1
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Ang G, Zhang A, Obrycki J, Sethuraman A. A high-quality genome of the convergent lady beetle, Hippodamia convergens. G3 (BETHESDA, MD.) 2024; 14:jkae083. [PMID: 38620009 DOI: 10.1093/g3journal/jkae083] [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: 09/25/2023] [Revised: 09/25/2023] [Accepted: 03/29/2024] [Indexed: 04/17/2024]
Abstract
Here, we describe a high-quality genome assembly and annotation of the convergent lady beetle, Hippodamia convergens (Coleoptera: Coccinellidae). The highest quality unmasked genome comprises 619 megabases (Mb) of chromosomal DNA, organized into 899 contigs, with a contig N50 score of 89 Mbps. The genome was assessed to be 96% complete (BUSCO). Reconstruction of a whole-genome phylogeny resolved H. convergens as sister to the Harlequin lady beetle, Harmonia axyridis, and nested within a clade of several known agricultural pests.
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Affiliation(s)
- Gavrila Ang
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Andrew Zhang
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
- National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - John Obrycki
- Department of Entomology, University of Kentucky, Lexington, KY 40506, USA
| | - Arun Sethuraman
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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2
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Shen R, Sylvester T, Shin NR, Zhan Z, Jin J, Yang D, McKenna DD, Liu X. Chromosome-level genome assembly of the snakefly Mongoloraphidia duomilia (Raphidioptera: Raphidiidae). Sci Data 2024; 11:579. [PMID: 38834590 DOI: 10.1038/s41597-024-03439-1] [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: 03/01/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024] Open
Abstract
Raphidioptera (snakeflies) are a holometabolan order with the least species diversity but play a pivotal role in understanding the origin of complete metamorphosis. Here, we provide an annotated, chromosome-level reference genome assembly for an Asian endemic snakefly Mongoloraphidia duomilia (Yang, 1998) of the family Raphidiidae, assembled using PacBio HiFi and Hi-C data from female specimens. The resulting assembly is 653.56 Mb, of which 97.90% is anchored into 13 chromosomes. The scaffold N50 is 53.50 Mb, and BUSCO completeness is 97.80%. Repetitive elements comprise 64.31% of the genome (366.04 Mb). We identified 599 noncoding RNAs and predicted 11,141 protein-coding genes in the genome (97.70% BUSCO completeness). The new snakefly genome will facilitate comparison of genome architecture across Neuropterida and Holometabola and shed light on the ecological and evolutionary transitions between Neuropterida and Coleopterida.
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Affiliation(s)
- Rongrong Shen
- Department of Entomology, China Agricultural University, Beijing, 100193, China
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Terrence Sylvester
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Na Ra Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Zhihong Zhan
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianfeng Jin
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, China.
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3
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Miles LS, Waterman H, Ayoub NA, Garb JE, Haney RA, Rosenberg MS, Krabbenhoft TJ, Verrelli BC. Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider. J Hered 2024; 115:241-252. [PMID: 38567866 DOI: 10.1093/jhered/esae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/19/2024] [Indexed: 05/12/2024] Open
Abstract
Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.
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Affiliation(s)
- Lindsay S Miles
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, United States
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Hannah Waterman
- Department of Biological Sciences and Research and Education in Energy, Environment, and Water Institute, University at Buffalo, Buffalo, NY, United States
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Robert A Haney
- Department of Biology, Ball State University, Muncie, IN, United States
| | - Michael S Rosenberg
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Trevor J Krabbenhoft
- Department of Biological Sciences and Research and Education in Energy, Environment, and Water Institute, University at Buffalo, Buffalo, NY, United States
| | - Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, United States
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4
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Bryant MJ, Coello AM, Glendening AM, Hilliman SA, Jara CF, Pring SS, Rodríguez Rivera A, Santiago Membreño J, Nigro L, Pauloski N, Graham MR, King T, Jockusch EL, O’Neill RJ, Wegrzyn JL, Santibáñez-López CE, Webster CN. Unveiling the Genetic Blueprint of a Desert Scorpion: A Chromosome-level Genome of Hadrurus arizonensis Provides the First Reference for Parvorder Iurida. Genome Biol Evol 2024; 16:evae097. [PMID: 38701023 PMCID: PMC11126328 DOI: 10.1093/gbe/evae097] [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: 03/22/2024] [Revised: 04/19/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024] Open
Abstract
Over 400 million years old, scorpions represent an ancient group of arachnids and one of the first animals to adapt to life on land. Presently, the lack of available genomes within scorpions hinders research on their evolution. This study leverages ultralong nanopore sequencing and Pore-C to generate the first chromosome-level assembly and annotation for the desert hairy scorpion, Hadrurus arizonensis. The assembled genome is 2.23 Gb in size with an N50 of 280 Mb. Pore-C scaffolding reoriented 99.6% of bases into nine chromosomes and BUSCO identified 998 (98.6%) complete arthropod single copy orthologs. Repetitive elements represent 54.69% of the assembled bases, including 872,874 (29.39%) LINE elements. A total of 18,996 protein-coding genes and 75,256 transcripts were predicted, and extracted protein sequences yielded a BUSCO score of 97.2%. This is the first genome assembled and annotated within the family Hadruridae, representing a crucial resource for closing gaps in genomic knowledge of scorpions, resolving arachnid phylogeny, and advancing studies in comparative and functional genomics.
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Affiliation(s)
- Meridia Jane Bryant
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Asher M Coello
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - A M Glendening
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Samuel A Hilliman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Carolina Fernanda Jara
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Samuel S Pring
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | | | | | - Lisa Nigro
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Nicole Pauloski
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Matthew R Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, USA
| | - Teisha King
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Elizabeth L Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Rachel J O’Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | | | - Cynthia N Webster
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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5
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Pawar S, Huxley PJ, Smallwood TRC, Nesbit ML, Chan AHH, Shocket MS, Johnson LR, Kontopoulos DG, Cator LJ. Variation in temperature of peak trait performance constrains adaptation of arthropod populations to climatic warming. Nat Ecol Evol 2024; 8:500-510. [PMID: 38273123 DOI: 10.1038/s41559-023-02301-8] [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: 05/22/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
The capacity of arthropod populations to adapt to long-term climatic warming is currently uncertain. Here we combine theory and extensive data to show that the rate of their thermal adaptation to climatic warming will be constrained in two fundamental ways. First, the rate of thermal adaptation of an arthropod population is predicted to be limited by changes in the temperatures at which the performance of four key life-history traits can peak, in a specific order of declining importance: juvenile development, adult fecundity, juvenile mortality and adult mortality. Second, directional thermal adaptation is constrained due to differences in the temperature of the peak performance of these four traits, with these differences expected to persist because of energetic allocation and life-history trade-offs. We compile a new global dataset of 61 diverse arthropod species which provides strong empirical evidence to support these predictions, demonstrating that contemporary populations have indeed evolved under these constraints. Our results provide a basis for using relatively feasible trait measurements to predict the adaptive capacity of diverse arthropod populations to geographic temperature gradients, as well as ongoing and future climatic warming.
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Affiliation(s)
- Samraat Pawar
- Department of Life Sciences, Imperial College London, Ascot, UK.
| | - Paul J Huxley
- Department of Life Sciences, Imperial College London, Ascot, UK.
- Department of Statistics, Virginia Tech, Blacksburg, VA, USA.
| | - Thomas R C Smallwood
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Miles L Nesbit
- Department of Life Sciences, Imperial College London, Ascot, UK
- The Pirbright Institute, Woking, UK
| | - Alex H H Chan
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Marta S Shocket
- Department of Geography, University of Florida, Gainesville, FL, USA
| | - Leah R Johnson
- Department of Statistics, Virginia Tech, Blacksburg, VA, USA
| | | | - Lauren J Cator
- Department of Life Sciences, Imperial College London, Ascot, UK.
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6
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Gallois M, Menoret D, Marques-Prieto S, Montigny A, Valenti P, Moussian B, Plaza S, Payre F, Chanut-Delalande H. Pri peptides temporally coordinate transcriptional programs during epidermal differentiation. SCIENCE ADVANCES 2024; 10:eadg8816. [PMID: 38335295 PMCID: PMC10857433 DOI: 10.1126/sciadv.adg8816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
To achieve a highly differentiated state, cells undergo multiple transcriptional processes whose coordination and timing are not well understood. In Drosophila embryonic epidermal cells, polished-rice (Pri) smORF peptides act as temporal mediators of ecdysone to activate a transcriptional program leading to cell shape remodeling. Here, we show that the ecdysone/Pri axis concomitantly represses the transcription of a large subset of cuticle genes to ensure proper differentiation of the insect exoskeleton. The repression relies on the transcription factor Ken and persists for several days throughout early larval stages, during which a soft cuticle allows larval crawling. The onset of these cuticle genes normally awaits the end of larval stages when the rigid pupal case assembles, and their premature expression triggers abnormal sclerotization of the larval cuticle. These results uncovered a temporal switch to set up distinct structures of cuticles adapted to the animal lifestyle and which might be involved in the evolutionary history of insects.
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Affiliation(s)
- Maylis Gallois
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Delphine Menoret
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Simon Marques-Prieto
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Audrey Montigny
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Philippe Valenti
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Bernard Moussian
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, CNRS/UPS/INPT, Auzeville-Tolosane, France
| | - François Payre
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Hélène Chanut-Delalande
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
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7
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Angst P, Dexter E, Stillman JH. Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae). G3 (BETHESDA, MD.) 2024; 14:jkad281. [PMID: 38079165 PMCID: PMC10849366 DOI: 10.1093/g3journal/jkad281] [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: 10/10/2023] [Accepted: 11/09/2023] [Indexed: 02/09/2024]
Abstract
Crabs are a large subtaxon of the Arthropoda, the most diverse and species-rich metazoan group. Several outstanding questions remain regarding crab diversification, including about the genomic capacitors of physiological and morphological adaptation, that cannot be answered with available genomic resources. Physiologically and ecologically diverse Anomuran porcelain crabs offer a valuable model for investigating these questions and hence genomic resources of these crabs would be particularly useful. Here, we present the first two genome assemblies of congeneric and sympatric Anomuran porcelain crabs, Petrolisthes cinctipes and Petrolisthes manimaculis from different microhabitats. Pacific Biosciences high-fidelity sequencing led to genome assemblies of 1.5 and 0.9 Gb, with N50s of 706.7 and 218.9 Kb, respectively. Their assembly length difference can largely be attributed to the different levels of interspersed repeats in their assemblies: The larger genome of P. cinctipes has more repeats (1.12 Gb) than the smaller genome of P. manimaculis (0.54 Gb). For obtaining high-quality annotations of 44,543 and 40,315 protein-coding genes in P. cinctipes and P. manimaculis, respectively, we used RNA-seq as part of a larger annotation pipeline. Contrarily to the large-scale differences in repeat content, divergence levels between the two species as estimated from orthologous protein-coding genes are moderate. These two high-quality genome assemblies allow future studies to examine the role of environmental regulation of gene expression in the two focal species to better understand physiological response to climate change, and provide the foundation for studies in fine-scale genome evolution and diversification of crabs.
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Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Eric Dexter
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Jonathon H Stillman
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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8
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Sylvester T, Adams R, Hunter WB, Li X, Rivera-Marchand B, Shen R, Shin NR, McKenna DD. The genome of the invasive and broadly polyphagous Diaprepes root weevil, Diaprepes abbreviatus (Coleoptera), reveals an arsenal of putative polysaccharide-degrading enzymes. J Hered 2024; 115:94-102. [PMID: 37878740 DOI: 10.1093/jhered/esad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/14/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
The Diaprepes root weevil (DRW), Diaprepes abbreviatus, is a broadly polyphagous invasive pest of agriculture in the southern United States and the Caribbean. Its genome was sequenced, assembled, and annotated to study genomic correlates of specialized plant-feeding and invasiveness and to facilitate the development of new methods for DRW control. The 1.69 Gb D. abbreviatus genome assembly was distributed across 653 contigs, with an N50 of 7.8 Mb and the largest contig of 62 Mb. Most of the genome was comprised of repetitive sequences, with 66.17% in transposable elements, 5.75% in macrosatellites, and 2.06% in microsatellites. Most expected orthologous genes were present and fully assembled, with 99.5% of BUSCO genes present and 1.5% duplicated. One hundred and nine contigs (27.19 Mb) were identified as putative fragments of the X and Y sex chromosomes, and homology assessment with other beetle X chromosomes indicated a possible sex chromosome turnover event. Genome annotation identified 18,412 genes, including 43 putative horizontally transferred (HT) loci. Notably, 258 genes were identified from gene families known to encode plant cell wall degrading enzymes and invertases, including carbohydrate esterases, polysaccharide lyases, and glycoside hydrolases (GH). GH genes were unusually numerous, with 239 putative genes representing 19 GH families. Interestingly, several other beetle species with large numbers of GH genes are (like D. abbreviatus) successful invasive pests of agriculture or forestry.
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Affiliation(s)
- Terrence Sylvester
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
| | - Richard Adams
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, United States
- Agricultural Statistics Laboratory, University of Arkansas, Fayetteville, AR, United States
| | - Wayne B Hunter
- USDA, ARS, U. S. Horticultural Research Laboratory, Fort Pierce, FL 34945, United States
| | - Xuankun Li
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Bert Rivera-Marchand
- Office of Academic Affairs, Polk State College, Lakeland Campus, Lakeland, FL, 33803, United States
| | - Rongrong Shen
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
| | - Na Ra Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
| | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
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9
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Mikhailova AA, Rinke S, Harrison MC. Genomic signatures of eusocial evolution in insects. CURRENT OPINION IN INSECT SCIENCE 2024; 61:101136. [PMID: 37922983 DOI: 10.1016/j.cois.2023.101136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
The genomes of eusocial insects allow the production and regulation of highly distinct phenotypes, largely independent of genotype. Although rare, eusociality has evolved convergently in at least three insect orders (Hymenoptera, Blattodea and Coleoptera). Despite such disparate origins, eusocial phenotypes show remarkable similarity, exhibiting long-lived reproductives and short-lived sterile workers and soldiers. In this article, we review current knowledge on genomic signatures of eusocial evolution. We confirm that especially an increased regulatory complexity and the adaptive evolution of chemical communication are common to several origins of eusociality. Furthermore, colony life itself can shape genomes of divergent taxa in a similar manner. Future research should be geared towards generating more high-quality genomic resources, especially in hitherto understudied clades, such as ambrosia beetles and termites. The application of more sophisticated tools such as machine learning techniques may allow the detection of more subtle convergent genomic footprints of eusociality.
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Affiliation(s)
- Alina A Mikhailova
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasße 1, 48149 Münster, Germany
| | - Sarah Rinke
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasße 1, 48149 Münster, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasße 1, 48149 Münster, Germany.
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10
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McCartney N, Kondakath G, Tai A, Trimmer BA. Functional annotation of insecta transcriptomes: A cautionary tale from Lepidoptera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 165:104038. [PMID: 37952902 DOI: 10.1016/j.ibmb.2023.104038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Functional annotation is a critical step in the analysis of genomic data, as it provides insight into the function of individual genes and the pathways in which they participate. Currently, there is no consensus on the best computational approach for assigning functional annotation. This study compares three functional annotation methods (BLAST, eggNOG-Mapper, and InterProScan) in their ability to assign Gene Ontology terms in two species of Insecta with differing levels of annotation, Bombyx mori and Manduca sexta. The methods were compared for their annotation coverage, number of term assignments, term agreement and non-overlapping terms. Here we show that there are large discrepancies in gene ontology term assignment among the three computational methods, which could lead to confounding interpretations of data and non-comparable results. This study provide insight into the strengths and weaknesses of each computational method and highlight the need for more standardized methods of functional annotation.
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Affiliation(s)
- Naya McCartney
- Department of Biology, Tufts University, 200 Boston Ave, Medford, MA, 02155, USA
| | - Gayathri Kondakath
- Department of Biology, Tufts University, 200 Boston Ave, Medford, MA, 02155, USA
| | - Albert Tai
- School of Medicine, Tufts University, 136 Harrison Ave, Boston, MA, 02111, USA
| | - Barry A Trimmer
- Department of Biology, Tufts University, 200 Boston Ave, Medford, MA, 02155, USA.
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11
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Bálint B, Merényi Z, Hegedüs B, Grigoriev IV, Hou Z, Földi C, Nagy LG. ContScout: sensitive detection and removal of contamination from annotated genomes. Nat Commun 2024; 15:936. [PMID: 38296951 PMCID: PMC10831095 DOI: 10.1038/s41467-024-45024-5] [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: 01/06/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024] Open
Abstract
Contamination of genomes is an increasingly recognized problem affecting several downstream applications, from comparative evolutionary genomics to metagenomics. Here we introduce ContScout, a precise tool for eliminating foreign sequences from annotated genomes. It achieves high specificity and sensitivity on synthetic benchmark data even when the contaminant is a closely related species, outperforms competing tools, and can distinguish horizontal gene transfer from contamination. A screen of 844 eukaryotic genomes for contamination identified bacteria as the most common source, followed by fungi and plants. Furthermore, we show that contaminants in ancestral genome reconstructions lead to erroneous early origins of genes and inflate gene loss rates, leading to a false notion of complex ancestral genomes. Taken together, we offer here a tool for sensitive removal of foreign proteins, identify and remove contaminants from diverse eukaryotic genomes and evaluate their impact on phylogenomic analyses.
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Affiliation(s)
- Balázs Bálint
- Synthetic and Systems Biology Unit, HUN-REN Biological Research Centre, Szeged, Szeged, 6726, Hungary
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, HUN-REN Biological Research Centre, Szeged, Szeged, 6726, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, HUN-REN Biological Research Centre, Szeged, Szeged, 6726, Hungary
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Zhihao Hou
- Synthetic and Systems Biology Unit, HUN-REN Biological Research Centre, Szeged, Szeged, 6726, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6720, Hungary
| | - Csenge Földi
- Synthetic and Systems Biology Unit, HUN-REN Biological Research Centre, Szeged, Szeged, 6726, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6720, Hungary
| | - László G Nagy
- Synthetic and Systems Biology Unit, HUN-REN Biological Research Centre, Szeged, Szeged, 6726, Hungary.
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12
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Sterling-Montealegre RA, Prada CF. Variability and evolution of gene order rearrangement in mitochondrial genomes of arthropods (except Hexapoda). Gene 2024; 892:147906. [PMID: 37844850 DOI: 10.1016/j.gene.2023.147906] [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: 06/07/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
In the species-rich Phylum Arthropoda, the mitochondrial genome is relatively well conserved both in terms of number and order of genes. However, specific clades have a 'typical' gene order that differs from the putative arthropod ancestral arrangement. The aim of this work was to compare the rate of mitochondrial gene rearrangements at inter- and intra-taxonomic levels in the Arthropoda and to postulate the most parsimonious ancestral orders representing the four major arthropod lineages. For this purpose, we performed a comparative genomic analysis of arthropod mitochondrial genomes available in the NCBI database. Using a combination of bioinformatics methods that examined mitochondrial gene rearrangements in 464 species of arthropods from three subphyla (Chelicerata, Myriapoda, and Crustacea [except Hexapoda, previously analyzed]), we observed differences in the rate of rearrangement within major lineages. A higher rate of mitochondrial genome rearrangement was observed in Crustacea and Chelicerata compared to Myriapoda. Likewise, early branching clades exhibit less variability in mitochondrial genome order than late branching clades, within each subphylum. We identified 'hot regions' in the mitochondrial genome of each studied subphylum, and postulated the most likely ancestral gene order in each subphylum and taxonomic order. Our work provides new evidence on the evolutionary dynamics of mitochondrial genome gene order in arthropods and new mitochondrial genome architectures in different taxonomic divisions within each major lineage of arthropods.
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Affiliation(s)
| | - Carlos Fernando Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia.
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13
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Francisco Barbosa F, Mermudes JRM, Russo CAM. Performance of tree-building methods using a morphological dataset and a well-supported Hexapoda phylogeny. PeerJ 2024; 12:e16706. [PMID: 38213769 PMCID: PMC10782957 DOI: 10.7717/peerj.16706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
Recently, many studies have addressed the performance of phylogenetic tree-building methods (maximum parsimony, maximum likelihood, and Bayesian inference), focusing primarily on simulated data. However, for discrete morphological data, there is no consensus yet on which methods recover the phylogeny with better performance. To address this lack of consensus, we investigate the performance of different methods using an empirical dataset for hexapods as a model. As an empirical test of performance, we applied normalized indices to effectively measure accuracy (normalized Robinson-Foulds metric, nRF) and precision, which are measured via resolution, one minus Colless' consensus fork index (1-CFI). Additionally, to further explore phylogenetic accuracy and support measures, we calculated other statistics, such as the true positive rate (statistical power) and the false positive rate (type I error), and constructed receiver operating characteristic plots to visualize the relationship between these statistics. We applied the normalized indices to the reconstructed trees from the reanalyses of an empirical discrete morphological dataset from extant Hexapoda using a well-supported phylogenomic tree as a reference. Maximum likelihood and Bayesian inference applying the k-state Markov (Mk) model (without or with a discrete gamma distribution) performed better, showing higher precision (resolution). Additionally, our results suggest that most available tree topology tests are reliable estimators of the performance measures applied in this study. Thus, we suggest that likelihood-based methods and tree topology tests should be used more often in phylogenetic tree studies based on discrete morphological characters. Our study provides a fair indication that morphological datasets have robust phylogenetic signal.
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Affiliation(s)
| | | | - Claudia A. M. Russo
- Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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14
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Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024; 2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.
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Affiliation(s)
- Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Frankfurt, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Ann Kathrin Huylmans
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Alun R C Jones
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Eckart Stolle
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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15
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Singleton M, Eisen M. Leveraging genomic redundancy to improve inference and alignment of orthologous proteins. G3 (BETHESDA, MD.) 2023; 13:jkad222. [PMID: 37770067 PMCID: PMC10700111 DOI: 10.1093/g3journal/jkad222] [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: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Identifying protein sequences with common ancestry is a core task in bioinformatics and evolutionary biology. However, methods for inferring and aligning such sequences in annotated genomes have not kept pace with the increasing scale and complexity of the available data. Thus, in this work, we implemented several improvements to the traditional methodology that more fully leverage the redundancy of closely related genomes and the organization of their annotations. Two highlights include the application of the more flexible k-clique percolation algorithm for identifying clusters of orthologous proteins and the development of a novel technique for removing poorly supported regions of alignments with a phylogenetic hidden Markov model (phylo-HMM). In making the latter, we wrote a fully documented Python package Homomorph that implements standard HMM algorithms and created a set of tutorials to promote its use by a wide audience. We applied the resulting pipeline to a set of 33 annotated Drosophila genomes, generating 22,813 orthologous groups and 8,566 high-quality alignments.
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Affiliation(s)
- Marc Singleton
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Michael Eisen
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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16
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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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17
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Nuss AB, Lomas JS, Reyes JB, Garcia-Cruz O, Lei W, Sharma A, Pham MN, Beniwal S, Swain ML, McVicar M, Hinne IA, Zhang X, Yim WC, Gulia-Nuss M. The highly improved genome of Ixodes scapularis with X and Y pseudochromosomes. Life Sci Alliance 2023; 6:e202302109. [PMID: 37813487 PMCID: PMC10561763 DOI: 10.26508/lsa.202302109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Ixodes scapularis, the black-legged tick, is the principal vector of the Lyme disease spirochete, Borrelia burgdorferi, and is responsible for most of the ∼470,000 estimated Lyme disease cases annually in the USA. Ixodes scapularis can transmit six additional pathogens of human health significance. Because of its medical importance, I. scapularis was the first tick genome to be sequenced and annotated. However, the first assembly, I. scapularis Wikel (IscaW), was highly fragmented because of the technical challenges posed by the long, repetitive genome sequences characteristic of arthropod genomes and the lack of long-read sequencing techniques. Although I. scapularis has emerged as a model for tick research because of the availability of new tools such as embryo injection and CRISPR-Cas9-mediated gene editing yet the lack of chromosome-scale scaffolds has slowed progress in tick biology and the development of tools for their control. Here we combine diverse technologies to produce the I. scapularis Gulia-Nuss (IscGN) genome assembly and gene set. We used DNA from eggs and male and female adult ticks and took advantage of Hi-C, PacBio HiFi sequencing, and Illumina short-read sequencing technologies to produce a chromosome-level assembly. In this work, we present the predicted pseudochromosomes consisting of 13 autosomes and the sex pseudochromosomes: X and Y, and a markedly improved genome annotation compared with the existing assemblies and annotations.
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Affiliation(s)
- Andrew B Nuss
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
- https://ror.org/01keh0577 Department of Agriculture, Veterinary, and Rangeland Sciences, The University of Nevada, Reno, NV, USA
| | - Johnathan S Lomas
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Jeremiah B Reyes
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
- https://ror.org/01keh0577 Nevada Bioinformatics Center, University of Nevada, Reno, NV, USA
| | - Omar Garcia-Cruz
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Wenlong Lei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Arvind Sharma
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Michael N Pham
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Saransh Beniwal
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
- https://ror.org/01keh0577 Department of Computer Science and Engineering, The University of Nevada, Reno, NV, USA
| | - Mia L Swain
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Molly McVicar
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Isaac Amankona Hinne
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Xingtan Zhang
- https://ror.org/01keh0577 Nevada Bioinformatics Center, University of Nevada, Reno, NV, USA
| | - Won C Yim
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Monika Gulia-Nuss
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
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18
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Oliveira IDS. An updated world checklist of velvet worms (Onychophora) with notes on nomenclature and status of names. Zookeys 2023; 1184:133-260. [PMID: 38023768 PMCID: PMC10680090 DOI: 10.3897/zookeys.1184.107286] [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: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 12/01/2023] Open
Abstract
More than a decade has passed since the publication of the only world checklist available for Onychophora. During this period, numerous nomenclatural acts and taxonomic changes have been suggested within the group and a wealth of novel data has been published on many taxa. Herein, the up-to-date taxonomic scenario within Onychophora is presented, with appraisal of name status. This checklist covers both extant (Peripatidae and Peripatopsidae) and fossil taxa, and each species is accompanied by information on synonyms, type designation, holotype location, type locality, and language of original description. Additional remarks include nomenclatural inconsistencies, synonymizations, name misspellings, conflicting collecting event data, availability of taxonomically informative molecular data, etc. According to the data, 237 species are currently assigned to Onychophora: 140 of Peripatopsidae, 92 of Peripatidae, and five fossil species with unclear relationship to extant taxa. Since the previous checklist, 37 species have been added to Onychophora, representing an increase of 18.5% in the diversity described for the group. Yet, taxonomic descriptions seem slow-paced, with an average of 3.6 onychophoran species being described annually. From the taxonomic standpoint, 216 species are valid, although many of them require morphological revision and molecular characterization; 21 species exhibit major taxonomic ambiguities and have been regarded as nomina dubia. Recurrent taxonomic issues identified in the literature include inaccurate collecting event data, doubtful taxonomic assignment of molecular sequences, and non-observance of nomenclatural rules. These and other taxonomic aspects are addressed herein in the light of the directives established by the International Code of Zoological Nomenclature.
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Affiliation(s)
- Ivo de Sena Oliveira
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, D-34132, Kassel, GermanyUniversity of KasselKasselGermany
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antônio Carlos 6627, 31270-901, Belo Horizonte, Minas Gerais, BrazilUniversidade Federal de Minas GeraisBelo HorizonteBrazil
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19
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Petrone ME, Parry R, Mifsud JCO, Van Brussel K, Vorhees I, Richards ZT, Holmes EC. Evidence for an ancient aquatic origin of the RNA viral order Articulavirales. Proc Natl Acad Sci U S A 2023; 120:e2310529120. [PMID: 37906647 PMCID: PMC10636315 DOI: 10.1073/pnas.2310529120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023] Open
Abstract
The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes the emergence of viruses in new hosts. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the RNA virus order Articulavirales, which includes the influenza viruses. We identified instances of Articulavirales in the invertebrate phylum Cnidaria (including corals), constituting a novel and divergent family that we provisionally named the "Cnidenomoviridae." We further extended the evolutionary history of the influenza virus lineage by identifying four divergent, fish-associated influenza-like viruses, thereby supporting the hypothesis that fish were among the first hosts of influenza viruses. In addition, we substantially expanded the phylogenetic diversity of quaranjaviruses and proposed that this genus be reclassified as a family-the "Quaranjaviridae." Within this putative family, we identified a novel arachnid-infecting genus, provisionally named "Cheliceravirus." Notably, we observed a close phylogenetic relationship between the Crustacea- and Chelicerata-infecting "Quaranjaviridae" that is inconsistent with virus-host codivergence. Together, these data suggest that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of the Articulavirales was likely shaped by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.
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Affiliation(s)
- Mary E. Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
| | - Rhys Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD4067, Australia
| | - Jonathon C. O. Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Ian Vorhees
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY14850
| | - Zoe T. Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA6102, Australia
- Collections and Research, Western Australian Museum, Welshpool, WA6106, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
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20
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Lee CE. Genome architecture underlying salinity adaptation in the invasive copepod Eurytemora affinis species complex: A review. iScience 2023; 26:107851. [PMID: 37752947 PMCID: PMC10518491 DOI: 10.1016/j.isci.2023.107851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
With climate change, habitat salinity is shifting rapidly throughout the globe. In addition, many destructive freshwater invaders are recent immigrants from saline habitats. Recently, populations of the copepod Eurytemora affinis species complex have invaded freshwater habitats multiple times independently from saline estuaries on three continents. This review discusses features of this species complex that could enhance their evolutionary potential during rapid environmental change. Remarkably, across independent freshwater invasions, natural selection has repeatedly favored the same alleles far more than expected. This high degree of parallelism is surprising, given the expectation of nonparallel evolution for polygenic adaptation. Factors such as population structure and the genome architecture underlying critical traits under selection might help drive rapid adaptation and parallel evolution. Given the preponderance of saline-to-freshwater invasions and climate-induced salinity change, the principles found here could provide invaluable insights into mechanisms operating in other systems and the potential for adaptation in a changing planet.
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Affiliation(s)
- Carol Eunmi Lee
- Department of Integrative Biology, University of Wisconsin, 430 Lincoln Drive, Birge Hall, Madison, WI 53706, USA
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21
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Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol 2023; 13:e10506. [PMID: 37791292 PMCID: PMC10542623 DOI: 10.1002/ece3.10506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 10/05/2023] Open
Abstract
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
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Affiliation(s)
- Kim L. Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - R. Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, University of FloridaGainesvilleFloridaUSA
| | - Tom Hill
- National Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research UnitUnited States Department of Agriculture: Agriculture Research Service Pacific Basin Agricultural Research CenterHiloHawaiiUSA
| | - Robert L. Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceKansasUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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22
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Gollapalli P, Rudrappa S, Kumar V, Santosh Kumar HS. Domain Architecture Based Methods for Comparative Functional Genomics Toward Therapeutic Drug Target Discovery. J Mol Evol 2023; 91:598-615. [PMID: 37626222 DOI: 10.1007/s00239-023-10129-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 08/06/2023] [Indexed: 08/27/2023]
Abstract
Genes duplicate, mutate, recombine, fuse or fission to produce new genes, or when genes are formed from de novo, novel functions arise during evolution. Researchers have tried to quantify the causes of these molecular diversification processes to know how these genes increase molecular complexity over a period of time, for instance protein domain organization. In contrast to global sequence similarity, protein domain architectures can capture key structural and functional characteristics, making them better proxies for describing functional equivalence. In Prokaryotes and eukaryotes it has proven that, domain designs are retained over significant evolutionary distances. Protein domain architectures are now being utilized to categorize and distinguish evolutionarily related proteins and find homologs among species that are evolutionarily distant from one another. Additionally, structural information stored in domain structures has accelerated homology identification and sequence search methods. Tools for functional protein annotation have been developed to discover, protein domain content, domain order, domain recurrence, and domain position as all these contribute to the prediction of protein functional accuracy. In this review, an attempt is made to summarise facts and speculations regarding the use of protein domain architecture and modularity to identify possible therapeutic targets among cellular activities based on the understanding their linked biological processes.
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Affiliation(s)
- Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Sushmitha Rudrappa
- Department of Biotechnology and Bioinformatics, Jnana Sahyadri Campus, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka, 577451, India
| | - Vadlapudi Kumar
- Department of Biochemistry, Davangere University, Shivagangothri, Davangere, Karnataka, 577007, India
| | - Hulikal Shivashankara Santosh Kumar
- Department of Biotechnology and Bioinformatics, Jnana Sahyadri Campus, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka, 577451, India.
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23
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Sharma PP. The Impact of Whole Genome Duplication on the Evolution of the Arachnids. Integr Comp Biol 2023; 63:825-842. [PMID: 37263789 DOI: 10.1093/icb/icad050] [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: 03/01/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023] Open
Abstract
The proliferation of genomic resources for Chelicerata in the past 10 years has revealed that the evolution of chelicerate genomes is more dynamic than previously thought, with multiple waves of ancient whole genome duplications affecting separate lineages. Such duplication events are fascinating from the perspective of evolutionary history because the burst of new gene copies associated with genome duplications facilitates the acquisition of new gene functions (neofunctionalization), which may in turn lead to morphological novelties and spur net diversification. While neofunctionalization has been invoked in several contexts with respect to the success and diversity of spiders, the overall impact of whole genome duplications on chelicerate evolution and development remains imperfectly understood. The purpose of this review is to examine critically the role of whole genome duplication on the diversification of the extant arachnid orders, as well as assess functional datasets for evidence of subfunctionalization or neofunctionalization in chelicerates. This examination focuses on functional data from two focal model taxa: the spider Parasteatoda tepidariorum, which exhibits evidence for an ancient duplication, and the harvestman Phalangium opilio, which exhibits an unduplicated genome. I show that there is no evidence that taxa with genome duplications are more successful than taxa with unduplicated genomes. I contend that evidence for sub- or neofunctionalization of duplicated developmental patterning genes in spiders is indirect or fragmentary at present, despite the appeal of this postulate for explaining the success of groups like spiders. Available expression data suggest that the condition of duplicated Hox modules may have played a role in promoting body plan disparity in the posterior tagma of some orders, such as spiders and scorpions, but functional data substantiating this postulate are critically missing. Spatiotemporal dynamics of duplicated transcription factors in spiders may represent cases of developmental system drift, rather than neofunctionalization. Developmental system drift may represent an important, but overlooked, null hypothesis for studies of paralogs in chelicerate developmental biology. To distinguish between subfunctionalization, neofunctionalization, and developmental system drift, concomitant establishment of comparative functional datasets from taxa exhibiting the genome duplication, as well as those that lack the paralogy, is sorely needed.
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Affiliation(s)
- Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
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24
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Ajayi OM, Wynne NE, Chen SC, Vinauger C, Benoit JB. Sleep: An Essential and Understudied Process in the Biology of Blood-Feeding Arthropods. Integr Comp Biol 2023; 63:530-547. [PMID: 37429615 PMCID: PMC10503478 DOI: 10.1093/icb/icad097] [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: 04/19/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023] Open
Abstract
Understanding the biology of blood-feeding arthropods is critical to managing them as vectors of etiological agents. Circadian rhythms act in the regulation of behavioral and physiological aspects such as blood feeding, immunity, and reproduction. However, the impact of sleep on these processes has been largely ignored in blood-feeding arthropods, but recent studies in mosquitoes show that sleep-like states directly impact host landing and blood feeding. Our focus in this review is on discussing the relationship between sleep and circadian rhythms in blood-feeding arthropods along with how unique aspects such as blood gluttony and dormancy can impact sleep-like states. We highlight that sleep-like states are likely to have profound impacts on vector-host interactions but will vary between lineages even though few direct studies have been conducted. A myriad of factors, such as artificial light, could directly impact the time and levels of sleep in blood-feeding arthropods and their roles as vectors. Lastly, we discuss underlying factors that make sleep studies in blood-feeding arthropods difficult and how these can be bypassed. As sleep is a critical factor in the fitness of animal systems, a lack of focus on sleep in blood-feeding arthropods represents a significant oversight in understanding their behavior and its role in pathogen transmission.
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Affiliation(s)
- Oluwaseun M Ajayi
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Nicole E Wynne
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Shyh-Chi Chen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Clément Vinauger
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
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25
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Attardo GM, Benoit JB, Michalkova V, Kondragunta A, Baumann AA, Weiss BL, Malacrida A, Scolari F, Aksoy S. Lipid metabolism dysfunction following symbiont elimination is linked to altered Kennedy pathway homeostasis. iScience 2023; 26:107108. [PMID: 37534171 PMCID: PMC10391724 DOI: 10.1016/j.isci.2023.107108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/27/2023] [Accepted: 06/08/2023] [Indexed: 08/04/2023] Open
Abstract
Lipid metabolism is critical for insect reproduction, especially for species that invest heavily in the early developmental stages of their offspring. The role of symbiotic bacteria during this process is understudied but likely essential. We examined the role of lipid metabolism during the interaction between the viviparous tsetse fly (Glossina morsitans morsitans) and its obligate endosymbiotic bacteria (Wigglesworthia glossinidia) during tsetse pregnancy. We observed increased CTP:phosphocholine cytidylyltransferase (cct1) expression during pregnancy, which is critical for phosphatidylcholine biosynthesis in the Kennedy pathway. Experimental removal of Wigglesworthia impaired lipid metabolism via disruption of the Kennedy pathway, yielding obese mothers whose developing progeny starve. Functional validation via experimental cct1 suppression revealed a phenotype similar to females lacking obligate Wigglesworthia symbionts. These results indicate that, in Glossina, symbiont-derived factors, likely B vitamins, are critical for the proper function of both lipid biosynthesis and lipolysis to maintain tsetse fly fecundity.
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Affiliation(s)
- Geoffrey M. Attardo
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Entomology and Nematology, Division of Agriculture and Natural Resources, University of California Davis, Davis, CA 95616, USA
| | - Joshua B. Benoit
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Veronika Michalkova
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Section of Molecular and Applied Zoology, Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alekhya Kondragunta
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Aaron A. Baumann
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Brian L. Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anna Malacrida
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
- Institute of Molecular Genetics (IGM), Italian National Research Council (CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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26
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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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27
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Adams SA, Graham NR, Holmquist AJ, Sheffer MM, Steigerwald EC, Sahasrabudhe R, Nguyen O, Beraut E, Fairbairn C, Sacco S, Seligmann W, Escalona M, Shaffer HB, Toffelmier E, Gillespie RG. Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae). J Hered 2023; 114:395-403. [PMID: 37042574 PMCID: PMC10287146 DOI: 10.1093/jhered/esad013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/27/2023] [Indexed: 04/13/2023] Open
Abstract
Climate-driven changes in hydrological regimes are of global importance and are particularly significant in riparian ecosystems. Riparian ecosystems in California provide refuge to many native and vulnerable species within a xeric landscape. California Tetragnatha spiders play a key role in riparian ecosystems, serving as a link between terrestrial and aquatic elements. Their tight reliance on water paired with the widespread distributions of many species make them ideal candidates to better understand the relative role of waterways versus geographic distance in shaping the population structure of riparian species. To assist in better understanding population structure, we constructed a reference genome assembly for Tetragnatha versicolor using long-read sequencing, scaffolded with proximity ligation Omni-C data. The near-chromosome-level assembly is comprised of 174 scaffolds spanning 1.06 Gb pairs, with a scaffold N50 of 64.1 Mb pairs and BUSCO completeness of 97.6%. This reference genome will facilitate future study of T. versicolor population structure associated with the rapidly changing environment of California.
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Affiliation(s)
- Seira A Adams
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
- Center for Population Biology, University of California, Davis, CA, United States
- Department of Evolution and Ecology, University of California, Davis, CA, United States
| | - Natalie R Graham
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
| | - Anna J Holmquist
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
| | - Monica M Sheffer
- Department of Biology, University of Washington, Seattle, WA, United States
- eScience Institute, University of Washington, Seattle, WA, United States
| | - Emma C Steigerwald
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute for Environment and Sustainability, University of California, Los Angeles, CA, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute for Environment and Sustainability, University of California, Los Angeles, CA, United States
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
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28
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Haberkorn C, David J, Henri H, Delpuech J, Lasseur R, Vavre F, Varaldi J. A major 6 Mb superlocus is involved in pyrethroid resistance in the common bed bug Cimex lectularius. Evol Appl 2023; 16:1012-1028. [PMID: 37216030 PMCID: PMC10197226 DOI: 10.1111/eva.13550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
In the last few years, the bed bug Cimex lectularius has been an increasing problem worldwide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancient-susceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes and was also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitutes a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.
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Affiliation(s)
- Chloé Haberkorn
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
- IZInovationLyonFrance
| | - Jean‐Philippe David
- Laboratoire d'Écologie AlpineUMR UGA‐USMB‐CNRS 5553 Université Grenoble Alpes CS 40700Grenoble cedex 9France
| | - Hélène Henri
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Jean‐Marie Delpuech
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | | | - Fabrice Vavre
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Julien Varaldi
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
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29
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Hotaling S, Desvignes T, Sproul JS, Lins LSF, Kelley JL. Pathways to polar adaptation in fishes revealed by long-read sequencing. Mol Ecol 2023; 32:1381-1397. [PMID: 35561000 DOI: 10.1111/mec.16501] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/31/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
Abstract
Long-read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage-specific loss of this cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.
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Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - John S Sproul
- Department of Biology, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Luana S F Lins
- Australian National Insect Collection, CSIRO, Canberra, Australia
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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30
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Benoit JB, McCluney KE, DeGennaro MJ, Dow JAT. Dehydration Dynamics in Terrestrial Arthropods: From Water Sensing to Trophic Interactions. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:129-149. [PMID: 36270273 PMCID: PMC9936378 DOI: 10.1146/annurev-ento-120120-091609] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Since the transition from water to land, maintaining water balance has been a key challenge for terrestrial arthropods. We explore factors that allow terrestrial arthropods to survive within a variably dry world and how they shape ecological interactions. Detection of water and hydration is critical for maintaining water content. Efficient regulation of internal water content is accomplished by excretory and osmoregulatory systems that balance water intake and loss. Biochemical and physiological responses are necessary as water content declines to prevent and repair the damage that occurs during dehydration. Desiccation avoidance can occur seasonally or daily via a move to more favorable areas. Dehydration and its avoidance have ecological impacts that extend beyond a single species to alter trophic interactions. As climate changes, evolutionary and ecological processes will be critical to species survival during drought.
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Affiliation(s)
- Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Kevin E McCluney
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, USA;
| | - Matthew J DeGennaro
- Department of Biological Sciences, Florida International University and Biomolecular Sciences Institute, Miami, Florida, USA;
| | - Julian A T Dow
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, United Kingdom;
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31
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Yan J, Zhang C, Zhang M, Zhou H, Zuo Z, Ding X, Zhang R, Li F, Gao Y. Chromosome-level genome assembly of the Colorado potato beetle, Leptinotarsa decemlineata. Sci Data 2023; 10:36. [PMID: 36653371 PMCID: PMC9849343 DOI: 10.1038/s41597-023-01950-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
The Colorado potato beetle (Leptinotarsa decemlineata) is one of the most notorious insect pests of potatoes globally. Here, we generated a high-quality chromosome-level genome assembly of L. decemlineata using a combination of the PacBio HiFi sequencing and Hi-C scaffolding technologies. The genome assembly (-1,008 Mb) is anchored to 18 chromosomes (17 + XO), with a scaffold N50 of 58.32 Mb. It contains 676 Mb repeat sequences and 29,606 protein-coding genes. The chromosome-level genome assembly of L. decemlineata provides in-depth knowledge and will be a helpful resource for the beetle and invasive biology research communities.
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Affiliation(s)
- Junjie Yan
- grid.410727.70000 0001 0526 1937State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Chaowei Zhang
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Mengdi Zhang
- grid.410727.70000 0001 0526 1937State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hang Zhou
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Zhangqi Zuo
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Xinhua Ding
- grid.433811.c0000 0004 1798 1482Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 China
| | - Runzhi Zhang
- grid.9227.e0000000119573309Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Fei Li
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Yulin Gao
- grid.410727.70000 0001 0526 1937State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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32
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Austin M, Clifford C, Rutt G, Price BW, Wallace I. The genome sequence of a caddisfly, Limnephilus lunatus (Curtis, 1834). Wellcome Open Res 2023; 8:25. [PMID: 37408608 PMCID: PMC10318372 DOI: 10.12688/wellcomeopenres.18752.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2022] [Indexed: 08/03/2023] Open
Abstract
We present a genome assembly from an individual Limnephilus lunatus (a caddisfly; Arthropoda; Insecta; Trichoptera; Limnephilidae). The genome sequence is 1,270 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases long.
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33
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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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34
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Moreyra NN, Almeida FC, Allan C, Frankel N, Matzkin LM, Hasson E. Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila. Mol Phylogenet Evol 2023; 178:107653. [PMID: 36404461 DOI: 10.1016/j.ympev.2022.107653] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/30/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
Cactophilic species of the Drosophila buzzatii cluster (repleta group) comprise an excellent model group to investigate genomic changes underlying adaptation to extreme climate conditions and host plants. In particular, these species form a tractable system to study the transition from chemically simpler breeding sites (like prickly pears of the genus Opuntia) to chemically more complex hosts (columnar cacti). Here, we report four highly contiguous genome assemblies of three species of the buzzatii cluster. Based on this genomic data and inferred phylogenetic relationships, we identified candidate taxonomically restricted genes (TRGs) likely involved in the evolution of cactophily and cactus host specialization. Functional enrichment analyses of TRGs within the buzzatii cluster identified genes involved in detoxification, water preservation, immune system response, anatomical structure development, and morphogenesis. In contrast, processes that regulate responses to stress, as well as the metabolism of nitrogen compounds, transport, and secretion were found in the set of species that are columnar cacti dwellers. These findings are in line with the hypothesis that those genomic changes brought about key mechanisms underlying the adaptation of the buzzatii cluster species to arid regions in South America.
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Affiliation(s)
- Nicolás Nahuel Moreyra
- Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina.
| | - Francisca Cunha Almeida
- Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina.
| | - Carson Allan
- Department of Entomology, University of Arizona, Tucson, AZ 85719, USA.
| | - Nicolás Frankel
- Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina.
| | | | - Esteban Hasson
- Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina.
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Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes. Int J Mol Sci 2022; 24:ijms24010649. [PMID: 36614092 PMCID: PMC9820851 DOI: 10.3390/ijms24010649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023] Open
Abstract
Lepidopteran species are mostly pests, causing serious annual economic losses. High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. Long-read sequencing technology and assembly algorithm advances have improved the ability to timeously produce high-quality genomes. Lepidoptera includes a wide variety of insects with high genetic diversity and heterozygosity. Therefore, the selection of an appropriate sequencing and assembly strategy to obtain high-quality genomic information is urgently needed. This research used silkworm as a model to test genome sequencing and assembly through high-coverage datasets by de novo assemblies. We report the first nearly complete telomere-to-telomere reference genome of silkworm Bombyx mori (P50T strain) produced by Pacific Biosciences (PacBio) HiFi sequencing, and highly contiguous and complete genome assemblies of two other silkworm strains by Oxford Nanopore Technologies (ONT) or PacBio continuous long-reads (CLR) that were unrepresented in the public database. Assembly quality was evaluated by use of BUSCO, Inspector, and EagleC. It is necessary to choose an appropriate assembler for draft genome construction, especially for low-depth datasets. For PacBio CLR and ONT sequencing, NextDenovo is superior. For PacBio HiFi sequencing, hifiasm is better. Quality assessment is essential for genome assembly and can provide better and more accurate results. For chromosome-level high-quality genome construction, we recommend using 3D-DNA with EagleC evaluation. Our study references how to obtain and evaluate high-quality genome assemblies, and is a resource for biological control, comparative genomics, and evolutionary studies of Lepidopteran pests and related species.
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Yuan R, Zheng B, Li Z, Ma X, Shu X, Qu Q, Ye X, Li S, Tang P, Chen X. The chromosome-level genome of Chinese praying mantis Tenodera sinensis (Mantodea: Mantidae) reveals its biology as a predator. Gigascience 2022; 12:giad090. [PMID: 37882605 PMCID: PMC10600911 DOI: 10.1093/gigascience/giad090] [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: 05/23/2023] [Revised: 09/17/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The Chinese praying mantis, Tenodera sinensis (Saussure), is a carnivorous insect that preys on a variety of arthropods and small vertebrates, including pest species. Several studies have been conducted to understand its behavior and physiology. However, there is limited knowledge about the genetic information underlying its genome evolution, digestive demands, and predatory behaviors. FINDINGS Here we have assembled the chromosome-level genome of T. sinensis, representing the first sequenced genome of the family Mantidae, with a genome size of 2.54 Gb and scaffold N50 of 174.78 Mb. Our analyses revealed that 98.6% of BUSCO genes are present, resulting in a well-annotated assembly compared to other insect genomes, containing 25,022 genes. The reconstructed phylogenetic analysis showed the expected topology placing the praying mantis in an appropriate position. Analysis of transposon elements suggested the Gypsy/Dirs family, which belongs to long terminal repeat (LTR) transposons, may be a key factor resulting in the larger genome size. The genome shows expansions in several digestion and detoxification associated gene families, including trypsin and glycosyl hydrolase (GH) genes, ATP-binding cassette (ABC) transporter, and carboxylesterase (CarE), reflecting the possible genomic basis of digestive demands. Furthermore, we have found 1 ultraviolet-sensitive opsin and 2 long-wavelength-sensitive (LWS) opsins, emphasizing the core role of LWS opsins in regulating predatory behaviors. CONCLUSIONS The high-quality genome assembly of the praying mantis provides a valuable repository for studying the evolutionary patterns of the mantis genomes and the gene expression profiles of insect predators.
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Affiliation(s)
- Ruizhong Yuan
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Boying Zheng
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Zekai Li
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Xingzhou Ma
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Xiaohan Shu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Qiuyu Qu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Xiqian Ye
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514779, China
| | - Pu Tang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Xuexin Chen
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
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37
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Panfilio KA, Chuva de Sousa Lopes SM. The extended analogy of extraembryonic development in insects and amniotes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210268. [PMID: 36252225 PMCID: PMC9574626 DOI: 10.1098/rstb.2021.0268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/14/2022] [Indexed: 12/22/2022] Open
Abstract
It is fascinating that the amnion and serosa/chorion, two extraembryonic (EE) tissues that are characteristic of the amniote vertebrates (mammals, birds and reptiles), have also independently evolved in insects. In this review, we offer the first detailed, macroevolutionary comparison of EE development and tissue biology across these animal groups. Some commonalities represent independent solutions to shared challenges for protecting the embryo (environmental assaults, risk of pathogens) and supporting its development, including clear links between cellular properties (e.g. polyploidy) and physiological function. Further parallels encompass developmental features such as the early segregation of the serosa/chorion compared to later, progressive differentiation of the amnion and formation of the amniotic cavity from serosal-amniotic folds as a widespread morphogenetic mode across species. We also discuss common developmental roles for orthologous transcription factors and BMP signalling in EE tissues of amniotes and insects, and between EE and cardiac tissues, supported by our exploration of new resources for global and tissue-specific gene expression. This highlights the degree to which general developmental principles and protective tissue features can be deduced from each of these animal groups, emphasizing the value of broad comparative studies to reveal subtle developmental strategies and answer questions that are common across species. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.
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Affiliation(s)
| | - Susana M. Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
- Department for Reproductive Medicine, Ghent University Hospital, 9000 Ghent, Belgium
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38
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Liénard MA, Valencia-Montoya WA, Pierce NE. Molecular advances to study the function, evolution and spectral tuning of arthropod visual opsins. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210279. [PMID: 36058235 PMCID: PMC9450095 DOI: 10.1098/rstb.2021.0279] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Visual opsins of vertebrates and invertebrates diversified independently and converged to detect ultraviolet to long wavelengths (LW) of green or red light. In both groups, colour vision largely derives from opsin number, expression patterns and changes in amino acids interacting with the chromophore. Functional insights regarding invertebrate opsin evolution have lagged behind those for vertebrates because of the disparity in genomic resources and the lack of robust in vitro systems to characterize spectral sensitivities. Here, we review bioinformatic approaches to identify and model functional variation in opsins as well as recently developed assays to measure spectral phenotypes. In particular, we discuss how transgenic lines, cAMP-spectroscopy and sensitive heterologous expression platforms are starting to decouple genotype–phenotype relationships of LW opsins to complement the classical physiological-behavioural-phylogenetic toolbox of invertebrate visual sensory studies. We illustrate the use of one heterologous method by characterizing novel LW Gq opsins from 10 species, including diurnal and nocturnal Lepidoptera, a terrestrial dragonfly and an aquatic crustacean, expressing them in HEK293T cells, and showing that their maximum absorbance spectra (λmax) range from 518 to 611 nm. We discuss the advantages of molecular approaches for arthropods with complications such as restricted availability, lateral filters, specialized photochemistry and/or electrophysiological constraints. This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
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Affiliation(s)
- Marjorie A Liénard
- Department of Biology, Lund University, 22362 Lund, Sweden.,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Wendy A Valencia-Montoya
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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Steenwyk JL, Goltz DC, Buida TJ, Li Y, Shen XX, Rokas A. OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. PLoS Biol 2022; 20:e3001827. [PMID: 36228036 PMCID: PMC9595520 DOI: 10.1371/journal.pbio.3001827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 10/25/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of selection, often rely on gene families of single-copy orthologs (SC-OGs). Large gene families with multiple homologs in 1 or more species-a phenomenon observed among several important families of genes such as transporters and transcription factors-are often ignored because identifying and retrieving SC-OGs nested within them is challenging. To address this issue and increase the number of markers used in molecular evolution studies, we developed OrthoSNAP, a software that uses a phylogenetic framework to simultaneously split gene families into SC-OGs and prune species-specific inparalogs. We term SC-OGs identified by OrthoSNAP as SNAP-OGs because they are identified using a splitting and pruning procedure analogous to snapping branches on a tree. From 415,129 orthologous groups of genes inferred across 7 eukaryotic phylogenomic datasets, we identified 9,821 SC-OGs; using OrthoSNAP on the remaining 405,308 orthologous groups of genes, we identified an additional 10,704 SNAP-OGs. Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar, even in complex datasets that contain a whole-genome duplication, complex patterns of duplication and loss, transcriptome data where each gene typically has multiple transcripts, and contentious branches in the tree of life. OrthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.
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Affiliation(s)
- Jacob L. Steenwyk
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (JLS); (AR)
| | - Dayna C. Goltz
- Independent Researcher, Nashville, Tennessee, United States of America
| | - Thomas J. Buida
- Independent Researcher, Nashville, Tennessee, United States of America
| | - Yuanning Li
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xing-Xing Shen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- * E-mail: (JLS); (AR)
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Iwasaki-Yokozawa S, Nanjo R, Akiyama-Oda Y, Oda H. Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider. BMC Biol 2022; 20:223. [PMID: 36203191 PMCID: PMC9535882 DOI: 10.1186/s12915-022-01421-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Background
The process of early development varies across the species-rich phylum Arthropoda. Owing to the limited research strategies for dissecting lineage-specific processes of development in arthropods, little is known about the variations in early arthropod development at molecular resolution. The Theridiidae spider, Parasteatoda tepidariorum, has its genome sequenced and could potentially contribute to dissecting early embryonic processes. Results We present genome-wide identification of candidate genes that exhibit locally restricted expression in germ disc forming stage embryos of P. tepidariorum, based on comparative transcriptomes of isolated cells from different regions of the embryo. A subsequent pilot screen by parental RNA interference identifies three genes required for body axis formation. One of them is a GATA-like gene that has been fast evolving after duplication and divergence from a canonical GATA family gene. This gene is designated fuchi nashi (fuchi) after its knockdown phenotypes, where the cell movement toward the formation of a germ disc was reversed. fuchi expression occurs in cells outside a forming germ disc and persists in the endoderm. Transcriptome and chromatin accessibility analyses of fuchi pRNAi embryos suggest that early fuchi activity regulates chromatin state and zygotic gene activation to promote endoderm specification and pattern formation. We also show that there are many uncharacterized genes regulated by fuchi. Conclusions Our genome-based research using an arthropod phylogenetically distant from Drosophila identifies a lineage-specific, fast-evolving gene with key developmental roles in one of the earliest, genome-wide regulatory events, and allows for molecular exploration of the developmental variations in early arthropod embryos. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01421-0.
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Affiliation(s)
- Sawa Iwasaki-Yokozawa
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan
| | - Ryota Nanjo
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Yasuko Akiyama-Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan.,Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Hiroki Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan.
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41
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De novo metatranscriptomic exploration of gene function in the millipede holobiont. Sci Rep 2022; 12:16173. [PMID: 36171216 PMCID: PMC9519908 DOI: 10.1038/s41598-022-19565-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Invertebrate-microbial associations are widespread in the biosphere and are often related to the function of novel genes, fitness advantages, and even speciation events. Despite ~ 13,000 species of millipedes identified across the world, millipedes and their gut microbiota are markedly understudied compared to other arthropods. Exploring the contribution of individual host-associated microbes is often challenging as many are uncultivable. In this study, we conducted metatranscriptomic profiling of different body segments of a millipede at the holobiont level. This is the first reported transcriptome assembly of a tropical millipede Telodeinopus aoutii (Demange, 1971), as well as the first study on any Myriapoda holobiont. High-throughput RNA sequencing revealed that Telodeinopus aoutii contained > 90% of the core Arthropoda genes. Proteobacteria, Bacteroidetes, Firmicutes, and Euryarchaeota represented dominant and functionally active phyla in the millipede gut, among which 97% of Bacteroidetes and 98% of Firmicutes were present exclusively in the hindgut. A total of 37,831 predicted protein-coding genes of millipede holobiont belonged to six enzyme classes. Around 35% of these proteins were produced by microbiota in the hindgut and 21% by the host in the midgut. Our results indicated that although major metabolic pathways operate at the holobiont level, the involvement of some host and microbial genes are mutually exclusive and microbes predominantly contribute to essential amino acid biosynthesis, short-chain fatty acid metabolism, and fermentation.
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42
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He S, Jiang B, Chakraborty A, Yu G. The Evolution of Glycoside Hydrolase Family 1 in Insects Related to Their Adaptation to Plant Utilization. INSECTS 2022; 13:786. [PMID: 36135486 PMCID: PMC9500737 DOI: 10.3390/insects13090786] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Insects closely interact with plants with multiple genes involved in their interactions. β-glucosidase, constituted mainly by glycoside hydrolase family 1 (GH1), is a crucial enzyme in insects to digest plant cell walls and defend against natural enemies with sequestered plant metabolites. To gain more insights into the role of this enzyme in plant-insect interactions, we analyzed the evolutionary history of the GH1 gene family with publicly available insect genomes. We found that GH1 is widely present in insects, while the gene numbers are significantly higher in insect herbivores directly feeding on plant cell walls than in other insects. After reconciling the insect GH1 gene tree with a species tree, we found that the patterns of duplication and loss of GH1 genes differ among insect orders, which may be associated with the evolution of their ecology. Furthermore, the majority of insects' GH1 genes were tandem-duplicated and subsequently went through neofunctionalization. This study shows the evolutionary history of an important gene family GH1 in insects and facilitates our understanding of the evolution of insect-plant interactions.
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Affiliation(s)
- Shulin He
- College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Bin Jiang
- College of Life Science, Anhui Normal University, Beijing Rd. 1, Wuhu 241000, China
| | - Amrita Chakraborty
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic
| | - Guozhi Yu
- College of Life Science, Sichuan Agricultural University, Xinkang Rd. 46, Ya’an 625014, China
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43
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Li Z, Li Y, Xue AZ, Dang V, Renee Holmes V, Spencer Johnston J, Barrick JE, Moran NA. The genomic basis of evolutionary novelties in a leafhopper. Mol Biol Evol 2022; 39:6677381. [PMID: 36026509 PMCID: PMC9450646 DOI: 10.1093/molbev/msac184] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the glassy-winged sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS and then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory.
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Affiliation(s)
- Zheng Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Yiyuan Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang, China
| | - Allen Z Xue
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Vy Dang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - V Renee Holmes
- Department of Entomology, Texas A&M University, College Station, TX,USA
| | | | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nancy A Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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Evidence that Transcriptional Alterations in Sarcoptes scabiei Are under Tight Post-Transcriptional (microRNA) Control. Int J Mol Sci 2022; 23:ijms23179719. [PMID: 36077116 PMCID: PMC9456212 DOI: 10.3390/ijms23179719] [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: 06/21/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Here, we explored transcriptomic differences among early egg (Ee), late egg (Le) and adult female (Af) stages of the scabies mite, Sarcoptes scabiei, using an integrative bioinformatic approach. We recorded a high, negative correlation between miRNAs and genes with decreased mRNA transcription between the developmental stages, indicating substantial post-transcriptional repression; we also showed a positive correlation between miRNAs and genes with increased mRNA transcription, suggesting indirect post-transcriptional regulation. The alterations in mRNA transcription between the egg and adult female stages of S. scabiei were inferred to be linked to metabolism (including carbohydrate and lipid degradation, amino acid and energy metabolism), environmental information processing (e.g., signal transduction and signalling molecules), genetic information processing (e.g., transcription and translation) and/or organismal systems. Taken together, these results provide insight into the transcription of this socioeconomically important parasitic mite, with a particular focus on the egg stage. This work encourages further, detailed laboratory studies of miRNA regulation across all developmental stages of S. scabiei and might assist in discovering new intervention targets in the egg stage of S. scabiei.
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Fujiwara M, Akiyama-Oda Y, Oda H. Virtual spherical-shaped multicellular platform for simulating the morphogenetic processes of spider-like body axis formation. Front Cell Dev Biol 2022; 10:932814. [PMID: 36036016 PMCID: PMC9411422 DOI: 10.3389/fcell.2022.932814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
Remodeling of multicellular architecture is a critical developmental process for shaping the axis of a bilaterally symmetric animal body and involves coordinated cell–cell interactions and cell rearrangement. In arthropods, the early embryonic process that leads to the segmented body axis varies at the cellular and molecular levels depending on the species. Developmental studies using insect and spider model species have provided specific examples of these diversified mechanisms that regulate axis formation and segmentation in arthropod embryos. However, there are few theoretical models for how diversity in the early embryonic process occurred during evolution, in part because of a limited computational infrastructure. We developed a virtual spherical-shaped multicellular platform to reproduce body axis-forming processes. Each virtual cell behaves according to the cell vertex model, with the computational program organized in a hierarchical order from cells and tissues to whole embryos. Using an initial set of two different mechanical states for cell differentiation and global directional signals that are linked to the planar polarity of each cell, the virtual cell assembly exhibited morphogenetic processes similar to those observed in spider embryos. We found that the development of an elongating body axis is achieved through implementation of an interactive cell polarity parameter associated with edge tension at the cell–cell adhesion interface, with no local control of the cell division rate and direction. We also showed that modifying the settings can cause variation in morphogenetic processes. This platform also can embed a gene network that generates waves of gene expression in a virtual dynamic multicellular field. This study provides a computational platform for testing the development and evolution of animal body patterns.
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Affiliation(s)
- Motohiro Fujiwara
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Japan
- *Correspondence: Motohiro Fujiwara, ; Hiroki Oda,
| | - Yasuko Akiyama-Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Japan
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Hiroki Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Japan
- Department of Biological Science, Graduate School of Science, Osaka University, Toyonaka, Japan
- *Correspondence: Motohiro Fujiwara, ; Hiroki Oda,
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The Unfolded-Protein Response Triggers the Arthropod Immune Deficiency Pathway. mBio 2022; 13:e0070322. [PMID: 35862781 PMCID: PMC9426425 DOI: 10.1128/mbio.00703-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The insect immune deficiency (IMD) pathway is a defense mechanism that senses and responds to Gram-negative bacteria. Ticks lack genes encoding upstream components that initiate the IMD pathway. Despite this deficiency, core signaling molecules are present and functionally restrict tick-borne pathogens. The molecular events preceding activation remain undefined. Here, we show that the unfolded-protein response (UPR) initiates the IMD network. The endoplasmic reticulum (ER) stress receptor IRE1α is phosphorylated in response to tick-borne bacteria but does not splice the mRNA encoding XBP1. Instead, through protein modeling and reciprocal pulldowns, we show that Ixodes IRE1α complexes with TRAF2. Disrupting IRE1α-TRAF2 signaling blocks IMD pathway activation and diminishes the production of reactive oxygen species. Through in vitro, in vivo, and ex vivo techniques, we demonstrate that the UPR-IMD pathway circuitry limits the Lyme disease-causing spirochete Borrelia burgdorferi and the rickettsial agents Anaplasma phagocytophilum and A. marginale (anaplasmosis). Altogether, our study uncovers a novel linkage between the UPR and the IMD pathway in arthropods. IMPORTANCE The ability of an arthropod to harbor and transmit pathogens is termed "vector competency." Many factors influence vector competency, including how arthropod immune processes respond to the microbe. Divergences in innate immunity between arthropods are increasingly being reported. For instance, although ticks lack genes encoding key upstream molecules of the immune deficiency (IMD) pathway, it is still functional and restricts causative agents of Lyme disease (Borrelia burgdorferi) and anaplasmosis (Anaplasma phagocytophilum). How the IMD pathway is activated in ticks without classically defined pathway initiators is not known. Here, we found that a cellular stress response network, the unfolded-protein response (UPR), functions upstream to induce the IMD pathway and restrict transmissible pathogens. Collectively, this explains how the IMD pathway can be activated in the absence of canonical pathway initiators. Given that the UPR is highly conserved, UPR-initiated immunity may be a fundamental principle impacting vector competency across arthropods.
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Ott LC, Mellata M. Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation. Front Microbiol 2022; 13:891548. [PMID: 35847067 PMCID: PMC9280185 DOI: 10.3389/fmicb.2022.891548] [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: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.
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Affiliation(s)
- Logan C. Ott
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Melha Mellata,
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Buellesbach J, Holze H, Schrader L, Liebig J, Schmitt T, Gadau J, Niehuis O. Genetic and genomic architecture of species-specific cuticular hydrocarbon variation in parasitoid wasps. Proc Biol Sci 2022; 289:20220336. [PMID: 35673870 PMCID: PMC9174729 DOI: 10.1098/rspb.2022.0336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cuticular hydrocarbons (CHCs) serve two fundamental functions in insects: protection against desiccation and chemical signalling. How the interaction of genes shapes CHC profiles, which are essential for insect survival, adaptation and reproductive success, is still poorly understood. Here we investigate the genetic and genomic basis of CHC biosynthesis and variation in parasitoid wasps of the genus Nasonia. We mapped 91 quantitative trait loci (QTL) explaining the variation of a total of 43 CHCs in F2 hybrid males from interspecific crosses between three Nasonia species. To identify candidate genes, we localized orthologues of CHC biosynthesis-related genes in the Nasonia genomes. We discovered multiple genomic regions where the location of QTL coincides with the location of CHC biosynthesis-related candidate genes. Most conspicuously, on a region close to the centromere of chromosome 1, multiple CHC biosynthesis-related candidate genes co-localize with several QTL explaining variation in methyl-branched alkanes. The genetic underpinnings behind this compound class are not well understood so far, despite their high potential for encoding chemical information as well as their prevalence in hymenopteran CHC profiles. Our study considerably extends our knowledge on the genetic architecture governing this important compound class, establishing a model for methyl-branched alkane genetics in the Hymenoptera in general.
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Affiliation(s)
- Jan Buellesbach
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, DE-48149 Münster, Germany
| | - Henrietta Holze
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, DE-48149 Münster, Germany
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, DE-48149 Münster, Germany
| | - Jürgen Liebig
- School of Life Sciences, Arizona State University, PO Box 874701, Tempe, AZ 85287-4501, USA
| | - Thomas Schmitt
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Juergen Gadau
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, DE-48149 Münster, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
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Nunes-da-Fonseca R. Editorial overview: Development and regulation: Lessons from a multispecies approach. CURRENT OPINION IN INSECT SCIENCE 2022; 51:100917. [PMID: 35358719 DOI: 10.1016/j.cois.2022.100917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Rodrigo Nunes-da-Fonseca
- Institute of Biodiversity and Sustainability-NUPEM, Universidade Federal do Rio de Janeiro, Av. São José do Barreto 764 Zip Code: 27965-045, Brazil.
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Smith ML, Vanderpool D, Hahn MW. Using all gene families vastly expands data available for phylogenomic inference. Mol Biol Evol 2022; 39:6596367. [PMID: 35642314 PMCID: PMC9178227 DOI: 10.1093/molbev/msac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail and by analyzing five additional data sets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other data sets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.
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Affiliation(s)
- Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana, USA
| | - Dan Vanderpool
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana, USA
| | - Matthew W Hahn
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana, USA
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