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Deem KD, Brisson JA. Problems with Paralogs: The Promise and Challenges of Gene Duplicates in Evo-Devo Research. Integr Comp Biol 2024; 64:556-564. [PMID: 38565319 PMCID: PMC11406157 DOI: 10.1093/icb/icae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/13/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
Gene duplicates, or paralogs, serve as a major source of new genetic material and comprise seeds for evolutionary innovation. While originally thought to be quickly lost or nonfunctionalized following duplication, now a vast number of paralogs are known to be retained in a functional state. Daughter paralogs can provide robustness through redundancy, specialize via sub-functionalization, or neo-functionalize to play new roles. Indeed, the duplication and divergence of developmental genes have played a monumental role in the evolution of animal forms (e.g., Hox genes). Still, despite their prevalence and evolutionary importance, the precise detection of gene duplicates in newly sequenced genomes remains technically challenging and often overlooked. This presents an especially pertinent problem for evolutionary developmental biology, where hypothesis testing requires accurate detection of changes in gene expression and function, often in nontraditional model species. Frequently, these analyses rely on molecular reagents designed within coding sequences that may be highly similar in recently duplicated paralogs, leading to cross-reactivity and spurious results. Thus, care is needed to avoid erroneously assigning diverged functions of paralogs to a single gene, and potentially misinterpreting evolutionary history. This perspective aims to overview the prevalence and importance of paralogs and to shed light on the difficulty of their detection and analysis while offering potential solutions.
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Affiliation(s)
- Kevin D Deem
- Department of Biology, University of Rochester, Rochester, NY, 14620
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2
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Treidel LA, Deem KD, Salcedo MK, Dickinson MH, Bruce HS, Darveau CA, Dickerson BH, Ellers O, Glass JR, Gordon CM, Harrison JF, Hedrick TL, Johnson MG, Lebenzon JE, Marden JH, Niitepõld K, Sane SP, Sponberg S, Talal S, Williams CM, Wold ES. Insect Flight: State of the Field and Future Directions. Integr Comp Biol 2024; 64:icae106. [PMID: 38982327 PMCID: PMC11406162 DOI: 10.1093/icb/icae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024] Open
Abstract
The evolution of flight in an early winged insect ancestral lineage is recognized as a key adaptation explaining the unparalleled success and diversification of insects. Subsequent transitions and modifications to flight machinery, including secondary reductions and losses, also play a central role in shaping the impacts of insects on broadscale geographic and ecological processes and patterns in the present and future. Given the importance of insect flight, there has been a centuries-long history of research and debate on the evolutionary origins and biological mechanisms of flight. Here, we revisit this history from an interdisciplinary perspective, discussing recent discoveries regarding the developmental origins, physiology, biomechanics, and neurobiology and sensory control of flight in a diverse set of insect models. We also identify major outstanding questions yet to be addressed and provide recommendations for overcoming current methodological challenges faced when studying insect flight, which will allow the field to continue to move forward in new and exciting directions. By integrating mechanistic work into ecological and evolutionary contexts, we hope that this synthesis promotes and stimulates new interdisciplinary research efforts necessary to close the many existing gaps about the causes and consequences of insect flight evolution.
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Affiliation(s)
- Lisa A Treidel
- School of Biological Sciences, University of Nebraska, Lincoln, Lincoln NE, 68588, USA
| | - Kevin D Deem
- Department of Biology, University of Rochester, Rochester NY, 14627, USA
| | - Mary K Salcedo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca NY, 14853, USA
| | - Michael H Dickinson
- Department of Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
| | | | - Charles-A Darveau
- Department of Biology, University of Ottawa, Ottawa Ontario, K1N 6N5, Canada
| | - Bradley H Dickerson
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA
| | - Olaf Ellers
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Jordan R Glass
- Department of Zoology & Physiology, University of Wyoming, Laramie, WY 82070, USA
| | - Caleb M Gordon
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT 06520-8109, USA
| | - Jon F Harrison
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Tyson L Hedrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meredith G Johnson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Jacqueline E Lebenzon
- Department of Integrative Biology, University of California, Berkeley, Berkeley CA, 94720, USA
| | - James H Marden
- Department of Biology, Pennsylvania State University, University Park, PA 16803, USA
| | | | - Sanjay P Sane
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065 India
| | - Simon Sponberg
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Stav Talal
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Caroline M Williams
- Department of Integrative Biology, University of California, Berkeley, Berkeley CA, 94720, USA
| | - Ethan S Wold
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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3
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Garrett D, Teakle G, Collier R, Bell JR, Cerezo-Medina S, Morales-Hojas R. Genome assembly and transcriptomic analysis to elucidate the ability of Nasonovia ribisnigri to break host plant resistance. INSECT MOLECULAR BIOLOGY 2024; 33:228-245. [PMID: 38348538 DOI: 10.1111/imb.12894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/09/2024] [Indexed: 02/27/2024]
Abstract
Aphid genomic resources enable the study of complex life history traits and provide information on vector biology, host adaption and speciation. The currant-lettuce aphid (Nasonovia ribisnigri (Hemiptera: Aphididae) (Mosley)) is a cosmopolitan pest of outdoor lettuce (Lactuca sativa (Asterales: Asteraceae) (Linnaeus)). Until recently, the use of resistant cultivars was an effective method for managing N. ribisnigri. A resistant cultivar containing a single gene (Nr-locus), introduced in the 1980s, conferred complete resistance to feeding. Overreliance of this Nr-locus in lettuce resulted in N. ribisnigri's ability to break resistance mechanism, with first reports during 2003. Our work attempts to understand which candidate gene(s) are associated with this resistance-breaking mechanism. We present two de novo draft assembles for N. ribisnigri genomes, corresponding to both avirulent (Nr-locus susceptible) and virulent (Nr-locus resistant) biotypes. Changes in gene expression of the two N. ribisnigri biotypes were investigated using transcriptomic analyses of RNA-sequencing (RNA-seq) data to understand the potential mechanisms of resistance to the Nr-locus in lettuce. The draft genome assemblies were 94.2% and 91.4% complete for the avirulent and virulent biotypes, respectively. Out of the 18,872 differentially expressed genes, a single gene/locus was identified in N. ribisnigri that was shared between two resistant-breaking biotypes. This locus was further explored and validated in Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) experiments and has predicted localisations in both the cytoplasm and nucleus. This is the first study to provide evidence that a single gene/locus is likely responsible for the ability of N. ribisnigri to overcome the Nr-locus resistance in the lettuce host.
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Affiliation(s)
- Dion Garrett
- Rothamsted Insect Survey, Rothamsted Research, Harpenden, UK
- Warwick Crop Centre, Wellesbourne Campus, University of Warwick, Warwick, UK
| | - Graham Teakle
- Warwick Crop Centre, Wellesbourne Campus, University of Warwick, Warwick, UK
| | - Rosemary Collier
- Warwick Crop Centre, Wellesbourne Campus, University of Warwick, Warwick, UK
| | - James R Bell
- Rothamsted Insect Survey, Rothamsted Research, Harpenden, UK
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
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4
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Yu J, Zhao W, Chen X, Lu H, Xiao Y, Li Q, Luo L, Kang L, Cui F. A plant virus manipulates the long-winged morph of insect vectors. Proc Natl Acad Sci U S A 2024; 121:e2315341121. [PMID: 38190519 PMCID: PMC10801844 DOI: 10.1073/pnas.2315341121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024] Open
Abstract
Wing dimorphism of insect vectors is a determining factor for viral long-distance dispersal and large-area epidemics. Although plant viruses affect the wing plasticity of insect vectors, the potential underlying molecular mechanisms have seldom been investigated. Here, we found that a planthopper-vectored rice virus, rice stripe virus (RSV), specifically induces a long-winged morph in male insects. The analysis of field populations demonstrated that the long-winged ratios of male insects are closely associated with RSV infection regardless of viral titers. A planthopper-specific and testis-highly expressed gene, Encounter, was fortuitously found to play a key role in the RSV-induced long-winged morph. Encounter resembles malate dehydrogenase in the sequence, but it does not have corresponding enzymatic activity. Encounter is upregulated to affect male wing dimorphism at early larval stages. Encounter is closely connected with the insulin/insulin-like growth factor signaling pathway as a downstream factor of Akt, of which the transcriptional level is activated in response to RSV infection, resulting in the elevated expression of Encounter. In addition, an RSV-derived small interfering RNA directly targets Encounter to enhance its expression. Our study reveals an unreported mechanism underlying the direct regulation by a plant virus of wing dimorphism in its insect vectors, providing the potential way for interrupting viral dispersal.
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Affiliation(s)
- Jinting Yu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Wan Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Xiaofang Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
| | - Hong Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
| | - Yan Xiao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Qiong Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
| | - Lan Luo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
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5
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Rimbault M, Legeai F, Peccoud J, Mieuzet L, Call E, Nouhaud P, Defendini H, Mahéo F, Marande W, Théron N, Tagu D, Le Trionnaire G, Simon JC, Jaquiéry J. Contrasting Evolutionary Patterns Between Sexual and Asexual Lineages in a Genomic Region Linked to Reproductive Mode Variation in the pea aphid. Genome Biol Evol 2023; 15:evad168. [PMID: 37717171 PMCID: PMC10538257 DOI: 10.1093/gbe/evad168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Although asexual lineages evolved from sexual lineages in many different taxa, the genetics of sex loss remains poorly understood. We addressed this issue in the pea aphid Acyrthosiphon pisum, whose natural populations encompass lineages performing cyclical parthenogenesis (CP) and producing one sexual generation per year, as well as obligate parthenogenetic (OP) lineages that can no longer produce sexual females but can still produce males. An SNP-based, whole-genome scan of CP and OP populations sequenced in pools (103 individuals from 6 populations) revealed that an X-linked region is associated with the variation in reproductive mode. This 840-kb region is highly divergent between CP and OP populations (FST = 34.9%), with >2,000 SNPs or short Indels showing a high degree of association with the phenotypic trait. In OP populations specifically, this region also shows reduced diversity and Tajima's D, consistent with the OP phenotype being a derived trait in aphids. Interestingly, the low genetic differentiation between CP and OP populations at the rest of the genome (FST = 2.5%) suggests gene flow between them. Males from OP lineages thus likely transmit their op allele to new genomic backgrounds. These genetic exchanges, combined with the selection of the OP and CP reproductive modes under different climates, probably contribute to the long-term persistence of the cp and op alleles.
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Affiliation(s)
- Maud Rimbault
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- University of Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, Poitiers CEDEX 9, France
| | - Lucie Mieuzet
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Elsa Call
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Pierre Nouhaud
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Hélène Defendini
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Frédérique Mahéo
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - William Marande
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Nicolas Théron
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Denis Tagu
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Gaël Le Trionnaire
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean-Christophe Simon
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Julie Jaquiéry
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
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6
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Guichard A, Legeai F, Tagu D, Lemaitre C. MTG-Link: leveraging barcode information from linked-reads to assemble specific loci. BMC Bioinformatics 2023; 24:284. [PMID: 37452278 PMCID: PMC10347852 DOI: 10.1186/s12859-023-05395-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. RESULTS We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. CONCLUSIONS MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.
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Affiliation(s)
- Anne Guichard
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France.
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France
| | - Denis Tagu
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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7
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Saleh Ziabari O, Li B, Hardy NB, Brisson JA. Aphid male wing polymorphisms are transient and have evolved repeatedly. Evolution 2023; 77:1056-1065. [PMID: 36773025 PMCID: PMC10078941 DOI: 10.1093/evolut/qpad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023]
Abstract
Polymorphic phenotypes have long been used to examine the maintenance of genetic variation within and between species. Most studies have focused on persistent polymorphisms, which are retained across species boundaries, and their positive effects on speciation rates. Far less is known about the macroevolutionary impacts of more transient polymorphisms, which are also common. Here we investigated male wing polymorphisms in aphids. We estimated the phylogenetic history of wing states across species, along with several other traits that could affect wing evolution. We found that male wing polymorphisms are transient: they are found in only ~4% of extant species, but have likely evolved repeatedly across the phylogeny. We reason that the repeated evolution of transient polymorphisms might be facilitated by the existence of the asexual female wing plasticity, which is common across aphids, and would maintain the wing development program even in species with wingless males. We also discovered that male wingedness correlates positively with host plant alternation and host plant breadth, and that winged morphs and wing polymorphisms may be associated with higher speciation rates. Our results provide new evolutionary insights into this well-studied group and suggest that even transient polymorphisms may impact species diversification rates.
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Affiliation(s)
- Omid Saleh Ziabari
- Department of Biology, University of Rochester, Rochester, United States
| | - Binshuang Li
- Department of Biology, University of Rochester, Rochester, United States
| | - Nate B Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, United States
| | - Jennifer A Brisson
- Department of Biology, University of Rochester, Rochester, United States
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8
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Yuan E, Guo H, Chen W, Du B, Mi Y, Qi Z, Yuan Y, Zhu-Salzman K, Ge F, Sun Y. A novel gene REPTOR2 activates the autophagic degradation of wing disc in pea aphid. eLife 2023; 12:e83023. [PMID: 36943031 PMCID: PMC10030113 DOI: 10.7554/elife.83023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
Wing dimorphism in insects is an evolutionarily adaptive trait to maximize insect fitness under various environments, by which the population could be balanced between dispersing and reproduction. Most studies concern the regulatory mechanisms underlying the stimulation of wing morph in aphids, but relatively little research addresses the molecular basis of wing loss. Here, we found that, while developing normally in winged-destined pea aphids, the wing disc in wingless-destined aphids degenerated 30-hr postbirth and that this degeneration was due to autophagy rather than apoptosis. Activation of autophagy in first instar nymphs reduced the proportion of winged aphids, and suppression of autophagy increased the proportion. REPTOR2, associated with TOR signaling pathway, was identified by RNA-seq as a differentially expressed gene between the two morphs with higher expression in the thorax of wingless-destined aphids. Further genetic analysis indicated that REPTOR2 could be a novel gene derived from a gene duplication event that occurred exclusively in pea aphids on autosome A1 but translocated to the sex chromosome. Knockdown of REPTOR2 reduced autophagy in the wing disc and increased the proportion of winged aphids. In agreement with REPTOR's canonical negative regulatory role of TOR on autophagy, winged-destined aphids had higher TOR expression in the wing disc. Suppression of TOR activated autophagy of the wing disc and decreased the proportion of winged aphids, and vice versa. Co-suppression of TOR and REPTOR2 showed that dsREPTOR2 could mask the positive effect of dsTOR on autophagy, suggesting that REPTOR2 acted as a key regulator downstream of TOR in the signaling pathway. These results revealed that the TOR signaling pathway suppressed autophagic degradation of the wing disc in pea aphids by negatively regulating the expression of REPTOR2.
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Affiliation(s)
- Erliang Yuan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of ScienceBeijingChina
| | - Huijuan Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of ScienceBeijingChina
| | - Weiyao Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of ScienceBeijingChina
| | - Bingru Du
- School of Life Science, Hebei UniversityBaodingChina
| | - Yingjie Mi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Zhaorui Qi
- School of Life Science, Hebei UniversityBaodingChina
| | - Yiyang Yuan
- Institute of Plant Protection, Shandong Academy of Agriculture SciencesJinanChina
| | - Keyan Zhu-Salzman
- Department of Entomology, Texas A&M UniversityCollege StationUnited States
| | - Feng Ge
- Institute of Plant Protection, Shandong Academy of Agriculture SciencesJinanChina
| | - Yucheng Sun
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of ScienceBeijingChina
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9
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San-Jose LM, Bestion E, Pellerin F, Richard M, Di Gesu L, Salmona J, Winandy L, Legrand D, Bonneaud C, Guillaume O, Calvez O, Elmer KR, Yurchenko AA, Recknagel H, Clobert J, Cote J. Investigating the genetic basis of vertebrate dispersal combining RNA-seq, RAD-seq and quantitative genetics. Mol Ecol 2023. [PMID: 36872057 DOI: 10.1111/mec.16916] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 01/17/2023] [Accepted: 02/06/2023] [Indexed: 03/07/2023]
Abstract
Although animal dispersal is known to play key roles in ecological and evolutionary processes such as colonization, population extinction and local adaptation, little is known about its genetic basis, particularly in vertebrates. Untapping the genetic basis of dispersal should deepen our understanding of how dispersal behaviour evolves, the molecular mechanisms that regulate it and link it to other phenotypic aspects in order to form the so-called dispersal syndromes. Here, we comprehensively combined quantitative genetics, genome-wide sequencing and transcriptome sequencing to investigate the genetic basis of natal dispersal in a known ecological and evolutionary model of vertebrate dispersal: the common lizard, Zootoca vivipara. Our study supports the heritability of dispersal in semi-natural populations, with less variation attributable to maternal and natal environment effects. In addition, we found an association between natal dispersal and both variation in the carbonic anhydrase (CA10) gene, and in the expression of several genes (TGFB2, SLC6A4, NOS1) involved in central nervous system functioning. These findings suggest that neurotransmitters (serotonin and nitric oxide) are involved in the regulation of dispersal and shaping dispersal syndromes. Several genes from the circadian clock (CRY2, KCTD21) were also differentially expressed between disperser and resident lizards, supporting that the circadian rhythm, known to be involved in long-distance migration in other taxa, might affect dispersal as well. Since neuronal and circadian pathways are relatively well conserved across vertebrates, our results are likely to be generalisable, and we therefore encourage future studies to further investigate the role of these pathways in shaping dispersal in vertebrates.
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Affiliation(s)
- Luis M San-Jose
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Elvire Bestion
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Félix Pellerin
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Murielle Richard
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Lucie Di Gesu
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Jordi Salmona
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Laurane Winandy
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Delphine Legrand
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Camille Bonneaud
- Centre for Ecology and Conservation, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Olivier Guillaume
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Olivier Calvez
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Andrey A Yurchenko
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Hans Recknagel
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jean Clobert
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Julien Cote
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
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10
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Zhang JL, Chen SJ, Liu XY, Moczek AP, Xu HJ. The transcription factor Zfh1 acts as a wing-morph switch in planthoppers. Nat Commun 2022; 13:5670. [PMID: 36167844 PMCID: PMC9515195 DOI: 10.1038/s41467-022-33422-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
Insect wing polyphenism is characterized by its ability to produce two or more distinct wing morphs from a single genotype in response to changing environments. However, the molecular basis of this phenomenon remains poorly understood. Here, we identified a zinc finger homeodomain transcription factor Zfh1 that acts as an upstream regulator for the development of long-winged (LW) or shorted-winged (SW) morphs in planthoppers. Knockdown of Zfh1 directs SW-destined nymphs to develop into LW morphs by down-regulating the transcriptional level of FoxO, a prominent downstream effector of the insulin/IGF signaling (IIS) pathway. The balance between transcriptional regulation via the Zfh1-FoxO cascade and post-translational regulation via the IIS-FoxO cascade provides a flexible regulatory mechanism for the development of alternative wing morphs. These findings help us understand how phenotypic diversity is generated by altering the activity of conserved proteins, and provide an extended framework for the evolution of wing morphological diversity in insects.
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Affiliation(s)
- Jin-Li Zhang
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu-Hang-Tang Ave, Hangzhou, China
| | - Sun-Jie Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu-Hang-Tang Ave, Hangzhou, China
| | - Xin-Yang Liu
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu-Hang-Tang Ave, Hangzhou, China
| | - Armin P Moczek
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN, 47405, USA
| | - Hai-Jun Xu
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu-Hang-Tang Ave, Hangzhou, China.
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11
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Bai Y, Pei XJ, Ban N, Chen N, Liu SN, Li S, Liu TX. Nutrition-dependent juvenile hormone sensitivity promotes flight-muscle degeneration during the aphid dispersal-reproduction transition. Development 2022; 149:275958. [DOI: 10.1242/dev.200891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
In insects, the loss of flight typically involves a dispersal-reproduction transition, but the underlying molecular mechanisms remain poorly understood. In the parthenogenetic pea aphid Acyrthosiphon pisum, winged females undergo flight-muscle degeneration after flight and feeding on new host plants. Similarly, topical application of a juvenile hormone (JH) mimic to starved aphids also induces flight-muscle degeneration. We found that feeding preferentially upregulated the expression of the JH receptor gene Met and a JH-inducible gene, Kr-h1, in the flight muscles, and, thus, enhanced tissue-specific JH sensitivity and signaling. RNAi-mediated knockdown of Kr-h1 prevented flight-muscle degeneration. Likewise, blocking nutritional signals by pharmacological inhibition of the target of rapamycin complex 1 (TORC1) impaired JH sensitivity of the flight muscles in feeding aphids and subsequently delayed muscle degeneration. RNA-sequencing analysis revealed that enhanced JH signaling inhibited the transcription of genes involved in the tricarboxylic acid cycle, likely resulting in reduction of the energy supply, mitochondrial dysfunction and muscle-fiber breakdown. This study shows that nutrient-dependent hormone sensitivity regulates developmental plasticity in a tissue-specific manner, emphasizing a relatively underappreciated mechanism of hormone sensitivity in modulating hormone signaling.
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Affiliation(s)
- Yu Bai
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University 1 , Guangzhou 510631 , China
- State Key Laboratory of Crop Stress Biology for Arid Areas and Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, Northwest A&F University 2 , Yangling 712100 , China
| | - Xiao-Jin Pei
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University 1 , Guangzhou 510631 , China
| | - Ning Ban
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University 3 , Qingdao 266109 , China
| | - Nan Chen
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University 1 , Guangzhou 510631 , China
| | - Su-Ning Liu
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University 1 , Guangzhou 510631 , China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University 1 , Guangzhou 510631 , China
| | - Tong-Xian Liu
- Institute of Entomology, Guizhou University 4 , Guiyang 550025 , China
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12
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Saleh Ziabari O, Zhong Q, Purandare SR, Reiter J, Zera AJ, Brisson JA. Pea aphid winged and wingless males exhibit reproductive, gene expression, and lipid metabolism differences. CURRENT RESEARCH IN INSECT SCIENCE 2022; 2:100039. [PMID: 36003264 PMCID: PMC9387497 DOI: 10.1016/j.cris.2022.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022]
Abstract
Alternative, intraspecific phenotypes offer an opportunity to identify the mechanistic basis of differences associated with distinctive life history strategies. Wing dimorphic insects, in which both flight-capable and flight-incapable individuals occur in the same population, are particularly well-studied in terms of why and how the morphs trade off flight for reproduction. Yet despite a wealth of studies examining the differences between female morphs, little is known about male differences, which could arise from different causes than those acting on females. Here we examined reproductive, gene expression, and biochemical differences between pea aphid (Acyrthosiphon pisum) winged and wingless males. We find that winged males are competitively superior in one-on-one mating circumstances, but wingless males reach reproductive maturity faster and have larger testes. We suggest that males tradeoff increased local matings with concurrent possible inbreeding for outbreeding and increased ability to find mates. At the mechanistic level, differential gene expression between the morphs revealed a possible role for activin and insulin signaling in morph differences; it also highlighted genes not previously identified as being functionally important in wing polymorphism, such as genes likely involved in sperm production. Further, we find that winged males have higher lipid levels, consistent with their use as flight fuel, but we find no consistent patterns of different levels of activity among five enzymes associated with lipid biosynthesis. Overall, our analyses provide evidence that winged versus wingless males exhibit differences at the reproductive, gene expression, and biochemical levels, expanding the field's understanding of the functional aspects of morph differences.
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Affiliation(s)
- Omid Saleh Ziabari
- Department of Biology, University of Rochester, Rochester, NY 14610, USA
| | - Qingyi Zhong
- Department of Biology, University of Rochester, Rochester, NY 14610, USA
| | - Swapna R. Purandare
- Current address: Department of Computational Biology, Indraprastha Institute of Information Technology Delhi; New Delhi, India
| | - Joel Reiter
- Department of Biology, University of Rochester, Rochester, NY 14610, USA
| | - Anthony J. Zera
- School of Biological Sciences, University of Nebraska-Lincoln
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13
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Wang L, Sun F, Wan ZY, Yang Z, Tay YX, Lee M, Ye B, Wen Y, Meng Z, Fan B, Alfiko Y, Shen Y, Piferrer F, Meyer A, Schartl M, Yue GH. Transposon-induced epigenetic silencing in the X chromosome as a novel form of dmrt1 expression regulation during sex determination in the fighting fish. BMC Biol 2022; 20:5. [PMID: 34996452 PMCID: PMC8742447 DOI: 10.1186/s12915-021-01205-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 12/03/2021] [Indexed: 01/14/2023] Open
Abstract
Background Fishes are the one of the most diverse groups of animals with respect to their modes of sex determination, providing unique models for uncovering the evolutionary and molecular mechanisms underlying sex determination and reversal. Here, we have investigated how sex is determined in a species of both commercial and ecological importance, the Siamese fighting fish Betta splendens. Results We conducted association mapping on four commercial and two wild populations of B. splendens. In three of the four commercial populations, the master sex determining (MSD) locus was found to be located in a region of ~ 80 kb on LG2 which harbours five protein coding genes, including dmrt1, a gene involved in male sex determination in different animal taxa. In these fish, dmrt1 shows a male-biased gonadal expression from undifferentiated stages to adult organs and the knockout of this gene resulted in ovarian development in XY genotypes. Genome sequencing of XX and YY genotypes identified a transposon, drbx1, inserted into the fourth intron of the X-linked dmrt1 allele. Methylation assays revealed that epigenetic changes induced by drbx1 spread out to the promoter region of dmrt1. In addition, drbx1 being inserted between two closely linked cis-regulatory elements reduced their enhancer activities. Thus, epigenetic changes, induced by drbx1, contribute to the reduced expression of the X-linked dmrt1 allele, leading to female development. This represents a previously undescribed solution in animals relying on dmrt1 function for sex determination. Differentiation between the X and Y chromosomes is limited to a small region of ~ 200 kb surrounding the MSD gene. Recombination suppression spread slightly out of the SD locus. However, this mechanism was not found in the fourth commercial stock we studied, or in the two wild populations analysed, suggesting that it originated recently during domestication. Conclusions Taken together, our data provide novel insights into the role of epigenetic regulation of dmrt1 in sex determination and turnover of SD systems and suggest that fighting fish are a suitable model to study the initial stages of sex chromosome evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01205-y.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Fei Sun
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Zituo Yang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Yi Xuan Tay
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - May Lee
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Baoqing Ye
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Yanfei Wen
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Zining Meng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Bin Fan
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, 529500, China
| | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Jakarta, Indonesia
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, China
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), 08003, Barcelona, Spain.
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, 97074, Wuerzburg, Germany. .,The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA.
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore. .,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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14
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Carpenter M, Peng L, Smith AH, Joffe J, O’Connor M, Oliver KM, Russell JA. Frequent Drivers, Occasional Passengers: Signals of Symbiont-Driven Seasonal Adaptation and Hitchhiking in the Pea Aphid, Acyrthosiphon pisum. INSECTS 2021; 12:805. [PMID: 34564245 PMCID: PMC8466206 DOI: 10.3390/insects12090805] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 12/25/2022]
Abstract
Insects harbor a variety of maternally inherited bacterial symbionts. As such, variation in symbiont presence/absence, in the combinations of harbored symbionts, and in the genotypes of harbored symbiont species provide heritable genetic variation of potential use in the insects' adaptive repertoires. Understanding the natural importance of symbionts is challenging but studying their dynamics over time can help to elucidate the potential for such symbiont-driven insect adaptation. Toward this end, we studied the seasonal dynamics of six maternally transferred bacterial symbiont species in the multivoltine pea aphid (Acyrthosiphon pisum). Our sampling focused on six alfalfa fields in southeastern Pennsylvania, and spanned 14 timepoints within the 2012 growing season, in addition to two overwintering periods. To test and generate hypotheses on the natural relevance of these non-essential symbionts, we examined whether symbiont dynamics correlated with any of ten measured environmental variables from the 2012 growing season, including some of known importance in the lab. We found that five symbionts changed prevalence across one or both overwintering periods, and that the same five species underwent such frequency shifts across the 2012 growing season. Intriguingly, the frequencies of these dynamic symbionts showed robust correlations with a subset of our measured environmental variables. Several of these trends supported the natural relevance of lab-discovered symbiont roles, including anti-pathogen defense. For a seventh symbiont-Hamiltonella defensa-studied previously across the same study periods, we tested whether a reported correlation between prevalence and temperature stemmed not from thermally varying host-level fitness effects, but from selection on co-infecting symbionts or on aphid-encoded alleles associated with this bacterium. In general, such "hitchhiking" effects were not evident during times with strongly correlated Hamiltonella and temperature shifts. However, we did identify at least one time period in which Hamiltonella spread was likely driven by selection on a co-infecting symbiont-Rickettsiella viridis. Recognizing the broader potential for such hitchhiking, we explored selection on co-infecting symbionts as a possible driver behind the dynamics of the remaining six species. Out of twelve examined instances of symbiont dynamics unfolding across 2-week periods or overwintering spans, we found eight in which the focal symbiont underwent parallel frequency shifts under single infection and one or more co-infection contexts. This supported the idea that phenotypic variation created by the presence/absence of individual symbionts is a direct target for selection, and that symbiont effects can be robust under co-habitation with other symbionts. Contrastingly, in two cases, we found that selection may target phenotypes emerging from symbiont co-infections, with specific species combinations driving overall trends for the focal dynamic symbionts, without correlated change under single infection. Finally, in three cases-including the one described above for Hamiltonella-our data suggested that incidental co-infection with a (dis)favored symbiont could lead to large frequency shifts for "passenger" symbionts, conferring no apparent cost or benefit. Such hitchhiking has rarely been studied in heritable symbiont systems. We propose that it is more common than appreciated, given the widespread nature of maternally inherited bacteria, and the frequency of multi-species symbiotic communities across insects.
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Affiliation(s)
- Melissa Carpenter
- Department of Biodiversity, Earth, and Environmental Science, Drexel University, 3250 Chestnut St., Philadelphia, PA 19104, USA; (M.C.); (A.H.S.); (M.O.)
| | - Linyao Peng
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA 19104, USA; (L.P.); (J.J.)
| | - Andrew H. Smith
- Department of Biodiversity, Earth, and Environmental Science, Drexel University, 3250 Chestnut St., Philadelphia, PA 19104, USA; (M.C.); (A.H.S.); (M.O.)
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA 19104, USA; (L.P.); (J.J.)
| | - Jonah Joffe
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA 19104, USA; (L.P.); (J.J.)
| | - Michael O’Connor
- Department of Biodiversity, Earth, and Environmental Science, Drexel University, 3250 Chestnut St., Philadelphia, PA 19104, USA; (M.C.); (A.H.S.); (M.O.)
| | - Kerry M. Oliver
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA 30602, USA;
| | - Jacob A. Russell
- Department of Biodiversity, Earth, and Environmental Science, Drexel University, 3250 Chestnut St., Philadelphia, PA 19104, USA; (M.C.); (A.H.S.); (M.O.)
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA 19104, USA; (L.P.); (J.J.)
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15
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Montejo-Kovacevich G, Salazar PA, Smith SH, Gavilanes K, Bacquet CN, Chan YF, Jiggins CD, Meier JI, Nadeau NJ. Genomics of altitude-associated wing shape in two tropical butterflies. Mol Ecol 2021; 30:6387-6402. [PMID: 34233044 DOI: 10.1111/mec.16067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/01/2021] [Indexed: 11/30/2022]
Abstract
Understanding how organisms adapt to their local environment is central to evolution. With new whole-genome sequencing technologies and the explosion of data, deciphering the genomic basis of complex traits that are ecologically relevant is becoming increasingly feasible. Here, we studied the genomic basis of wing shape in two Neotropical butterflies that inhabit large geographical ranges. Heliconius butterflies at high elevations have been shown to generally have rounder wings than those in the lowlands. We reared over 1,100 butterflies from 71 broods of H. erato and H. melpomene in common-garden conditions and showed that wing aspect ratio, that is, elongatedness, is highly heritable in both species and that elevation-associated wing aspect ratio differences are maintained. Genome-wide associations with a published data set of 666 whole genomes from across a hybrid zone, uncovered a highly polygenic basis to wing aspect ratio variation in the wild. We identified several genes that have roles in wing morphogenesis or wing aspect ratio variation in Drosophila flies, making them promising candidates for future studies. There was little evidence for molecular parallelism in the two species, with only one shared candidate gene, nor for a role of the four known colour pattern loci, except for optix in H. erato. Thus, we present the first insights into the heritability and genomic basis of within-species wing aspect ratio in two Heliconius species, adding to a growing body of evidence that polygenic adaptation may underlie many ecologically relevant traits.
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Affiliation(s)
| | | | - Sophie H Smith
- Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | | | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Joana I Meier
- Department of Zoology, University of Cambridge, Cambridge, UK.,St John's College, University of Cambridge, Cambridge, UK
| | - Nicola J Nadeau
- Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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16
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Male-Biased microRNA Discovery in the Pea Aphid. INSECTS 2021; 12:insects12060533. [PMID: 34201015 PMCID: PMC8228725 DOI: 10.3390/insects12060533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/18/2022]
Abstract
Epigenetic mechanisms modulate gene expression levels during development, shaping how a single genome produces a diversity of phenotypes. Here, we begin to explore the epigenetic regulation of sexual dimorphism in pea aphids (Acyrthosiphon pisum) by focusing on microRNAs. Previous analyses of microRNAs in aphids have focused solely on females, so we performed deep sequencing of a sample containing early-stage males. We used this sample, plus samples from Genbank, to find 207 novel pea aphid microRNA coding loci. We localized microRNA loci to a chromosome-level assembly of the pea aphid genome and found that those on the X chromosome have lower overall expression compared to those on autosomes. We then identified a set of 19 putative male-biased microRNAs and found them enriched on the X chromosome. Finally, we performed protein-coding RNA-Seq of first instar female and male pea aphids to identify genes with lower expression in males. 10 of these genes were predicted targets of the 19 male-biased microRNAs. Our study provides the most complete set of microRNAs in the pea aphid to date and serves as foundational work for future studies on the epigenetic control of sexual dimorphism.
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17
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Gutiérrez-Valencia J, Hughes PW, Berdan EL, Slotte T. The Genomic Architecture and Evolutionary Fates of Supergenes. Genome Biol Evol 2021; 13:6178796. [PMID: 33739390 PMCID: PMC8160319 DOI: 10.1093/gbe/evab057] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2021] [Indexed: 12/25/2022] Open
Abstract
Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic architecture as well as the mode of origin of supergenes across diverse organismal systems. Although the role of genomic architecture for the origin of supergenes has been much discussed, differences in the genomic architecture also subsequently affect the evolutionary trajectory of supergenes and the rate of degeneration of supergene haplotypes. In this review, we synthesize recent genomic work and historical models of supergene evolution, highlighting how the genomic architecture of supergenes affects their evolutionary fate. We discuss how recent findings on classic supergenes involved in governing ant colony social form, mimicry in butterflies, and heterostyly in flowering plants relate to theoretical expectations. Furthermore, we use forward simulations to demonstrate that differences in genomic architecture affect the degeneration of supergenes. Finally, we discuss implications of the evolution of supergene haplotypes for the long-term fate of balanced polymorphisms governed by supergenes.
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Affiliation(s)
- Juanita Gutiérrez-Valencia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
| | - P William Hughes
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
| | - Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
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18
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Gibert JM. [Phenotypic plasticity in insects]. Biol Aujourdhui 2020; 214:33-44. [PMID: 32773028 DOI: 10.1051/jbio/2020005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Indexed: 11/14/2022]
Abstract
Insects represent 85% of the animals. They have adapted to many environments and play a major role in ecosystems. Many insect species exhibit phenotypic plasticity. We here report on the mechanisms involved in phenotypic plasticity of different insects (aphids, migratory locust, map butterfly, honeybee) and also on the nutritional size plasticity in Drosophila and the plasticity of the wing eye-spots of the butterfly Bicyclus anynana. We also describe in more detail our work concerning the thermal plasticity of pigmentation in Drosophila. We have shown that the expression of the tan, yellow and Ddc genes, encoding enzymes of the melanin synthesis pathway, is modulated by temperature and that it is a consequence, at least in part, of the temperature-sensitive expression of the bab locus genes that repress them.
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Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), UMR7622, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement (IBPS-LBD), 75005 Paris, France
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