51
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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: 5] [Impact Index Per Article: 2.5] [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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52
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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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53
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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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54
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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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55
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Two Novel Iflaviruses Discovered in Bat Samples in Washington State. Viruses 2022; 14:v14050994. [PMID: 35632735 PMCID: PMC9143909 DOI: 10.3390/v14050994] [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: 04/15/2022] [Revised: 05/04/2022] [Accepted: 05/04/2022] [Indexed: 02/01/2023] Open
Abstract
Arthropods are integral to ecosystem equilibrium, serving as both a food source for insectivores and supporting plant reproduction. Members of the Iflaviridae family in the order Picornavirales are frequently found in RNA sequenced from arthropods, who serve as their hosts. Here we implement a metagenomic deep sequencing approach followed by rapid amplification of cDNA ends (RACE) on viral RNA isolated from wild and captured bat guano in Washington State at two separate time points. From these samples we report the complete genomes of two novel viruses in the family Iflaviridae. The first virus, which we call King virus, is 46% identical by nucleotide to the lethal honeybee virus, deformed wing virus, while the second virus which we call Rolda virus, shares 39% nucleotide identity to deformed wing virus. King and Rolda virus genomes are 10,183 and 8934 nucleotides in length, respectively. Given these iflaviruses were detected in guano from captive bats whose sole food source was the Tenebrio spp. mealworm, we anticipate this invertebrate may be a likely host. Using the NCBI Sequence Read Archive, we found that these two viruses are located in six continents and have been isolated from a variety of arthropod and mammalian specimens.
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56
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Liu H, Jiang F, Wang S, Wang H, Wang A, Zhao H, Xu D, Yang B, Fan W. Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens). Gigascience 2022; 11:6563153. [PMID: 35373834 PMCID: PMC8978299 DOI: 10.1093/gigascience/giac009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/24/2021] [Accepted: 01/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background The globe skimmer dragonfly (Pantala flavescens) is a notable Odonata insect distributed in nature fields and farmlands worldwide, and it is commonly recognized as a natural enemy because it preys on agricultural pests and health pests. As one of the sister groups of winged insects, odonatan species are key to understanding the evolution of insect wings. Findings We present a high-quality reference genome of P. flavescens, which is the first chromosome-level genome in the Palaeoptera (Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.9%) of contig sequences were clustered, ordered, and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The X chromosome was identified by sequence coverage depth. The repetitive sequences and gene density of the X chromosome are similar to those of autosomal sequences, but the X chromosome shows a much lower degree of heterozygosity. Our analysis shows that the effective population size experienced 3 declining events, which may have been caused by climate change and environmental pollution. Conclusions The genome of P. flavescens provides more information on the biology and evolution of insects and will help for the use of this species in pest control.
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Affiliation(s)
- Hangwei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hanbo Zhao
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Boyuan Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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57
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Reynolds M, de Oliveira L, Vosburg C, Paris T, Massimino C, Norus J, Ortiz Y, Espino M, Davis N, Masse R, Neiman A, Holcomb R, Gervais K, Kemp M, Hoang M, Shippy TD, Hosmani PS, Flores-Gonzalez M, Pelz-Stelinski K, Qureshi JA, Mueller LA, Hunter WB, Benoit JB, Brown SJ, D’Elia T, Saha S. Annotation of putative circadian rhythm-associated genes in Diaphorina citri (Hemiptera: Liviidae). GIGABYTE 2022; 2022:gigabyte48. [PMID: 36824532 PMCID: PMC9662589 DOI: 10.46471/gigabyte.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/28/2022] [Indexed: 11/09/2022] Open
Abstract
The circadian rhythm involves multiple genes that generate an internal molecular clock, allowing organisms to anticipate environmental conditions produced by the Earth's rotation on its axis. Here, we present the results of the manual curation of 27 genes that are associated with circadian rhythm in the genome of Diaphorina citri, the Asian citrus psyllid. This insect is the vector for the bacterial pathogen Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease (Huanglongbing). This disease severely affects citrus industries and has drastically decreased crop yields worldwide. Based on cry1 and cry2 identified in the psyllid genome, D. citri likely possesses a circadian model similar to the lepidopteran butterfly, Danaus plexippus. Manual annotation will improve the quality of circadian rhythm gene models, allowing the future development of molecular therapeutics, such as RNA interference or antisense technologies, to target these genes to disrupt the psyllid biology.
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Affiliation(s)
- Max Reynolds
- Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Chad Vosburg
- Indian River State College, Fort Pierce, FL 34981, USA,Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Thomson Paris
- Entomology and Nematology Department, University of Florida, North Florida Research and Education Center, Research Road, Quincy 32351, Florida, USA
| | | | - Jordan Norus
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Yasmin Ortiz
- Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Nina Davis
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Ron Masse
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Alan Neiman
- Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Kylie Gervais
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Melissa Kemp
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Maria Hoang
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Teresa D. Shippy
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Kirsten Pelz-Stelinski
- Department of Entomology and Nematology, University of Florida, Lake Alfred, FL 33850, USA
| | - Jawwad A. Qureshi
- Indian River Research and Education Center, University of Florida, IFAS, 2199 South Rock Road, Fort Pierce, FL 34945-3138, USA,Southwest Florida Research and Education Center, University of Florida, IFAS, 2685 State Road 29 North, Immokalee, FL 34142, USA
| | | | - Wayne B. Hunter
- USDA-ARS, US Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Susan J. Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Tom D’Elia
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Surya Saha
- Boyce Thompson Institute, Ithaca, NY 14853, USA,Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA, Corresponding author. E-mail:
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58
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Horn T, Narov KD, Panfilio KA. Persistent Parental RNAi in the Beetle Tribolium castaneum Involves Maternal Transmission of Long Double-Stranded RNA. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100064. [PMID: 36620196 PMCID: PMC9744488 DOI: 10.1002/ggn2.202100064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Indexed: 01/11/2023]
Abstract
Parental RNA interference (pRNAi) is a powerful and widely used method for gene-specific knockdown. Yet in insects its efficacy varies between species, and how the systemic response is transmitted from mother to offspring remains elusive. Using the beetle Tribolium castaneum, an RT-qPCR strategy to distinguish the presence of double-stranded RNA (dsRNA) from endogenous mRNA is reported. It is found that injected dsRNA is directly transmitted into the egg and persists throughout embryogenesis. Despite this depletion of dsRNA from the mother, it is shown that strong pRNAi can persist for months before waning at strain-specific rates. In seeking the receptor proteins for cellular uptake of long dsRNA into the egg, a phylogenomics profiling approach of candidate proteins is also presented. A visualization strategy based on taxonomically hierarchical assessment of orthology clustering data to rapidly assess gene age and copy number changes, refined by sequence-based evidence, is demonstrated. Repeated losses of SID-1-like channel proteins in the arthropods, including wholesale loss in the Heteroptera (true bugs), which are nonetheless highly sensitive to pRNAi, are thereby documented. Overall, practical considerations for insect pRNAi against a backdrop of outstanding questions on the molecular mechanism of dsRNA transmission for long-term, systemic knockdown are elucidated.
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Affiliation(s)
- Thorsten Horn
- Institute for Zoology: Developmental BiologyUniversity of CologneZülpicher Straße 47b50674CologneGermany
| | - Kalin D. Narov
- School of Life SciencesUniversity of WarwickGibbet Hill CampusCoventryCV4 7ALUK
| | - Kristen A. Panfilio
- Institute for Zoology: Developmental BiologyUniversity of CologneZülpicher Straße 47b50674CologneGermany,School of Life SciencesUniversity of WarwickGibbet Hill CampusCoventryCV4 7ALUK
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59
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Sethuraman A, Tovar A, Welch W, Dettmers R, Arce C, Skaggs T, Rothenberg A, Saisho R, Summerhays B, Cartmill R, Grenier C, Vasquez Y, Vansant H, Obrycki J. Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior. G3 GENES|GENOMES|GENETICS 2022; 12:6499286. [PMID: 35100359 PMCID: PMC8896016 DOI: 10.1093/g3journal/jkac001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/21/2021] [Indexed: 11/14/2022]
Abstract
Abstract
Dinocampus coccinellae (Hymenoptera: Braconidae) is a generalist parasitoid wasp that parasitizes >50 species of predatory lady beetles (Coleoptera: Coccinellidae), with thelytokous parthenogeny as its primary mode of reproduction. Here, we present the first high-quality genome of D. coccinellae using a combination of short- and long-read sequencing technologies, followed by assembly and scaffolding of chromosomal segments using Chicago + HiC technologies. We also present a first-pass ab initio and a reference-based genome annotation and resolve timings of divergence and evolution of (1) solitary behavior vs eusociality, (2) arrhenotokous vs thelytokous parthenogenesis, and (3) rates of gene loss and gain among Hymenopteran lineages. Our study finds (1) at least 2 independent origins of eusociality and solitary behavior among Hymenoptera, (2) 2 independent origins of thelytokous parthenogenesis from ancestral arrhenotoky, and (3) accelerated rates of gene duplications, loss, and gain along the lineages leading to D. coccinellae. Our work both affirms the ancient divergence of Braconid wasps from ancestral Hymenopterans and accelerated rates of evolution in response to adaptations to novel hosts, including polyDNA viral coevolution.
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Affiliation(s)
- Arun Sethuraman
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Alicia Tovar
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Walker Welch
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Ryan Dettmers
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Camila Arce
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Timothy Skaggs
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Alexander Rothenberg
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Roxane Saisho
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Bryce Summerhays
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Ryan Cartmill
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Christy Grenier
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
| | - Yumary Vasquez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92096, USA
- Department of Life and Environmental Systems, University of California Merced, Merced, CA 95343, USA
| | - Hannah Vansant
- 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
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60
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Heckenhauer J, Frandsen PB, Sproul JS, Li Z, Paule J, Larracuente AM, Maughan PJ, Barker MS, Schneider JV, Stewart RJ, Pauls SU. Genome size evolution in the diverse insect order Trichoptera. Gigascience 2022; 11:6537159. [PMID: 35217860 PMCID: PMC8881205 DOI: 10.1093/gigascience/giac011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/25/2021] [Accepted: 01/21/2022] [Indexed: 12/30/2022] Open
Abstract
Background Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. Results We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). Conclusion Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.
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Affiliation(s)
- Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.,Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | - Paul B Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.,Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA.,Data Science Lab, Smithsonian Institution, Washington, DC 20560, USA
| | - John S Sproul
- Department of Biology, University of Rochester, Rochester, NY 14620, USA.,Department of Biology, University of Nebraska Omaha, Omaha, NE 68182, USA
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | | | - Peter J Maughan
- Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Julio V Schneider
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | - Russell J Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.,Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany.,Institute for Insect Biotechnology, Justus-Liebig-University, Gießen 35390, Germany
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61
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A Review on Transcriptional Responses of Interactions between Insect Vectors and Plant Viruses. Cells 2022; 11:cells11040693. [PMID: 35203347 PMCID: PMC8870222 DOI: 10.3390/cells11040693] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/03/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
This review provides a synopsis of transcriptional responses pertaining to interactions between plant viruses and the insect vectors that transmit them in diverse modes. In the process, it attempts to catalog differential gene expression pertinent to virus–vector interactions in vectors such as virus reception, virus cell entry, virus tissue tropism, virus multiplication, and vector immune responses. Whiteflies, leafhoppers, planthoppers, and thrips are the main insect groups reviewed, along with aphids and leaf beetles. Much of the focus on gene expression pertinent to vector–virus interactions has centered around whole-body RNA extraction, whereas data on virus-induced tissue-specific gene expression in vectors is limited. This review compares transcriptional responses in different insect groups following the acquisition of non-persistent, semi-persistent, and persistent (non-propagative and propagative) plant viruses and identifies parallels and divergences in gene expression patterns. Understanding virus-induced changes in vectors at a transcriptional level can aid in the identification of candidate genes for targeting with RNAi and/or CRISPR editing in insect vectors for management approaches.
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62
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Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). BMC Genomics 2022; 23:90. [PMID: 35100986 PMCID: PMC8805230 DOI: 10.1186/s12864-022-08299-w] [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: 08/11/2021] [Accepted: 01/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the genus Novius Mulsant, 1846 (= Rodolia Mulsant, 1850) (Coleoptera, Coccinellidae), play important roles in the biological control of cotton cushion scale pests, especially those belonging to Icerya. Since the best-known species, the vedalia beetle Novius cardinalis (Mulsant, 1850) was introduced into California from Australia, more than a century of successful use in classical biological control, some species of Novius have begun to exhibit some field adaptations to novel but related prey species. Despite their economic importance, relatively little is known about the underlying genetic adaptations associated with their feeding habits. Knowledge of the genome sequence of Novius is a major step towards further understanding its biology and potential applications in pest control. RESULTS We report the first high-quality genome sequence for Novius pumilus (Weise, 1892), a representative specialist of Novius. Computational Analysis of gene Family Evolution (CAFE) analysis showed that several orthogroups encoding chemosensors, digestive, and immunity-related enzymes were significantly expanded (P < 0.05) in N. pumilus compared to the published genomes of other four ladybirds. Furthermore, some of these orthogroups were under significant positive selection pressure (P < 0.05). Notably, transcriptome profiling demonstrated that many genes among the significantly expanded and positively selected orthogroups, as well as genes related to detoxification were differentially expressed, when N. pumilus feeding on the nature prey Icerya compared with the no feeding set. We speculate that these genes are vital in the Icerya adaptation of Novius species. CONCLUSIONS We report the first Novius genome thus far. In addition, we provide comprehensive transcriptomic resources for N. pumilus. The results from this study may be helpful for understanding the association of the evolution of genes related to chemosensing, digestion, detoxification and immunity with the prey adaptation of insect predators. This will provide a reference for future research and utilization of Novius in biological control programs. Moreover, understanding the possible molecular mechanisms of prey adaptation also inform mass rearing of N. pumilus and other Novius, which may benefit pest control.
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63
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Engelhardt J, Scheer O, Stadler PF, Prohaska SJ. Evolution of DNA Methylation Across Ecdysozoa. J Mol Evol 2022; 90:56-72. [PMID: 35089376 PMCID: PMC8821070 DOI: 10.1007/s00239-021-10042-0] [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] [Received: 07/14/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022]
Abstract
DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as Drosophila melanogaster and Caenorhabditis elegans. We report here a comprehensive study of the presence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa, covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada. Three of these phyla have not been investigated for the presence of DNA methylation before. We observe that the loss of individual DNMTs independently occurred multiple times across ecdysozoan phyla. We computationally predict the presence of DNA methylation based on CpG rates in coding sequences using an implementation of Gaussian Mixture Modeling, MethMod. Integrating both analysis we predict two previously unknown losses of DNA methylation in Ecdysozoa, one within Chelicerata (Mesostigmata) and one in Tardigrada. In the early-branching Ecdysozoa Priapulus caudatus, we predict the presence of a full set of DNMTs and the presence of DNA methylation. We are therefore showing a very diverse and independent evolution of DNA methylation in different ecdysozoan phyla spanning a phylogenetic range of more than 700 million years.
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Affiliation(s)
- Jan Engelhardt
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany. .,Computational EvoDevo Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany. .,Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany. .,Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Oliver Scheer
- Computational EvoDevo Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.,Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.,Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.,The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA.,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia
| | - Sonja J Prohaska
- Computational EvoDevo Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.,Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.,The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA.,Complexity Science Hub Vienna, Josefstädter Str. 39, 1080, Vienna, Austria
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64
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Breeschoten T, van der Linden CFH, Ros VID, Schranz ME, Simon S. Expanding the Menu: Are Polyphagy and Gene Family Expansions Linked across Lepidoptera? Genome Biol Evol 2022; 14:6482744. [PMID: 34951642 PMCID: PMC8725640 DOI: 10.1093/gbe/evab283] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 12/31/2022] Open
Abstract
Evolutionary expansions and contractions of gene families are often correlated with key innovations and/or ecological characteristics. In butterflies and moths (Lepidoptera), expansions of gene families involved in detoxification of plant specialized metabolites are hypothesized to facilitate a polyphagous feeding style. However, analyses supporting this hypothesis are mostly based on a limited number of lepidopteran species. We applied a phylogenomics approach, using 37 lepidopteran genomes, to analyze if gene family evolution (gene gain and loss) is associated with the evolution of polyphagy. Specifically, we compared gene counts and evolutionary gene gain and loss rates of gene families involved in adaptations with plant feeding. We correlated gene evolution to host plant family range (phylogenetic diversity) and specialized metabolite content of plant families (functional metabolite diversity). We found a higher rate for gene loss than gene gain in Lepidoptera, a potential consequence of genomic rearrangements and deletions after (potentially small-scale) duplication events. Gene family expansions and contractions varied across lepidopteran families, and were associated to host plant use and specialization levels. Within the family Noctuidae, a higher expansion rate for gene families involved in detoxification can be related to the large number of polyphagous species. However, gene family expansions are observed in both polyphagous and monophagous lepidopteran species and thus seem to be species-specific in the taxa sampled. Nevertheless, a significant positive correlation of gene counts of the carboxyl- and choline esterase and glutathione-S-transferase detoxification gene families with the level of polyphagy was identified across Lepidoptera.
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Affiliation(s)
| | | | - Vera I D Ros
- Laboratory of Virology, Wageningen University & Research, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, The Netherlands
| | - Sabrina Simon
- Biosystematics Group, Wageningen University & Research, The Netherlands
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65
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Abstract
In less than 25 y, the field of animal genome science has transformed from a discipline seeking its first glimpses into genome sequences across the Tree of Life to a global enterprise with ambitions to sequence genomes for all of Earth's eukaryotic diversity [H. A. Lewin et al., Proc. Natl. Acad. Sci. U.S.A. 115, 4325-4333 (2018)]. As the field rapidly moves forward, it is important to take stock of the progress that has been made to best inform the discipline's future. In this Perspective, we provide a contemporary, quantitative overview of animal genome sequencing. We identified the best available genome assemblies in GenBank, the world's most extensive genetic database, for 3,278 unique animal species across 24 phyla. We assessed taxonomic representation, assembly quality, and annotation status for major clades. We show that while tremendous taxonomic progress has occurred, stark disparities in genomic representation exist, highlighted by a systemic overrepresentation of vertebrates and underrepresentation of arthropods. In terms of assembly quality, long-read sequencing has dramatically improved contiguity, whereas gene annotations are available for just 34.3% of taxa. Furthermore, we show that animal genome science has diversified in recent years with an ever-expanding pool of researchers participating. However, the field still appears to be dominated by institutions in the Global North, which have been listed as the submitting institution for 77% of all assemblies. We conclude by offering recommendations for improving genomic resource availability and research value while also broadening global representation.
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66
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Cerca J, Armstrong EE, Vizueta J, Fernández R, Dimitrov D, Petersen B, Prost S, Rozas J, Petrov D, Gillespie RG. The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders. Genome Biol Evol 2021; 13:evab262. [PMID: 34849853 PMCID: PMC8693713 DOI: 10.1093/gbe/evab262] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 01/07/2023] Open
Abstract
Spiders (Araneae) have a diverse spectrum of morphologies, behaviors, and physiologies. Attempts to understand the genomic-basis of this diversity are often hindered by their large, heterozygous, and AT-rich genomes with high repeat content resulting in highly fragmented, poor-quality assemblies. As a result, the key attributes of spider genomes, including gene family evolution, repeat content, and gene function, remain poorly understood. Here, we used Illumina and Dovetail Chicago technologies to sequence the genome of the long-jawed spider Tetragnatha kauaiensis, producing an assembly distributed along 3,925 scaffolds with an N50 of ∼2 Mb. Using comparative genomics tools, we explore genome evolution across available spider assemblies. Our findings suggest that the previously reported and vast genome size variation in spiders is linked to the different representation and number of transposable elements. Using statistical tools to uncover gene-family level evolution, we find expansions associated with the sensory perception of taste, immunity, and metabolism. In addition, we report strikingly different histories of chemosensory, venom, and silk gene families, with the first two evolving much earlier, affected by the ancestral whole genome duplication in Arachnopulmonata (∼450 Ma) and exhibiting higher numbers. Together, our findings reveal that spider genomes are highly variable and that genomic novelty may have been driven by the burst of an ancient whole genome duplication, followed by gene family and transposable element expansion.
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Affiliation(s)
- José Cerca
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, California, USA
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Norway
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ellie E Armstrong
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, California, USA
- Department of Biology, Stanford University, California, USA
| | - Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
| | - Rosa Fernández
- Institute of Evolutionary Biology (CSIC—Universitat Pompeu Fabra), Barcelona, Spain
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Norway
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Stefan Prost
- Central Research Laboratories, Natural History Museum Vienna, Vienna, Austria
- University of Veterinary Medicine, Konrad Lorenz Institute of Ethology, Vienna, Austria
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Dmitri Petrov
- Department of Biology, Stanford University, California, USA
| | - Rosemary G Gillespie
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, California, USA
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67
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Van Damme K, Cornetti L, Fields PD, Ebert D. Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution. Syst Biol 2021; 71:777-787. [PMID: 34850935 PMCID: PMC9203061 DOI: 10.1093/sysbio/syab094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 11/28/2022] Open
Abstract
Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the “Gymnomera”). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]
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Affiliation(s)
- Kay Van Damme
- Centre for Academic Heritage and Archives & Ghent University Botanical Garden, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Tvärminne Zoological Station (TZS), University of Helsinki, J.A. Palménin tie 260, Hanko, Finland
| | - Luca Cornetti
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter D Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
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68
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Walsh AT, Triant DA, Le Tourneau JJ, Shamimuzzaman M, Elsik CG. Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. Nucleic Acids Res 2021; 50:D1032-D1039. [PMID: 34747465 PMCID: PMC8728238 DOI: 10.1093/nar/gkab1018] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 01/02/2023] Open
Abstract
We report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies. With a reorganized website, HGD continues to provide the HymenopteraMine genomic data mining warehouse and JBrowse/Apollo genome browsers integrated with BLAST. We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. We have also generated orthology datasets that encompass all HGD species and provide orthologue clusters for fourteen taxonomic groups. The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads.
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Affiliation(s)
- Amy T Walsh
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Deborah A Triant
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | - Md Shamimuzzaman
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Christine G Elsik
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.,Division of Plant Science & Technology, University of Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
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69
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Lafuente E, Lürig MD, Rövekamp M, Matthews B, Buser C, Vorburger C, Räsänen K. Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.748212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Interactions between organisms and their environments are central to how biological diversity arises and how natural populations and ecosystems respond to environmental change. These interactions involve processes by which phenotypes are affected by or respond to external conditions (e.g., via phenotypic plasticity or natural selection) as well as processes by which organisms reciprocally interact with the environment (e.g., via eco-evolutionary feedbacks). Organism-environment interactions can be highly dynamic and operate on different hierarchical levels, from genes and phenotypes to populations, communities, and ecosystems. Therefore, the study of organism-environment interactions requires integrative approaches and model systems that are suitable for studies across different hierarchical levels. Here, we introduce the freshwater isopod Asellus aquaticus, a keystone species and an emerging invertebrate model system, as a prime candidate to address fundamental questions in ecology and evolution, and the interfaces therein. We review relevant fields of research that have used A. aquaticus and draft a set of specific scientific questions that can be answered using this species. Specifically, we propose that studies on A. aquaticus can help understanding (i) the influence of host-microbiome interactions on organismal and ecosystem function, (ii) the relevance of biotic interactions in ecosystem processes, and (iii) how ecological conditions and evolutionary forces facilitate phenotypic diversification.
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70
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Pu J, Wang Z, Cong H, Chin JSR, Justen J, Finet C, Yew JY, Chung H. Repression precedes independent evolutionary gains of a highly specific gene expression pattern. Cell Rep 2021; 37:109896. [PMID: 34706247 PMCID: PMC8578697 DOI: 10.1016/j.celrep.2021.109896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 08/24/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
Highly specific expression patterns can be caused by the overlapping activities of activator and repressor sequences in enhancers. However, few studies illuminate how these sequences evolve in the origin of new enhancers. Here, we show that expression of the bond gene in the semicircular wall epithelium (swe) of the Drosophila melanogaster male ejaculatory bulb (EB) is controlled by an enhancer consisting of an activator region that requires Abdominal-B driving expression in the entire EB and a repressor region that restricts this expression to the EB swe. Although this expression pattern is independently gained in the distantly related Scaptodrosophila lebanonensis and does not require Abdominal-B, we show that functionally similar repressor sequences are present in Scaptodrosophila and also in species that do not express bond in the EB. We suggest that during enhancer evolution, repressor sequences can precede the evolution of activator sequences and may lead to similar but independently evolved expression patterns. Pu et al. show that the independent gain of a highly specific expression pattern across distantly related species may be because of the preexistence of repressor sequences that precedes the diversification of these species. This may reflect a general mechanism underlying the evolution of highly specific enhancers.
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Affiliation(s)
- Jian Pu
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA.
| | - Zinan Wang
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Haosu Cong
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Jacqueline S R Chin
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A(∗)STAR), Brenner Centre for Molecular Medicine, Singapore 117609, Singapore
| | - Jessa Justen
- Laboratory of Cellular and Molecular Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Cédric Finet
- Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore
| | - Joanne Y Yew
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Henry Chung
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
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71
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Tihelka E, Cai C, Giacomelli M, Lozano-Fernandez J, Rota-Stabelli O, Huang D, Engel MS, Donoghue PCJ, Pisani D. The evolution of insect biodiversity. Curr Biol 2021; 31:R1299-R1311. [PMID: 34637741 DOI: 10.1016/j.cub.2021.08.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.
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Affiliation(s)
- Erik Tihelka
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | - Chenyang Cai
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | | | - Jesus Lozano-Fernandez
- School of Biological Sciences, University of Bristol, Bristol, UK; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige, Italy; Center Agriculture Food Environment, University of Trento, 38010 San Michele all Adige, Italy
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Michael S Engel
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, KS, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK.
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72
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Leask M, Lovegrove M, Walker A, Duncan E, Dearden P. Evolution and genomic organization of the insect sHSP gene cluster and coordinate regulation in phenotypic plasticity. BMC Ecol Evol 2021; 21:154. [PMID: 34348652 PMCID: PMC8336396 DOI: 10.1186/s12862-021-01885-8] [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: 12/21/2020] [Accepted: 07/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background Conserved syntenic gene complexes are rare in Arthropods and likely only retained due to functional constraint. Numerous sHSPs have been identified in the genomes of insects, some of which are located clustered in close proximity. Previous phylogenetic analyses of these clustered sHSP have been limited to a small number of holometabolous insect species and have not determined the pattern of evolution of the clustered sHSP genes (sHSP-C) in insect or Arthropod lineages. Results Using eight genomes from representative insect orders and three non-insect arthropod genomes we have identified that a syntenic cluster of sHSPs (sHSP-C) is a hallmark of most Arthropod genomes. Using 11 genomes from Hymenopteran species our phylogenetic analyses have refined the evolution of the sHSP-C in Hymenoptera and found that the sHSP-C is order-specific with evidence of birth-and-death evolution in the hymenopteran lineage. Finally we have shown that the honeybee sHSP-C is co-ordinately expressed and is marked by genomic features, including H3K27me3 histone marks consistent with coordinate regulation, during honeybee ovary activation. Conclusions The syntenic sHSP-C is present in most insect genomes, and its conserved coordinate expression and regulation implies that it is an integral genomic component of environmental response in arthropods. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01885-8.
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Affiliation(s)
- Megan Leask
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Mackenzie Lovegrove
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Abigail Walker
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Elizabeth Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter Dearden
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
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73
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Hotaling S, Sproul JS, Heckenhauer J, Powell A, Larracuente AM, Pauls SU, Kelley JL, Frandsen PB. Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing. Genome Biol Evol 2021; 13:evab138. [PMID: 34152413 PMCID: PMC8358217 DOI: 10.1093/gbe/evab138] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
The first insect genome assembly (Drosophila melanogaster) was published two decades ago. Today, nuclear genome assemblies are available for a staggering 601 insect species representing 20 orders. In this study, we analyzed the most-contiguous assembly for each species and provide a "state-of-the-field" perspective, emphasizing taxonomic representation, assembly quality, gene completeness, and sequencing technologies. Relative to species richness, genomic efforts have been biased toward four orders (Diptera, Hymenoptera, Collembola, and Phasmatodea), Coleoptera are underrepresented, and 11 orders still lack a publicly available genome assembly. The average insect genome assembly is 439.2 Mb in length with 87.5% of single-copy benchmarking genes intact. Most notable has been the impact of long-read sequencing; assemblies that incorporate long reads are ∼48× more contiguous than those that do not. We offer four recommendations as we collectively continue building insect genome resources: 1) seek better integration between independent research groups and consortia, 2) balance future sampling between filling taxonomic gaps and generating data for targeted questions, 3) take advantage of long-read sequencing technologies, and 4) expand and improve gene annotations.
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Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - John S Sproul
- Department of Biology, University of Rochester, New York, USA
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Ashlyn Powell
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | | | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Giessen, Germany
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Paul B Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG), Frankfurt, Germany
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
- Data Science Lab, Smithsonian Institution, Washington, District of Columbia, USA
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74
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Pak N, Wu S, Gibson JF. The evolution of marine dwelling in Diptera. Ecol Evol 2021; 11:11440-11448. [PMID: 34429931 PMCID: PMC8366842 DOI: 10.1002/ece3.7935] [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: 05/10/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 11/06/2022] Open
Abstract
Marine dwelling in Diptera has been relatively unexplored and the frequency of transitions to the marine environment and the evolutionary history remain poorly understood. By reviewing records from the World Register of Marine Species and using ancestral state reconstruction methods, we build on the fly tree of life phylogeny and ecological descriptions of marine life history. Our ancestral state reconstruction analyses suggest marine dwelling is lacking as an ancestral trait for the most recent common ancestor to Diptera. While many transitions in Empidoidea, Sciomyzoidea, Tipulomorpha, and Culicomorpha seem to have been gradual, other transitions in Tephritoidea and Tabanomorpha were found likely to have been stochastic occurrences. From the collection of 532 marine species, we reveal several independent transitions to the marine environment throughout the fly tree of life. Considering the results from our analysis, we outline potential adaptations for marine flies and discuss the barriers of colonizing the marine environment and the implications to the mechanisms for salt tolerance.
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Affiliation(s)
- Nina Pak
- Department of Environmental Science, Policy, & ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Stephanie Wu
- Department of Environmental Science, Policy, & ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
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75
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Shrestha AMS, I Lilagan CA, B Guiao JE, R Romana-Eguia MR, Ablan Lagman MC. Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across sites of varying climate profiles. BMC Genomics 2021; 22:580. [PMID: 34325654 PMCID: PMC8323281 DOI: 10.1186/s12864-021-07891-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/14/2021] [Indexed: 11/30/2022] Open
Abstract
Background The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab juveniles from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response. Results We present the first ever transcriptome assembly of S. serrata obtained from a data set containing 66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Our assembly contains many almost full-length transcripts – 5229 shrimp and 3049 fruit fly proteins have alignments that cover >80% of their sequence lengths to a contig. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat-stress response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis showed that between Cagayan and Bataan, there were 389 genes associated with 48 signaling and stress-response pathways, for which there was an effect of site in the response to heat; and between Cagayan and Bicol, there were 101 such genes affecting 8 pathways. Conclusion In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-07891-w).
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Affiliation(s)
- Anish M S Shrestha
- Bioinformatics Lab, Advanced Research Institute for Informatics, Computing, and Networking (AdRIC), De La Salle University, Manila, Philippines. .,Software Technology Department, College of Computer Studies, De La Salle University, Manila, Philippines.
| | - Crissa Ann I Lilagan
- Software Technology Department, College of Computer Studies, De La Salle University, Manila, Philippines.,Practical Genomics Laboratory, Center for Natural Science and Environment Research, De La Salle University, Manila, Philippines.,Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Joyce Emlyn B Guiao
- Bioinformatics Lab, Advanced Research Institute for Informatics, Computing, and Networking (AdRIC), De La Salle University, Manila, Philippines.,Mathematics and Statistics Department, College of Science, De La Salle University, Manila, Philippines
| | - Maria Rowena R Romana-Eguia
- Aquaculture Department, Southeast Asian Fisheries Development Center, Binangoan, 1940 Rizal, Philippines.,Biology Department, College of Science, De La Salle University, Manila, Philippines
| | - Ma Carmen Ablan Lagman
- Practical Genomics Laboratory, Center for Natural Science and Environment Research, De La Salle University, Manila, Philippines.,Biology Department, College of Science, De La Salle University, Manila, Philippines
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76
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Lima LF, Torres AQ, Jardim R, Mesquita RD, Schama R. Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias. BMC Genomics 2021; 22:562. [PMID: 34289811 PMCID: PMC8296651 DOI: 10.1186/s12864-021-07886-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/13/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Arthropoda, the most numerous and diverse metazoan phylum, has species in many habitats where they encounter various microorganisms and, as a result, mechanisms for pathogen recognition and elimination have evolved. The Toll pathway, involved in the innate immune system, was first described as part of the developmental pathway for dorsal-ventral differentiation in Drosophila. Its later discovery in vertebrates suggested that this system was extremely conserved. However, there is variation in presence/absence, copy number and sequence divergence in various genes along the pathway. As most studies have only focused on Diptera, for a comprehensive and accurate homology-based approach it is important to understand gene function in a number of different species and, in a group as diverse as insects, the use of species belonging to different taxonomic groups is essential. RESULTS We evaluated the diversity of Toll pathway gene families in 39 Arthropod genomes, encompassing 13 different Insect Orders. Through computational methods, we shed some light into the evolution and functional annotation of protein families involved in the Toll pathway innate immune response. Our data indicates that: 1) intracellular proteins of the Toll pathway show mostly species-specific expansions; 2) the different Toll subfamilies seem to have distinct evolutionary backgrounds; 3) patterns of gene expansion observed in the Toll phylogenetic tree indicate that homology based methods of functional inference might not be accurate for some subfamilies; 4) Spatzle subfamilies are highly divergent and also pose a problem for homology based inference; 5) Spatzle subfamilies should not be analyzed together in the same phylogenetic framework; 6) network analyses seem to be a good first step in inferring functional groups in these cases. We specifically show that understanding Drosophila's Toll functions might not indicate the same function in other species. CONCLUSIONS Our results show the importance of using species representing the different orders to better understand insect gene content, origin and evolution. More specifically, in intracellular Toll pathway gene families the presence of orthologues has important implications for homology based functional inference. Also, the different evolutionary backgrounds of Toll gene subfamilies should be taken into consideration when functional studies are performed, especially for TOLL9, TOLL, TOLL2_7, and the new TOLL10 clade. The presence of Diptera specific clades or the ones lacking Diptera species show the importance of overcoming the Diptera bias when performing functional characterization of Toll pathways.
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Affiliation(s)
- Letícia Ferreira Lima
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - André Quintanilha Torres
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - Rafael Dias Mesquita
- Laboratório de Bioinformática, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular-INCT-EM, Rio de Janeiro, Brazil
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular-INCT-EM, Rio de Janeiro, Brazil.
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77
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Denecke S, Rankić I, Driva O, Kalsi M, Luong NBH, Buer B, Nauen R, Geibel S, Vontas J. Comparative and functional genomics of the ABC transporter superfamily across arthropods. BMC Genomics 2021; 22:553. [PMID: 34281528 PMCID: PMC8290562 DOI: 10.1186/s12864-021-07861-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/23/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The ATP-binding cassette (ABC) transporter superfamily is comprised predominantly of proteins which directly utilize energy from ATP to move molecules across the plasma membrane. Although they have been the subject of frequent investigation across many taxa, arthropod ABCs have been less well studied. While the manual annotation of ABC transporters has been performed in many arthropods, there has so far been no systematic comparison of the superfamily within this order using the increasing number of sequenced genomes. Furthermore, functional work on these genes is limited. RESULTS Here, we developed a standardized pipeline to annotate ABCs from predicted proteomes and used it to perform comparative genomics on ABC families across arthropod lineages. Using Kruskal-Wallis tests and the Computational Analysis of gene Family Evolution (CAFE), we were able to observe significant expansions of the ABC-B full transporters (P-glycoproteins) in Lepidoptera and the ABC-H transporters in Hemiptera. RNA-sequencing of epithelia tissues in the Lepidoptera Helicoverpa armigera showed that the 7 P-glycoprotein paralogues differ substantially in their tissue distribution, suggesting a spatial division of labor. It also seems that functional redundancy is a feature of these transporters as RNAi knockdown showed that most transporters are dispensable with the exception of the highly conserved gene Snu, which is probably due to its role in cuticular formation. CONCLUSIONS We have performed an annotation of the ABC superfamily across > 150 arthropod species for which good quality protein annotations exist. Our findings highlight specific expansions of ABC transporter families which suggest evolutionary adaptation. Future work will be able to use this analysis as a resource to provide a better understanding of the ABC superfamily in arthropods.
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Affiliation(s)
- Shane Denecke
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece.
| | - Ivan Rankić
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
| | - Olympia Driva
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece
| | - Megha Kalsi
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece
| | - Ngoc Bao Hang Luong
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece
| | - Benjamin Buer
- CropScience Division, Bayer AG, R&D Pest Control, D-40789, Monheim, Germany
| | - Ralf Nauen
- CropScience Division, Bayer AG, R&D Pest Control, D-40789, Monheim, Germany
| | - Sven Geibel
- CropScience Division, Bayer AG, R&D Pest Control, D-40789, Monheim, Germany
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece.,Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Athens, Greece
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78
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Novikova EL, Kulakova MA. There and Back Again: Hox Clusters Use Both DNA Strands. J Dev Biol 2021; 9:28. [PMID: 34287306 PMCID: PMC8293171 DOI: 10.3390/jdb9030028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.
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Affiliation(s)
- Elena L. Novikova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Milana A. Kulakova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
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79
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Yan Z, Smith ML, Du P, Hahn MW, Nakhleh L. Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs. Syst Biol 2021; 71:367-381. [PMID: 34245291 PMCID: PMC8978208 DOI: 10.1093/sysbio/syab056] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
Many recent phylogenetic methods have focused on accurately inferring species
trees when there is gene tree discordance due to incomplete lineage sorting
(ILS). For almost all of these methods, and for phylogenetic methods in general,
the data for each locus are assumed to consist of orthologous, single-copy
sequences. Loci that are present in more than a single copy in any of the
studied genomes are excluded from the data. These steps greatly reduce the
number of loci available for analysis. The question we seek to answer in this
study is: what happens if one runs such species tree inference methods on data
where paralogy is present, in addition to or without ILS being present? Through
simulation studies and analyses of two large biological data sets, we show that
running such methods on data with paralogs can still provide accurate results.
We use multiple different methods, some of which are based directly on the
multispecies coalescent model, and some of which have been proven to be
statistically consistent under it. We also treat the paralogous loci in multiple
ways: from explicitly denoting them as paralogs, to randomly selecting one copy
per species. In all cases, the inferred species trees are as accurate as
equivalent analyses using single-copy orthologs. Our results have significant
implications for the use of ILS-aware phylogenomic analyses, demonstrating that
they do not have to be restricted to single-copy loci. This will greatly
increase the amount of data that can be used for phylogenetic inference.[Gene
duplication and loss; incomplete lineage sorting; multispecies coalescent;
orthology; paralogy.]
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Affiliation(s)
- Zhi Yan
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
| | - Peng Du
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Matthew W Hahn
- Department of Biology and Department of Computer Science, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA.,Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
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80
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Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, Paten B, Penso-Dolfin L, Wang L, Chang Y, Gao Q, Ma L, Ma L, Zhang Z, Zhang H, Zhang H, Ruzzante L, Robertson HM, Zhu Y, Liu Y, Yang H, Ding L, Wang Q, Ma D, Xu W, Liang C, Itgen MW, Mee L, Cao G, Zhang Z, Sadd BM, Hahn MW, Schaack S, Barribeau SM, Williams PH, Waterhouse RM, Mueller RL. Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits. Mol Biol Evol 2021; 38:486-501. [PMID: 32946576 PMCID: PMC7826183 DOI: 10.1093/molbev/msaa240] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships, whereas incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.
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Affiliation(s)
- Cheng Sun
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaxing Huang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaomeng Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Su
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gregg W C Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Mengya Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Saverio Vicario
- Institute of Atmospheric Pollution Research-Italian National Research Council C/O Department of Physics, University of Bari, Bari, Italy
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA.,Department of Cytology and Genetics, Tomsk State University, Tomsk, Russian Federation
| | - Semen M Bondarenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA
| | - Martin Hasselmann
- Department of Livestock Population Genomics, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Chang N Kim
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA
| | | | - Li Wang
- 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
| | - Yuxiao Chang
- 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
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ling Ma
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lina Ma
- China National Center for Bioinformation & Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- China National Center for Bioinformation & Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Hongbo Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Huahao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Livio Ruzzante
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL
| | - Yihui Zhu
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA
| | - Yanjie Liu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huipeng Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lele Ding
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Quangui Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongna Ma
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilin Xu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Liang
- Institute of Sericultural and Apiculture, Yunnan Academy of Agricultural Sciences, Mengzi, China
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Lauren Mee
- Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ze Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Ben M Sadd
- School of Biological Sciences, Illinois State University, Normal, IL
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN.,Department of Computer Science, Indiana University, Bloomington, IN
| | | | - Seth M Barribeau
- Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Paul H Williams
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
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81
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Koiwai K, Koyama T, Tsuda S, Toyoda A, Kikuchi K, Suzuki H, Kawano R. Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process. eLife 2021; 10:e66954. [PMID: 34132195 PMCID: PMC8266392 DOI: 10.7554/elife.66954] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/15/2021] [Indexed: 01/03/2023] Open
Abstract
Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been reported, showing that the morphological characteristics are not sufficient to resolve their actual roles. Our present study using single-cell RNA sequencing revealed six types of hemocytes of Marsupenaeus japonicus based on their transcriptional profiles. We identified markers of each subpopulation and predicted the differentiation pathways involved in their maturation. We also predicted cell growth factors that might play crucial roles in hemocyte differentiation. Different immune roles among these subpopulations were suggested from the analysis of differentially expressed immune-related genes. These results provide a unified classification of shrimp hemocytes, which improves the understanding of its immune system.
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Affiliation(s)
- Keiichiro Koiwai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and TechnologyKoganeiJapan
- Laboratory of Genome Science, Tokyo University of Marine Science and TechnologyMinatoJapan
| | - Takashi Koyama
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of TokyoHamamatsuJapan
- Graduate School of Fisheries and Environmental Sciences, Nagasaki UniversityNagasakiJapan
| | | | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of GeneticsMishimaJapan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of TokyoHamamatsuJapan
| | - Hiroaki Suzuki
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo UniversityBunkyoJapan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and TechnologyKoganeiJapan
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82
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Insights into the genomic evolution of insects from cricket genomes. Commun Biol 2021; 4:733. [PMID: 34127782 PMCID: PMC8203789 DOI: 10.1038/s42003-021-02197-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Most of our knowledge of insect genomes comes from Holometabolous species, which undergo complete metamorphosis and have genomes typically under 2 Gb with little signs of DNA methylation. In contrast, Hemimetabolous insects undergo the presumed ancestral process of incomplete metamorphosis, and have larger genomes with high levels of DNA methylation. Hemimetabolous species from the Orthopteran order (grasshoppers and crickets) have some of the largest known insect genomes. What drives the evolution of these unusual insect genome sizes, remains unknown. Here we report the sequencing, assembly and annotation of the 1.66-Gb genome of the Mediterranean field cricket Gryllus bimaculatus, and the annotation of the 1.60-Gb genome of the Hawaiian cricket Laupala kohalensis. We compare these two cricket genomes with those of 14 additional insects and find evidence that hemimetabolous genomes expanded due to transposable element activity. Based on the ratio of observed to expected CpG sites, we find higher conservation and stronger purifying selection of methylated genes than non-methylated genes. Finally, our analysis suggests an expansion of the pickpocket class V gene family in crickets, which we speculate might play a role in the evolution of cricket courtship, including their characteristic chirping. Ylla, Extavour et al. use genomic data from crickets to investigate the evolution of large genome sizes and DNA methylation events in insects. Their findings indicate that transposable element activity drove genome expansion in hemimetabolous insects, such as crickets and grasshoppers, and that DNA methylation is predominant in conserved genes.
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83
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Lukicheva S, Flot JF, Mardulyn P. Genome Assembly of the Cold-Tolerant Leaf Beetle Gonioctena quinquepunctata, an Important Resource for Studying Its Evolution and Reproductive Barriers between Species. Genome Biol Evol 2021; 13:6296840. [PMID: 34115123 PMCID: PMC8290105 DOI: 10.1093/gbe/evab134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Coleoptera is the most species-rich insect order, yet is currently underrepresented in genomic databases. An assembly was generated for ca. 1.7 Gb genome of the leaf beetle Gonioctena quinquepunctata by first assembling long-sequence reads (Oxford Nanopore; ± 27-fold coverage) and subsequently polishing the resulting assembly with short sequence reads (Illumina; ± 85-fold coverage). The unusually large size (most Coleoptera species are associated with a reported size below 1 Gb) was at least partially attributed to the presence of a large fraction of repeated elements (73.8%). The final assembly was characterized by an N50 length of 432 kb and a BUSCO score of 95.5%. The heterozygosity rate was ± 0.6%. Automated genome annotation informed by RNA-Seq resulted in 40,568 predicted proteins, which is much larger than the typical range 17,000–23,000 predicted for other Coleoptera. However, no evidence of a genome duplication was detected. This new reference genome will contribute to our understanding of genetic variation in the Coleoptera. Among others, it will also allow exploring reproductive barriers between species, investigating introgression in the nuclear genome, and identifying genes involved in resistance to extreme climate conditions.
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Affiliation(s)
- Svitlana Lukicheva
- Evolutionary Biology and Ecology & Interuniversity Institute of Bioinformatics in Brussels - (IB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Jean-François Flot
- Evolutionary Biology and Ecology & Interuniversity Institute of Bioinformatics in Brussels - (IB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology & Interuniversity Institute of Bioinformatics in Brussels - (IB), Université Libre de Bruxelles (ULB), Brussels, Belgium
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84
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Provazníková I, Hejníčková M, Visser S, Dalíková M, Carabajal Paladino LZ, Zrzavá M, Voleníková A, Marec F, Nguyen P. Large-scale comparative analysis of cytogenetic markers across Lepidoptera. Sci Rep 2021; 11:12214. [PMID: 34108567 PMCID: PMC8190105 DOI: 10.1038/s41598-021-91665-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/24/2021] [Indexed: 11/25/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) allows identification of particular chromosomes and their rearrangements. Using FISH with signal enhancement via antibody amplification and enzymatically catalysed reporter deposition, we evaluated applicability of universal cytogenetic markers, namely 18S and 5S rDNA genes, U1 and U2 snRNA genes, and histone H3 genes, in the study of the karyotype evolution in moths and butterflies. Major rDNA underwent rather erratic evolution, which does not always reflect chromosomal changes. In contrast, the hybridization pattern of histone H3 genes was well conserved, reflecting the stable organisation of lepidopteran genomes. Unlike 5S rDNA and U1 and U2 snRNA genes which we failed to detect, except for 5S rDNA in a few representatives of early diverging lepidopteran lineages. To explain the negative FISH results, we used quantitative PCR and Southern hybridization to estimate the copy number and organization of the studied genes in selected species. The results suggested that their detection was hampered by long spacers between the genes and/or their scattered distribution. Our results question homology of 5S rDNA and U1 and U2 snRNA loci in comparative studies. We recommend the use of histone H3 in studies of karyotype evolution.
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Affiliation(s)
- Irena Provazníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martina Hejníčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Sander Visser
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | | | - Magda Zrzavá
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Anna Voleníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - František Marec
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic.
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85
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Ellis EA, Storer CG, Kawahara AY. De novo genome assemblies of butterflies. Gigascience 2021; 10:6291117. [PMID: 34076242 PMCID: PMC8170690 DOI: 10.1093/gigascience/giab041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/22/2020] [Accepted: 05/05/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The availability of thousands of genomes has enabled new advancements in biology. However, many genomes have not been investigated for their quality. Here we examine quality trends in a taxonomically diverse and well-known group, butterflies (Papilionoidea), and provide draft, de novo assemblies for all available butterfly genomes. Owing to massive genome sequencing investment and taxonomic curation, this is an excellent group to explore genome quality. FINDINGS We provide de novo assemblies for all 822 available butterfly genomes and interpret their quality in terms of completeness and continuity. We identify the 50 highest quality genomes across butterflies and conclude that the ringlet, Aphantopus hyperantus, has the highest quality genome. Our post-processing of draft genome assemblies identified 118 butterfly genomes that should not be reused owing to contamination or extremely low quality. However, many draft genomes are of high utility, especially because permissibility of low-quality genomes is dependent on the objective of the study. Our assemblies will serve as a key resource for papilionid genomics, especially for researchers without computational resources. CONCLUSIONS Quality metrics and assemblies are typically presented with annotated genome accessions but rarely with de novo genomes. We recommend that studies presenting genome sequences provide the assembly and some metrics of quality because quality will significantly affect downstream results. Transparency in quality metrics is needed to improve the field of genome science and encourage data reuse.
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Affiliation(s)
- Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611-2710, USA
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611-2710, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611-2710, USA
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86
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Jockusch EL, Fisher CR. Something old, something new, something borrowed, something red: the origin of ecologically relevant novelties in Hemiptera. Curr Opin Genet Dev 2021; 69:154-162. [PMID: 34058515 DOI: 10.1016/j.gde.2021.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/19/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
Comparative transcriptomics, applied in an evolutionary context, has transformed the possibilities for studying phenotypic evolution in non-model taxa. We review recent discoveries about the development of novel, ecologically relevant phenotypes in hemipteran insects. These discoveries highlight the diverse genomic substrates of novelty: 'something old', when novelty results from changes in the regulation of existing genes or gene duplication; 'something new', wherein lineage-restricted genes contribute to the evolution of new phenotypes; and 'something borrowed', showcasing contributions of horizontal gene transfer to the evolution of novelty, including carotenoid synthesis (resulting in 'something red'). These findings show the power and flexibility of comparative transcriptomic approaches for expanding beyond the 'toolkit' model for the evolution of development. We conclude by raising questions about the relationship between new genes and new traits and outlining a research framework for answering them in Hemiptera.
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Affiliation(s)
- Elizabeth L Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd., U-3043, Storrs, CT 06269, USA.
| | - Cera R Fisher
- Cornell University, Department of Entomology, 2126 Comstock Hall, Ithaca, NY 14853, USA
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87
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Yi SV, Goodisman MAD. The impact of epigenetic information on genome evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200114. [PMID: 33866804 DOI: 10.1098/rstb.2020.0114] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Epigenetic information affects gene function by interacting with chromatin, while not changing the DNA sequence itself. However, it has become apparent that the interactions between epigenetic information and chromatin can, in fact, indirectly lead to DNA mutations and ultimately influence genome evolution. This review evaluates the ways in which epigenetic information affects genome sequence and evolution. We discuss how DNA methylation has strong and pervasive effects on DNA sequence evolution in eukaryotic organisms. We also review how the physical interactions arising from the connections between histone proteins and DNA affect DNA mutation and repair. We then discuss how a variety of epigenetic mechanisms exert substantial effects on genome evolution by suppressing the movement of transposable elements. Finally, we examine how genome expansion through gene duplication is also partially controlled by epigenetic information. Overall, we conclude that epigenetic information has widespread indirect effects on DNA sequences in eukaryotes and represents a potent cause and constraint of genome evolution. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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88
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Ferguson KB, Visser S, Dalíková M, Provazníková I, Urbaneja A, Pérez‐Hedo M, Marec F, Werren JH, Zwaan BJ, Pannebakker BA, Verhulst EC. Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest. INSECT MOLECULAR BIOLOGY 2021; 30:188-209. [PMID: 33305885 PMCID: PMC8048687 DOI: 10.1111/imb.12688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/25/2020] [Accepted: 12/07/2020] [Indexed: 05/14/2023]
Abstract
Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.
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Affiliation(s)
- K. B. Ferguson
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - S. Visser
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - M. Dalíková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - I. Provazníková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- European Molecular Biology LaboratoryHeidelbergGermany
| | - A. Urbaneja
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - M. Pérez‐Hedo
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - F. Marec
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
| | - J. H. Werren
- Department of BiologyUniversity of RochesterRochesterNew YorkUSA
| | - B. J. Zwaan
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - B. A. Pannebakker
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - E. C. Verhulst
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
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89
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Ritchie AM, Stark TL, Liberles DA. Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework. BMC Ecol Evol 2021; 21:39. [PMID: 33691618 PMCID: PMC7944921 DOI: 10.1186/s12862-021-01770-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/25/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Recovering the historical patterns of selection acting on a protein coding sequence is a major goal of evolutionary biology. Mutation-selection models address this problem by explicitly modelling fixation rates as a function of site-specific amino acid fitness values.However, they are restricted in their utility for investigating directional evolution because they require prior knowledge of the locations of fitness changes in the lineages of a phylogeny. RESULTS We apply a modified mutation-selection methodology that relaxes assumptions of equlibrium and time-reversibility. Our implementation allows us to identify branches where adaptive or compensatory shifts in the fitness landscape have taken place, signalled by a change in amino acid fitness profiles. Through simulation and analysis of an empirical data set of [Formula: see text]-lactamase genes, we test our ability to recover the position of adaptive events within the tree and successfully reconstruct initial codon frequencies and fitness profile parameters generated under the non-stationary model. CONCLUSION We demonstrate successful detection of selective shifts and identification of the affected branch on partitions of 300 codons or more. We successfully reconstruct fitness parameters and initial codon frequencies in simulated data and demonstrate that failing to account for non-equilibrium evolution can increase the error in fitness profile estimation. We also demonstrate reconstruction of plausible shifts in amino acid fitnesses in the bacterial [Formula: see text]-lactamase family and discuss some caveats for interpretation.
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Affiliation(s)
- Andrew M Ritchie
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, USA
| | - Tristan L Stark
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, USA
| | - David A Liberles
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, USA.
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90
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Brevik K, Bueno EM, McKay S, Schoville SD, Chen YH. Insecticide exposure affects intergenerational patterns of DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata. Evol Appl 2021; 14:746-757. [PMID: 33767749 PMCID: PMC7980262 DOI: 10.1111/eva.13153] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/23/2022] Open
Abstract
Insecticide use is pervasive as a selective force in modern agroecosystems. Insect herbivores exposed to these insecticides have been able to rapidly evolve resistance to them, but how they are able to do so is poorly understood. One possible but largely unexplored explanation is that exposure to sublethal doses of insecticides may alter epigenetic patterns that are heritable. For instance, epigenetic mechanisms, such as DNA methylation that modifies gene expression without changing the underlying genetic code, may facilitate the emergence of resistant phenotypes in complex ways. We assessed the effects of sublethal insecticide exposure, with the neonicotinoid imidacloprid, on DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata, examining both global changes in DNA methylation and specific changes found within genes and transposable elements. We found that exposure to insecticide led to decreases in global DNA methylation for parent and F2 generations and that many of the sites of changes in methylation are found within genes associated with insecticide resistance, such as cytochrome P450s, or within transposable elements. Exposure to sublethal doses of insecticide caused heritable changes in DNA methylation in an agricultural insect herbivore. Therefore, epigenetics may play a role in insecticide resistance, highlighting a fundamental mechanism of evolution while informing how we might better coexist with insect species in agroecosystems.
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Affiliation(s)
- Kristian Brevik
- Department of Plant and Soil ScienceUniversity of VermontBurlingtonVTUSA
| | - Erika M. Bueno
- Department of Plant and Soil ScienceUniversity of VermontBurlingtonVTUSA
| | - Stephanie McKay
- Department of Animal and Veterinary SciencesUniversity of VermontBurlingtonVTUSA
| | | | - Yolanda H. Chen
- Department of Plant and Soil ScienceUniversity of VermontBurlingtonVTUSA
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91
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Li HS, Huang YH, Chen ML, Ren Z, Qiu BY, De Clercq P, Heckel G, Pang H. Genomic insight into diet adaptation in the biological control agent Cryptolaemus montrouzieri. BMC Genomics 2021; 22:135. [PMID: 33632122 PMCID: PMC7905881 DOI: 10.1186/s12864-021-07442-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/10/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The ladybird beetle Cryptolaemus montrouzieri Mulsant, 1853 (Coleoptera, Coccinellidae) is used worldwide as a biological control agent. It is a predator of various mealybug pests, but it also feeds on alternative prey and can be reared on artificial diets. Relatively little is known about the underlying genetic adaptations of its feeding habits. RESULTS We report the first high-quality genome sequence for C. montrouzieri. We found that the gene families encoding chemosensors and digestive and detoxifying enzymes among others were significantly expanded or contracted in C. montrouzieri in comparison to published genomes of other beetles. Comparisons of diet-specific larval development, survival and transcriptome profiling demonstrated that differentially expressed genes on unnatural diets as compared to natural prey were enriched in pathways of nutrient metabolism, indicating that the lower performance on the tested diets was caused by nutritional deficiencies. Remarkably, the C. montrouzieri genome also showed a significant expansion in an immune effector gene family. Some of the immune effector genes were dramatically downregulated when larvae were fed unnatural diets. CONCLUSION We suggest that the evolution of genes related to chemosensing, digestion, and detoxification but also immunity might be associated with diet adaptation of an insect predator. These findings help explain why this predatory ladybird has become a successful biological control agent and will enable the optimization of its mass rearing and use in biological control programs.
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Affiliation(s)
- Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mei-Lan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong, China.,School of Environment and Life Science, Nanning Normal University, Nanning, 530001, China
| | - Zhan Ren
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bo-Yuan Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Patrick De Clercq
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong, China.
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92
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Bain SA, Marshall H, de la Filia AG, Laetsch DR, Husnik F, Ross L. Sex-specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination. Mol Ecol 2021; 30:5687-5703. [PMID: 33629415 DOI: 10.1111/mec.15842] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/27/2020] [Accepted: 02/09/2021] [Indexed: 12/16/2022]
Abstract
Phenotypic differences between sexes are often mediated by differential expression and alternative splicing of genes. However, the mechanisms that regulate these expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, paternal genome elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. Planococcus citri has no sex chromosomes and both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. Here, we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole-genome bisulphite sequencing. We identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifest as more uniform low levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq, we identify extensive sex-specific gene expression and alternative splicing, but we find no correlation with cis-acting DNA methylation.
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Affiliation(s)
- Stevie A Bain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Hollie Marshall
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Filip Husnik
- Evolution, Cell Biology, and Symbiosis Unit, Okinawa Institute of Science and Technology, Kunigami-gun, Japan
| | - Laura Ross
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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93
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New Approaches for Inferring Phylogenies in the Presence of Paralogs. Trends Genet 2021; 37:174-187. [DOI: 10.1016/j.tig.2020.08.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 12/18/2022]
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94
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Olsen LK, Heckenhauer J, Sproul JS, Dikow RB, Gonzalez VL, Kweskin MP, Taylor AM, Wilson SB, Stewart RJ, Zhou X, Holzenthal R, Pauls SU, Frandsen PB. Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera). Genome Biol Evol 2021; 13:6121109. [PMID: 33501983 PMCID: PMC7936034 DOI: 10.1093/gbe/evab013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2021] [Indexed: 12/20/2022] Open
Abstract
Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators. Knowledge on the genomic diversity of caddisflies can facilitate comparative and phylogenetic studies thereby allowing scientists to better understand the evolutionary history of caddisflies. Although Trichoptera are the most diverse aquatic insect order, they remain poorly represented in terms of genomic resources. To date, all long-read based genomes have been sequenced from individuals in the retreat-making suborder, Annulipalpia, leaving ∼275 Ma of evolution without high-quality genomic resources. Here, we report the first long-read based de novo genome assemblies of two tube case-making Trichoptera from the suborder Integripalpia, Agrypnia vestita Walker and Hesperophylax magnus Banks. We find that these tube case-making caddisflies have genome sizes that are at least 3-fold larger than those of currently sequenced annulipalpian genomes and that this pattern is at least partly driven by major expansion of repetitive elements. In H. magnus, long interspersed nuclear elements alone exceed the entire genome size of some annulipalpian counterparts suggesting that caddisflies have high potential as a model for understanding genome size evolution in diverse insect lineages.
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Affiliation(s)
- Lindsey K Olsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.,Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - John S Sproul
- Department of Biology, University of Rochester, New York, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA
| | - Vanessa L Gonzalez
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Matthew P Kweskin
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Adam M Taylor
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Seth B Wilson
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Russell J Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ralph Holzenthal
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, USA
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.,Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany.,Institute of Insect Biotechnology, Justus-Liebig University, Gießen, Germany
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA
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95
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Li HS, Tang XF, Huang YH, Xu ZY, Chen ML, Du XY, Qiu BY, Chen PT, Zhang W, Ślipiński A, Escalona HE, Waterhouse RM, Zwick A, Pang H. Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles. BMC Biol 2021; 19:7. [PMID: 33446206 PMCID: PMC7807722 DOI: 10.1186/s12915-020-00945-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/22/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) has been documented in many herbivorous insects, conferring the ability to digest plant material and promoting their remarkable ecological diversification. Previous reports suggest HGT of antibacterial enzymes may have contributed to the insect immune response and limit bacterial growth. Carnivorous insects also display many evolutionary successful lineages, but in contrast to the plant feeders, the potential role of HGTs has been less well-studied. RESULTS Using genomic and transcriptomic data from 38 species of ladybird beetles, we identified a set of bacterial cell wall hydrolase (cwh) genes acquired by this group of beetles. Infection with Bacillus subtilis led to upregulated expression of these ladybird cwh genes, and their recombinantly produced proteins limited bacterial proliferation. Moreover, RNAi-mediated cwh knockdown led to downregulation of other antibacterial genes, indicating a role in antibacterial immune defense. cwh genes are rare in eukaryotes, but have been maintained in all tested Coccinellinae species, suggesting that this putative immune-related HGT event played a role in the evolution of this speciose subfamily of predominant predatory ladybirds. CONCLUSION Our work demonstrates that, in a manner analogous to HGT-facilitated plant feeding, enhanced immunity through HGT might have played a key role in the prey adaptation and niche expansion that promoted the diversification of carnivorous beetle lineages. We believe that this represents the first example of immune-related HGT in carnivorous insects with an association with a subsequent successful species radiation.
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Affiliation(s)
- Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xue-Fei Tang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ze-Yu Xu
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mei-Lan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- School of Environment and Life Science, Nanning Normal University, Nanning, 530001, China
| | - Xue-Yong Du
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Bo-Yuan Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Pei-Tao Chen
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Hermes E Escalona
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China.
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96
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Allio R, Nabholz B, Wanke S, Chomicki G, Pérez-Escobar OA, Cotton AM, Clamens AL, Kergoat GJ, Sperling FAH, Condamine FL. Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nat Commun 2021; 12:354. [PMID: 33441560 PMCID: PMC7806994 DOI: 10.1038/s41467-020-20507-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/03/2020] [Indexed: 01/29/2023] Open
Abstract
The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic insect-plant interaction between swallowtail butterflies and the highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient host-plant shifts. This evolutionary framework provides a valuable opportunity for repeated tests of genomic signatures of macroevolutionary changes and estimation of diversification rates across their phylogeny. We find that host-plant shifts in butterflies are associated with both genome-wide adaptive molecular evolution (more genes under positive selection) and repeated bursts of speciation rates, contributing to an increase in global diversification through time. Our study links ecological changes, genome-wide adaptations and macroevolutionary consequences, lending support to the importance of ecological interactions as evolutionary drivers over long time periods.
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Affiliation(s)
- Rémi Allio
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Benoit Nabholz
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - Guillaume Chomicki
- Department of Bioscience, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | | | - Adam M Cotton
- 86/2 Moo 5, Tambon Nong Kwai, Hang Dong, Chiang Mai, Thailand
| | - Anne-Laure Clamens
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Gaël J Kergoat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada
| | - Fabien L Condamine
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada.
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97
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Sheffer MM, Hoppe A, Krehenwinkel H, Uhl G, Kuss AW, Jensen L, Jensen C, Gillespie RG, Hoff KJ, Prost S. Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation. Gigascience 2021; 10:giaa148. [PMID: 33410470 PMCID: PMC7788392 DOI: 10.1093/gigascience/giaa148] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/17/2020] [Accepted: 11/20/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Argiope bruennichi, the European wasp spider, has been investigated intensively as a focal species for studies on sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies. FINDINGS We generated, de novo, a 1.67 Gb genome assembly of A. bruennichi using 21.8× Pacific Biosciences sequencing, polished with 19.8× Illumina paired-end sequencing data, and proximity ligation (Hi-C)-based scaffolding. This resulted in an N50 scaffold size of 124 Mb and an N50 contig size of 288 kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high-quality assembly. CONCLUSIONS We present the first chromosome-level genome assembly in the order Araneae. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation not only in A. bruennichi but also in arachnids overall, shedding light on questions such as the genomic architecture of traits, whole-genome duplication, and the genomic mechanisms behind silk and venom evolution.
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Affiliation(s)
- Monica M Sheffer
- Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, 17489 Greifswald, Germany
| | - Anica Hoppe
- Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17489 Greifswald, Germany
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Henrik Krehenwinkel
- Department of Biogeography, University of Trier, Universitätsring 15, 54296 Trier, Germany
| | - Gabriele Uhl
- Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, 17489 Greifswald, Germany
| | - Andreas W Kuss
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Lars Jensen
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Corinna Jensen
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Rosemary G Gillespie
- Department of Environmental Science Policy and Management, University of California Berkeley, 130 Mulford Hall #3114, Berkeley, CA, 94720, USA
| | - Katharina J Hoff
- Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17489 Greifswald, Germany
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Gardens of South Africa, 232 Boom St., Pretoria 0001, South Africa
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98
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Mendes FK, Vanderpool D, Fulton B, Hahn MW. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 2020; 36:5516-5518. [PMID: 33325502 DOI: 10.1093/bioinformatics/btaa1022] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/12/2020] [Accepted: 11/30/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Genome sequencing projects have revealed frequent gains and losses of genes between species. Previous versions of our software, CAFE (Computational Analysis of gene Family Evolution), have allowed researchers to estimate parameters of gene gain and loss across a phylogenetic tree. However, the underlying model assumed that all gene families had the same rate of evolution, despite evidence suggesting a large amount of variation in rates among families. RESULTS Here we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modelling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts. AVAILABILITY CAFE 5 source code, documentation, test data, and a detailed manual with examples are freely available at https://github.com/hahnlab/CAFE5/releases.
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Affiliation(s)
- Fábio K Mendes
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Dan Vanderpool
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ben Fulton
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,University Information Technology Services Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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99
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Cohen ZP, Brevik K, Chen YH, Hawthorne DJ, Weibel BD, Schoville SD. Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata, Say). Mol Ecol 2020; 30:237-254. [PMID: 33095936 DOI: 10.1111/mec.15703] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 09/28/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
Abstract
Contextualizing evolutionary history and identifying genomic features of an insect that might contribute to its pest status is important in developing early detection and control tactics. In order to understand the evolution of pestiferousness, which we define as the accumulation of traits that contribute to an insect population's success in an agroecosystem, we tested the importance of known genomic properties associated with rapid adaptation in the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say. Within the leaf beetle genus Leptinotarsa, only CPB, and a few populations therein, has risen to pest status on cultivated nightshades, Solanum. Using whole genomes from ten closely related Leptinotarsa species native to the United States, we reconstructed a high-quality species tree and used this phylogenetic framework to assess evolutionary patterns in four genomic features of rapid adaptation: standing genetic variation, gene family expansion and contraction, transposable element abundance and location, and positive selection at protein-coding genes. Throughout approximately 20 million years of history, Leptinotarsa species show little evidence of gene family turnover and transposable element variation. However, there is a clear pattern of CPB experiencing higher rates of positive selection on protein-coding genes. We determine that these rates are associated with greater standing genetic variation due to larger effective population size, which supports the theory that the demographic history contributes to rates of protein evolution. Furthermore, we identify a suite of coding genes under positive selection that are putatively associated with pestiferousness in the Colorado potato beetle lineage. They are involved in the biological processes of xenobiotic detoxification, chemosensation and hormone function.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristian Brevik
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - Yolanda H Chen
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - David J Hawthorne
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Benjamin D Weibel
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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100
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Weisman CM, Murray AW, Eddy SR. Many, but not all, lineage-specific genes can be explained by homology detection failure. PLoS Biol 2020; 18:e3000862. [PMID: 33137085 PMCID: PMC7660931 DOI: 10.1371/journal.pbio.3000862] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 11/12/2020] [Accepted: 09/21/2020] [Indexed: 12/21/2022] Open
Abstract
Genes for which homologs can be detected only in a limited group of evolutionarily related species, called “lineage-specific genes,” are pervasive: Essentially every lineage has them, and they often comprise a sizable fraction of the group’s total genes. Lineage-specific genes are often interpreted as “novel” genes, representing genetic novelty born anew within that lineage. Here, we develop a simple method to test an alternative null hypothesis: that lineage-specific genes do have homologs outside of the lineage that, even while evolving at a constant rate in a novelty-free manner, have merely become undetectable by search algorithms used to infer homology. We show that this null hypothesis is sufficient to explain the lack of detected homologs of a large number of lineage-specific genes in fungi and insects. However, we also find that a minority of lineage-specific genes in both clades are not well explained by this novelty-free model. The method provides a simple way of identifying which lineage-specific genes call for special explanations beyond homology detection failure, highlighting them as interesting candidates for further study. Lineage-specific gene families may arise from evolutionary innovations such as de novo gene origination, or may simply mean that a similarity search program failed to identify more distant homologs. A new computational method for modeling the expected decay of similarity search scores with evolutionary distance allows distinction between the two explanations.
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Affiliation(s)
- Caroline M. Weisman
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Andrew W. Murray
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Sean R. Eddy
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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