Balmand S, Beranger L, Blanc C, Bonnamour A, Boulesteix M, Burlet N, Calevro F, Callaerts P, Chancy T, Charles H, Colella S, Da Silva Barbosa A, Dell'Aglio E, Di Genova A, Febvay G, Gabaldón T, Galvão Ferrarini M, Gerber A, Gillet B, Hubley R, Hughes S, Jacquin-Joly E, Maire J, Marcet-Houben M, Masson F, Meslin C, Montagné N, Moya A, Ribeiro de Vasconcelos AT, Richard G, Rosen J, Sagot MF, Smit AFA, Storer JM, Vincent-Monegat C, Vallier A, Vigneron A, Zaidman-Rémy A, Zamoum W, Vieira C, Rebollo R, Latorre A, Heddi A. The transposable element-rich genome of the cereal pest Sitophilus oryzae. BMC Biol 2021; 19:241. [PMID: 34749730 PMCID: PMC8576890 DOI: 10.1186/s12915-021-01158-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. RESULTS We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. CONCLUSIONS Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.
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Affiliation(s)
- Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Carlos Vargas-Chávez
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Present Address: Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Clément Goubert
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, New York, 14853, USA
- Present Address: Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Séverine Balmand
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Louis Beranger
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Caroline Blanc
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aymeric Bonnamour
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Matthieu Boulesteix
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Federica Calevro
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Patrick Callaerts
- Department of Human Genetics, Laboratory of Behavioral and Developmental Genetics, KU Leuven, University of Leuven, B-3000, Leuven, Belgium
| | - Théo Chancy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | - Stefano Colella
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, INRAE, SupAgro, Univ Montpellier, Montpellier, France
| | - André Da Silva Barbosa
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Elisa Dell'Aglio
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Alex Di Genova
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
- Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gérard Febvay
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Toni Gabaldón
- Life Sciences, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Mechanisms of Disease, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Institut Catalan de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Alexandra Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | | | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Justin Maire
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Florent Masson
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain
| | | | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653, Le Rheu, France
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | | | | | | | - Agnès Vallier
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aurélien Vigneron
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Department of Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, 55128, Mainz, Germany
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Waël Zamoum
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France.
- ERABLE European Team, INRIA, Rhône-Alpes, France.
| | - Rita Rebollo
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain.
| | - Abdelaziz Heddi
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
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Deep Conservation of Hid-Like RHG Gene Family Homologs in Winged Insects Revealed by "Taxon Hopping" BLAST. INSECTS 2021; 12:insects12110957. [PMID: 34821758 PMCID: PMC8620624 DOI: 10.3390/insects12110957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022]
Abstract
Together with sickle (skl), the Drosophila paralogs reaper (rpr), head involution defective (hid), and grim (RHG) control a critical switch in the induction of programmed cell death. RHG homologs have been identified in other dipteran and lepidopteran species but not beyond. Revisiting this issue with a "taxon hopping" BLAST search strategy in current genome and transcriptome resources, I detected high confidence RHG homologs in Coleoptera, Hymenoptera, Hemiptera, and Dictyoptera. Analyses of gene structure and protein sequence conservation revealed aconserved splicing pattern and highly conserved amino acid residues at both the N- and C-terminal ends that identify hid as the most ancestrally organized RHG gene family member in Drosophila. hid-like RHG homologs were also detected in mosquitoes, redefining their michelob_x (mx) genes as an expansion of derived RHG homologs. Only singleton homologs were detected in the large majority of other insect clades. Lepidopteran RHG homologs, however, stand out by producing an evolutionarily-derived splice isoform, identified in previous work, in addition to the newly detected hid-like isoform. Exceptional sequence diversification of select RHG homologs at the family- and genus-level explain their previous elusiveness in important insect genome model species like the red flour beetle Tribolium castaneum and the pea aphid Acyrthosiphon pisum. Combined, these findings expand the minimal age of the RHG gene family by about 100 million years and open new avenues for molecular cell death studies in insects.
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Montino A, Balakrishnan K, Dippel S, Trebels B, Neumann P, Wimmer EA. Mutually Exclusive Expression of Closely Related Odorant-Binding Proteins 9A and 9B in the Antenna of the Red Flour Beetle Tribolium castaneum. Biomolecules 2021; 11:1502. [PMID: 34680135 PMCID: PMC8533528 DOI: 10.3390/biom11101502] [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: 08/30/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 01/01/2023] Open
Abstract
Olfaction is crucial for insects to find food sources, mates, and oviposition sites. One of the initial steps in olfaction is facilitated by odorant-binding proteins (OBPs) that translocate hydrophobic odorants through the aqueous olfactory sensilla lymph to the odorant receptor complexes embedded in the dendritic membrane of olfactory sensory neurons. The Tribolium castaneum (Coleoptera, Tenebrionidae) OBPs encoded by the gene pair TcasOBP9A and TcasOBP9B represent the closest homologs to the well-studied Drosophila melanogaster OBP Lush (DmelOBP76a), which mediates pheromone reception. By an electroantennographic analysis, we can show that these two OBPs are not pheromone-specific but rather enhance the detection of a broad spectrum of organic volatiles. Both OBPs are expressed in the antenna but in a mutually exclusive pattern, despite their homology and gene pair character by chromosomal location. A phylogenetic analysis indicates that this gene pair arose at the base of the Cucujiformia, which dates the gene duplication event to about 200 Mio years ago. Therefore, this gene pair is not the result of a recent gene duplication event and the high sequence conservation in spite of their expression in different sensilla is potentially the result of a common function as co-OBPs.
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Affiliation(s)
- Alice Montino
- GZMB, Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, Ernst-Caspari-Haus, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany; (A.M.); (S.D.)
- Goettingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, Georg-August University School of Science, University of Goettingen, 37077 Goettingen, Germany
| | - Karthi Balakrishnan
- Department of Forest Zoology and Forest Conservation, Buesgen-Institute, Georg-August-University Goettingen, Buesgenweg 3, 37077 Goettingen, Germany;
| | - Stefan Dippel
- GZMB, Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, Ernst-Caspari-Haus, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany; (A.M.); (S.D.)
- Department of Biology—Animal Physiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany;
| | - Björn Trebels
- Department of Biology—Animal Physiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany;
| | - Piotr Neumann
- GZMB, Department of Molecular Structural Biology, Institute of Microbiology & Genetics, Ernst-Caspari-Haus, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany;
| | - Ernst A. Wimmer
- GZMB, Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, Ernst-Caspari-Haus, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany; (A.M.); (S.D.)
- Goettingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, Georg-August University School of Science, University of Goettingen, 37077 Goettingen, Germany
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47
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Ogata N. Whole-Genome Sequence of the Trypoxylus dichotomus Japanese rhinoceros beetle. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000487. [PMID: 34723147 PMCID: PMC8553429 DOI: 10.17912/micropub.biology.000487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/06/2022]
Abstract
The draft whole-genome sequence of the Japanese rhinoceros beetle, Trypoxylus dichotomus was obtained using long-read PacBio sequence technology. The final assembled genome consisted of 739 Mbp in 2,347 contigs, with 24.5× mean coverage and a G+C content of 35.99%.
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Affiliation(s)
- Norichika Ogata
- Nihon BioData Corporation,
Correspondence to: Norichika Ogata ()
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48
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Garcia-Perez NC, Bucher G, Buescher M. Shaking hands is a homeodomain transcription factor that controls axon outgrowth of central complex neurons in the insect model Tribolium. Development 2021; 148:272435. [PMID: 34415334 PMCID: PMC8543150 DOI: 10.1242/dev.199368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/09/2021] [Indexed: 01/22/2023]
Abstract
Gene regulatory mechanisms that specify subtype identity of central complex (CX) neurons are the subject of intense investigation. The CX is a compartment within the brain common to all insect species and functions as a ‘command center’ that directs motor actions. It is made up of several thousand neurons, with more than 60 morphologically distinct identities. Accordingly, transcriptional programs must effect the specification of at least as many neuronal subtypes. We demonstrate a role for the transcription factor Shaking hands (Skh) in the specification of embryonic CX neurons in Tribolium. The developmental dynamics of skh expression are characteristic of terminal selectors of subtype identity. In the embryonic brain, skh expression is restricted to a subset of neurons, many of which survive to adulthood and contribute to the mature CX. skh expression is maintained throughout the lifetime in at least some CX neurons. skh knockdown results in axon outgrowth defects, thus preventing the formation of an embryonic CX primordium. The previously unstudied Drosophila skh shows a similar embryonic expression pattern, suggesting that subtype specification of CX neurons may be conserved. Summary: A detailed examination of the developmental expression of the homeodomain transcription factor Shaking hands in Tribolium reveals a role in the formation of the central complex primordium.
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Affiliation(s)
- Natalia Carolina Garcia-Perez
- Johann Friedrich Blumenbach Institute of Zoology, GZMB, Department of Evolutionary Developmental Genetics, University of Goettingen, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
| | - Gregor Bucher
- Johann Friedrich Blumenbach Institute of Zoology, GZMB, Department of Evolutionary Developmental Genetics, University of Goettingen, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
| | - Marita Buescher
- Johann Friedrich Blumenbach Institute of Zoology, GZMB, Department of Evolutionary Developmental Genetics, University of Goettingen, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
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The β 2Tubulin, Rad50-ATPase and enolase cis-regulatory regions mediate male germline expression in Tribolium castaneum. Sci Rep 2021; 11:18131. [PMID: 34518617 PMCID: PMC8438054 DOI: 10.1038/s41598-021-97443-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/19/2021] [Indexed: 11/19/2022] Open
Abstract
Genetics-based pest management processes, including the sterile insect technique, are an effective method for the control of some pest insects. However, current SIT methods are not directly transferable to many important pest insect species due to the lack of genetic sexing strains. Genome editing is revolutionizing the way we conduct genetics in insects, including in Tribolium castaneum, an important genetic model and agricultural pest. We identified orthologues of β2Tubulin, Rad50-ATPase and enolase in T. castaneum. Using RT-PCR, we confirmed that these genes are predominantly expressed in the testis. PiggyBac-based transformation of T. castaneum cis-regulatory regions derived from Tc-β2t, Tc-rad50 or Tc-eno resulted in EGFP expression specifically in the T. castaneum testis. Additionally, we determined that each of these regulatory regions regulates EGFP expression in different cell types of the male gonad. Cis-regulatory regions from Tc-β2t produced EGFP expression throughout spermatogenesis and also in mature sperms; Tc-rad50 resulted in expression only in the haploid spermatid, while Tc-eno expressed EGFP in late spermatogenesis. In summary, the regulatory cis-regions characterized in this study are not only suited to study male gonadal function but could be used for development of transgenic sexing strains that produce one sex in pest control strategies.
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Powell D, Groβe-Wilde E, Krokene P, Roy A, Chakraborty A, Löfstedt C, Vogel H, Andersson MN, Schlyter F. A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest. Commun Biol 2021; 4:1059. [PMID: 34504275 PMCID: PMC8429705 DOI: 10.1038/s42003-021-02602-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
Conifer-feeding bark beetles are important herbivores and decomposers in forest ecosystems. These species complete their life cycle in nutritionally poor substrates and some can kill enormous numbers of trees during population outbreaks. The Eurasian spruce bark beetle (Ips typographus) can destroy >100 million m3 of spruce in a single year. We report a 236.8 Mb I. typographus genome assembly using PacBio long-read sequencing. The final phased assembly has a contig N50 of 6.65 Mb in 272 contigs and is predicted to contain 23,923 protein-coding genes. We reveal expanded gene families associated with plant cell wall degradation, including pectinases, aspartyl proteases, and glycosyl hydrolases. This genome sequence from the genus Ips provides timely resources to address questions about the evolutionary biology of the true weevils (Curculionidae), one of the most species-rich animal families. In forests of today, increasingly stressed by global warming, this draft genome may assist in developing pest control strategies to mitigate outbreaks.
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Affiliation(s)
- Daniel Powell
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Excellent Team for Mitigation (ETM), Kamýcká 129, Praha 6, Suchdol, Czech Republic
- Department of Biology, Lund University, Lund, Sweden
- Global Change Ecology Research Group, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Ewald Groβe-Wilde
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Excellent Team for Mitigation (ETM), Kamýcká 129, Praha 6, Suchdol, Czech Republic
| | - Paal Krokene
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Amit Roy
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Excellent Team for Mitigation (ETM), Kamýcká 129, Praha 6, Suchdol, Czech Republic
| | - Amrita Chakraborty
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, EVA 4.0 Unit, Kamýcká 129, Praha 6, Suchdol, Czech Republic
| | | | - Heiko Vogel
- Entomology Department, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Fredrik Schlyter
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Excellent Team for Mitigation (ETM), Kamýcká 129, Praha 6, Suchdol, Czech Republic
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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