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Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
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Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
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2
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Tendolkar A, Mazo-Vargas A, Livraghi L, Hanly JJ, Van Horne KC, Gilbert LE, Martin A. Cis-regulatory modes of Ultrabithorax inactivation in butterfly forewings. eLife 2024; 12:RP90846. [PMID: 38261357 PMCID: PMC10945631 DOI: 10.7554/elife.90846] [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] [Indexed: 01/24/2024] Open
Abstract
Hox gene clusters encode transcription factors that drive regional specialization during animal development: for example the Hox factor Ubx is expressed in the insect metathoracic (T3) wing appendages and differentiates them from T2 mesothoracic identities. Hox transcriptional regulation requires silencing activities that prevent spurious activation and regulatory crosstalks in the wrong tissues, but this has seldom been studied in insects other than Drosophila, which shows a derived Hox dislocation into two genomic clusters that disjoined Antennapedia (Antp) and Ultrabithorax (Ubx). Here, we investigated how Ubx is restricted to the hindwing in butterflies, amidst a contiguous Hox cluster. By analysing Hi-C and ATAC-seq data in the butterfly Junonia coenia, we show that a Topologically Associated Domain (TAD) maintains a hindwing-enriched profile of chromatin opening around Ubx. This TAD is bordered by a Boundary Element (BE) that separates it from a region of joined wing activity around the Antp locus. CRISPR mutational perturbation of this BE releases ectopic Ubx expression in forewings, inducing homeotic clones with hindwing identities. Further mutational interrogation of two non-coding RNA encoding regions and one putative cis-regulatory module within the Ubx TAD cause rare homeotic transformations in both directions, indicating the presence of both activating and repressing chromatin features. We also describe a series of spontaneous forewing homeotic phenotypes obtained in Heliconius butterflies, and discuss their possible mutational basis. By leveraging the extensive wing specialization found in butterflies, our initial exploration of Ubx regulation demonstrates the existence of silencing and insulating sequences that prevent its spurious expression in forewings.
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Affiliation(s)
- Amruta Tendolkar
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
| | - Anyi Mazo-Vargas
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
| | - Luca Livraghi
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
| | - Joseph J Hanly
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
- Smithsonian Tropical Research InstitutePanama CityPanama
| | - Kelsey C Van Horne
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
| | - Lawrence E Gilbert
- Department of Integrative Biology, University of Texas – AustinAustinUnited States
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
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3
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Murugesan SN, Monteiro A. Butterfly eyespots exhibit unique patterns of open chromatin. F1000Res 2023; 12:1428. [PMID: 38778811 PMCID: PMC11109672 DOI: 10.12688/f1000research.133789.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/02/2023] [Indexed: 05/25/2024] Open
Abstract
Background: How the precise spatial regulation of genes is correlated with spatial variation in chromatin accessibilities is not yet clear. Previous studies that analysed chromatin from homogenates of whole-body parts of insects found little variation in chromatin accessibility across those parts, but single-cell studies of Drosophila brains showed extensive spatial variation in chromatin accessibility across that organ. In this work we studied the chromatin accessibility of butterfly wing tissue fated to differentiate distinct colors and patterns in pupal wings of Bicyclus anynana. Methods: We dissected small eyespot and adjacent control tissues from 3h pupae and performed ATAC-Seq to identify the chromatin accessibility differences between different sections of the wings. Results: We observed that three dissected wing regions showed unique chromatin accessibilities. Open chromatin regions specific to eyespot color patterns were highly enriched for binding motifs recognized by Suppressor of Hairless (Su(H)), Krüppel (Kr), Buttonhead (Btd) and Nubbin (Nub) transcription factors. Genes in the vicinity of the eyespot-specific open chromatin regions included those involved in wound healing and SMAD signal transduction pathways, previously proposed to be involved in eyespot development. Conclusions: We conclude that eyespot and non-eyespot tissue samples taken from the same wing have distinct patterns of chromatin accessibility, possibly driven by the eyespot-restricted expression of potential pioneer factors, such as Kr.
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Affiliation(s)
| | - Antónia Monteiro
- Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
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4
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Mazo-Vargas A, Langmüller AM, Wilder A, van der Burg KRL, Lewis JJ, Messer PW, Zhang L, Martin A, Reed RD. Deep cis-regulatory homology of the butterfly wing pattern ground plan. Science 2022; 378:304-308. [PMID: 36264807 DOI: 10.1126/science.abi9407] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Butterfly wing patterns derive from a deeply conserved developmental ground plan yet are diverse and evolve rapidly. It is poorly understood how gene regulatory architectures can accommodate both deep homology and adaptive change. To address this, we characterized the cis-regulatory evolution of the color pattern gene WntA in nymphalid butterflies. Comparative assay for transposase-accessible chromatin using sequencing (ATAC-seq) and in vivo deletions spanning 46 cis-regulatory elements across five species revealed deep homology of ground plan-determining sequences, except in monarch butterflies. Furthermore, noncoding deletions displayed both positive and negative regulatory effects that were often broad in nature. Our results provide little support for models predicting rapid enhancer turnover and suggest that deeply ancestral, multifunctional noncoding elements can underlie rapidly evolving trait systems.
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Affiliation(s)
- Anyi Mazo-Vargas
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Anna M Langmüller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Alexis Wilder
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | | | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Linlin Zhang
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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5
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Wang S, Teng D, Li X, Yang P, Da W, Zhang Y, Zhang Y, Liu G, Zhang X, Wan W, Dong Z, Wang D, Huang S, Jiang Z, Wang Q, Lohman DJ, Wu Y, Zhang L, Jia F, Westerman E, Zhang L, Wang W, Zhang W. The evolution and diversification of oakleaf butterflies. Cell 2022; 185:3138-3152.e20. [PMID: 35926506 DOI: 10.1016/j.cell.2022.06.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 01/20/2022] [Accepted: 06/22/2022] [Indexed: 10/16/2022]
Abstract
Oakleaf butterflies in the genus Kallima have a polymorphic wing phenotype, enabling these insects to masquerade as dead leaves. This iconic example of protective resemblance provides an interesting evolutionary paradigm that can be employed to study biodiversity. We integrated multi-omic data analyses and functional validation to infer the evolutionary history of Kallima species and investigate the genetic basis of their variable leaf wing patterns. We find that Kallima butterflies diversified in the eastern Himalayas and dispersed to East and Southeast Asia. Moreover, we find that leaf wing polymorphism is controlled by the wing patterning gene cortex, which has been maintained in Kallima by long-term balancing selection. Our results provide macroevolutionary and microevolutionary insights into a model species originating from a mountain ecosystem.
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Affiliation(s)
- Shuting Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Dequn Teng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Peiwen Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wa Da
- Tibet Plateau Institute of Biology, Lhasa, Tibet 850001, China
| | - Yiming Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yubo Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Guichun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | | | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Zhiwei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Donghui Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; National Teaching Center for Experimental Biology, Peking University, Beijing 100871, China
| | - Shun Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhisheng Jiang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qingyi Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - David J Lohman
- Biology Department, City College of New York, City University of New York, New York, NY 10031, USA; Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA; Entomology Section, National Museum of Natural History, Manila 1000, Philippines
| | - Yongjie Wu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Fenghai Jia
- Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, China
| | - Erica Westerman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing 100871, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; Center for Excellence in Animal Evolution and Genetics, Kunming 650223, China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Institute of Ecology, Peking University, Beijing 100871, China; Institute for Tibetan Plateau Research, Peking University, Beijing 100871, China.
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6
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Tian S, Monteiro A. A transcriptomic atlas underlying developmental plasticity of seasonal forms of Bicyclus anynana butterflies. Mol Biol Evol 2022; 39:msac126. [PMID: 35679434 PMCID: PMC9218548 DOI: 10.1093/molbev/msac126] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/10/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Organisms residing in regions with alternating seasons often develop different phenotypes, or forms, in each season. These forms are often adaptations to each season and result from an altered developmental response to specific environmental cues such as temperature. While multiple studies have examined form-specific gene expression profiles in a diversity of species, little is known about how environments and developmental transitions, cued by hormone pulses, alter post-transcriptional patterns. In this study, we examine how gene expression, alternative splicing, and miRNA-mediated gene silencing in Bicyclus anynana butterfly hindwing tissue, varies across two rearing temperatures at four developmental timepoints. These timepoints flank two temperature-sensitive periods that coincide with two pulses of the insect hormone 20E. Our results suggest that developmental transitions, coincident with 20E pulses, elicit a greater impact on all these transcriptomic patterns than rearing temperatures per se. More similar transcriptomic patterns are observed pre-20E pulses than those observed post-20E pulses. We also found functionally distinct sets of differentially expressed and differentially spliced genes in the seasonal forms. Furthermore, around 10% of differentially expressed genes are predicted to be direct targets of, and regulated by, differentially expressed miRNAs between the seasonal forms. Many differentially expressed genes, miRNAs, or differentially spliced genes potentially regulate eyespot size plasticity, and we validated the differential splicing pattern of one such gene, daughterless. We present a comprehensive and interactive transcriptomic atlas of the hindwing tissue of both seasonal forms of B. anynana throughout development, a model organism of seasonal plasticity.
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Affiliation(s)
- Shen Tian
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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7
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Abstract
Epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are increasingly targeted in studies of natural populations. Here, I review some of the insights gained from this research, examine some of the methods currently in use and discuss some of the challenges that researchers working on natural populations are likely to face when probing epigenetic mechanisms. While studies supporting the involvement of epigenetic mechanisms in generating phenotypic variation in natural populations are amassing, many of these studies are currently correlative in nature. Thus, while empirical data point to widespread contributions of epigenetic mechanisms in generating phenotypic variation, there are still concerns as to whether epigenetic variation is instead ultimately controlled by genetic variation. Disentangling these two sources of variation will be a key to resolving the debate about the importance of epigenetic mechanisms, and studies on natural populations that partition the relative contribution of genetic and epigenetic factors to phenotypic variation can play an important role in this debate.
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Affiliation(s)
- Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden.,Centre for Biodiversity Dynamics, Norwegian University for Science and Technology, Trondheim, Norway
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8
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MAPK-mediated transcription factor GATAd contributes to Cry1Ac resistance in diamondback moth by reducing PxmALP expression. PLoS Genet 2022; 18:e1010037. [PMID: 35113858 PMCID: PMC8846524 DOI: 10.1371/journal.pgen.1010037] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/15/2022] [Accepted: 01/12/2022] [Indexed: 12/12/2022] Open
Abstract
The benefits of biopesticides and transgenic crops based on the insecticidal Cry-toxins from Bacillus thuringiensis (Bt) are considerably threatened by insect resistance evolution, thus, deciphering the molecular mechanisms underlying insect resistance to Bt products is of great significance to their sustainable utilization. Previously, we have demonstrated that the down-regulation of PxmALP in a strain of Plutella xylostella (L.) highly resistant to the Bt Cry1Ac toxin was due to a hormone-activated MAPK signaling pathway and contributed to the resistance phenotype. However, the underlying transcriptional regulatory mechanism remains enigmatic. Here, we report that the PxGATAd transcription factor (TF) is responsible for the differential expression of PxmALP observed between the Cry1Ac susceptible and resistant strains. We identified that PxGATAd directly activates PxmALP expression via interacting with a non-canonical but specific GATA-like cis-response element (CRE) located in the PxmALP promoter region. A six-nucleotide insertion mutation in this cis-acting element of the PxmALP promoter from the resistant strain resulted in repression of transcriptional activity, affecting the regulatory performance of PxGATAd. Furthermore, silencing of PxGATAd in susceptible larvae reduced the expression of PxmALP and susceptibility to Cry1Ac toxin. Suppressing PxMAP4K4 expression in the resistant larvae transiently recovered both the expression of PxGATAd and PxmALP, indicating that the PxGATAd is a positive responsive factor involved in the activation of PxmALP promoter and negatively regulated by the MAPK signaling pathway. Overall, this study deciphers an intricate regulatory mechanism of PxmALP gene expression and highlights the concurrent involvement of both trans-regulatory factors and cis-acting elements in Cry1Ac resistance development in lepidopteran insects. Gene expression and regulation are associated with adaptive evolution in living organisms. The rapid evolution of insect resistance to Bt insecticidal Cry toxins is frequently associated with reduced expression of diverse midgut genes that code for Cry-toxin receptors. Nonetheless, our current knowledge about the regulation of gene expression of these pivotal receptor genes in insects is limited. Membrane-bound alkaline phosphatase (mALP) is a known receptor for Cry1Ac toxin in diverse insects and here, we report the transcriptional regulatory mechanism of the PxmALP gene related to Cry1Ac resistance in P. xylostella. We identified a MAPK signaling pathway that negatively regulates the PxGATAd transcriptional factor which is involved in the differential expression of PxmALP via interacting with the PxmALP promoter. Furthermore, a cis-acting element mutation repressing the regulatory activity of PxGATAd for PxmALP expression in the Cry1Ac resistant strain was identified. Our study provides an insight into the precise transcriptional regulatory mechanism that regulates PxmALP expression and is involved in the evolution of Bt Cry1Ac resistance in P. xylostella, which provides a paradigm for decoding the regulation landscape of midgut Cry-toxin receptor genes in insects.
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9
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Sigrist-Flores SC, Castañeda-Partida L, Campos-Aguilar M, Santos-Cruz LF, Miranda-Gutierrez A, Gallardo-Ortíz IA, Villalobos-Molina R, Dueñas-García IE, Heres-Pulido ME, Piedra-Ibarra E, Rosales-García VH, Jimenez-Flores R, Ponciano-Gómez A. Variation in resistance to oxidative stress in Oregon-(R)R-flare and Canton-S strains of Drosophila melanogaster. Toxicol Res (Camb) 2021; 10:817-823. [PMID: 34484673 DOI: 10.1093/toxres/tfab066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/07/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
All aerobic organisms are susceptible to damage by reactive oxygen species (ROS). ROS-induced damage has been associated with aging and diseases such as metabolic syndrome and cancer. However, not all organisms develop these diseases, nor do they age at the same rate; this is partially due to resistance to oxidative stress, a quantitative trait attributable to the interaction of factors including genetics and environmental. Drosophila melanogaster represents an ideal system to study how genetic variation can affect resistance to oxidative stress. In this work, oxidative stress (total and mitochondrial ROS), antioxidant response, and Cap 'n' collar isoform C and Spineless gene expression, one pesticide resistant (Oregon R(R)-flare) and wild-type (Canton-S) strains of D. melanogaster, were analyzed to test resistance to basal oxidative stress. ROS, catalase, and superoxide dismutase were determined by flow cytometry, and Cap 'n' collar isoform C and Spineless expression by qRT-PCR. The intensity of oxidative stress due to the pro-oxidant zearalenone in both was evaluated by flow cytometry. Data confirm expected differences in oxidative stress between strains that differ in Cyp450s levels. The Oregon (R)R-flare showed greater ROS, total and mitochondrial, compared to Canton-S. Regarding oxidative stress genes expression Cap 'n' collar isoform C and Spineless (Ss), Oregon R(R)-flare strain showed higher expression. In terms of response to zearalenone mycotoxin, Canton-S showed higher ROS concentration. Our data show variation in the resistance to oxidative stress among these strains of D. melanogaster.
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Affiliation(s)
- Santiago Cristobal Sigrist-Flores
- Laboratorio de Inmunología (UMF), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla, C.P. 54090, Estado de México, México
| | - Laura Castañeda-Partida
- Toxicología Genética, Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla C.P. 54090, Estado de México, México
| | - Myriam Campos-Aguilar
- Laboratorio de Inmunología (UMF), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla, C.P. 54090, Estado de México, México
| | - Luis Felipe Santos-Cruz
- Toxicología Genética, Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla C.P. 54090, Estado de México, México
| | - Aranza Miranda-Gutierrez
- Laboratorio de Inmunología (UMF), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla, C.P. 54090, Estado de México, México
| | - I A Gallardo-Ortíz
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla C.P. 54090, Estado de México, México
| | - R Villalobos-Molina
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla C.P. 54090, Estado de México, México
| | - Irma Elena Dueñas-García
- Toxicología Genética, Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla C.P. 54090, Estado de México, México
| | - María Eugenia Heres-Pulido
- Toxicología Genética, Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla C.P. 54090, Estado de México, México
| | - Elías Piedra-Ibarra
- Fisiología Vegetal (UBIPRO), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla C.P. 54090, Estado de México, México
| | - Víctor Hugo Rosales-García
- Laboratorios Nacionales de Servicios Experimentales, Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional. Ciudad de México, La Laguna Ticoman, Gustavo A. Madero, 07340 Mexico City, México
| | - Rafael Jimenez-Flores
- Laboratorio de Inmunología (UMF), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla, C.P. 54090, Estado de México, México
| | - Alberto Ponciano-Gómez
- Laboratorio de Inmunología (UMF), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Barrios N° 1, Los Reyes Iztacala, Tlalnepantla, C.P. 54090, Estado de México, México
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10
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Zhang L, Steward RA, Wheat CW, Reed RD. High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui. Genome Biol Evol 2021; 13:evab145. [PMID: 34282459 PMCID: PMC8290113 DOI: 10.1093/gbe/evab145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
The painted lady butterfly, Vanessa cardui, has the longest migration routes, the widest hostplant diversity, and one of the most complex wing patterns of any insect. Due to minimal culturing requirements, easily characterized wing pattern elements, and technical feasibility of CRISPR/Cas9 genome editing, V. cardui is emerging as a functional genomics model for diverse research programs. Here, we report a high-quality, annotated genome assembly of the V. cardui genome, generated using 84× coverage of PacBio long-read data, which we assembled into 205 contigs with a total length of 425.4 Mb (N50 = 10.3 Mb). The genome was very complete (single-copy complete Benchmarking Universal Single-Copy Orthologs [BUSCO] 97%), with contigs assembled into presumptive chromosomes using synteny analyses. Our annotation used embryonic, larval, and pupal transcriptomes, and 20 transcriptomes across five different wing developmental stages. Gene annotations showed a high level of accuracy and completeness, with 14,437 predicted protein-coding genes. This annotated genome assembly constitutes an important resource for diverse functional genomic studies ranging from the developmental genetic basis of butterfly color pattern, to coevolution with diverse hostplants.
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Affiliation(s)
- Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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11
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Lewis JJ, Cicconardi F, Martin SH, Reed RD, Danko CG, Montgomery SH. The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies. Genome Biol Evol 2021; 13:evab128. [PMID: 34117762 PMCID: PMC8290107 DOI: 10.1093/gbe/evab128] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
In butterflies and moths, which exhibit highly variable sex determination mechanisms, the homogametic Z chromosome is deeply conserved and is featured in many genome assemblies. The evolution and origin of the female W sex chromosome, however, remains mostly unknown. Previous studies have proposed that a ZZ/Z0 sex determination system is ancestral to Lepidoptera, and that W chromosomes may originate from sex-linked B chromosomes. Here, we sequence and assemble the female Dryas iulia genome into 32 highly contiguous ordered and oriented chromosomes, including the Z and W sex chromosomes. We then use sex-specific Hi-C, ATAC-seq, PRO-seq, and whole-genome DNA sequence data sets to test if features of the D. iulia W chromosome are consistent with a hypothesized B chromosome origin. We show that the putative W chromosome displays female-associated DNA sequence, gene expression, and chromatin accessibility to confirm the sex-linked function of the W sequence. In contrast with expectations from studies of homologous sex chromosomes, highly repetitive DNA content on the W chromosome, the sole presence of domesticated repetitive elements in functional DNA, and lack of sequence homology with the Z chromosome or autosomes is most consistent with a B chromosome origin for the W, although it remains challenging to rule out extensive sequence divergence. Synteny analysis of the D. iulia W chromosome with other female lepidopteran genome assemblies shows no homology between W chromosomes and suggests multiple, independent origins of the W chromosome from a B chromosome likely occurred in butterflies.
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Affiliation(s)
- James J Lewis
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Francesco Cicconardi
- School of Biological Sciences, University of Bristol, United Kingdom
- Department of Zoology, University of Cambridge, United Kingdom
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
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12
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Tendolkar A, Pomerantz AF, Heryanto C, Shirk PD, Patel NH, Martin A. Ultrabithorax Is a Micromanager of Hindwing Identity in Butterflies and Moths. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.643661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The forewings and hindwings of butterflies and moths (Lepidoptera) are differentiated from each other, with segment-specific morphologies and color patterns that mediate a wide range of functions in flight, signaling, and protection. The Hox geneUltrabithorax(Ubx) is a master selector gene that differentiates metathoracic from mesothoracic identities across winged insects, and previous work has shown this role extends to at least some of the color patterns from the butterfly hindwing. Here we used CRISPR targeted mutagenesis to generateUbxloss-of-function somatic mutations in two nymphalid butterflies (Junonia coenia,Vanessa cardui) and a pyralid moth (Plodia interpunctella). The resulting mosaic clones yielded hindwing-to-forewing transformations, showingUbxis necessary for specifying many aspects of hindwing-specific identities, including scale morphologies, color patterns, and wing venation and structure. These homeotic phenotypes showed cell-autonomous, sharp transitions between mutant and non-mutant scales, except for clones that encroached into the border ocelli (eyespots) and resulted in composite and non-autonomous effects on eyespot ring determination. In the pyralid moth, homeotic clones converted the folding and depigmented hindwing into rigid and pigmented composites, affected the wing-coupling frenulum, and induced ectopic scent-scales in male androconia. These data confirmUbxis a master selector of lepidopteran hindwing identity and suggest it acts on many gene regulatory networks involved in wing development and patterning.
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13
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van der Burg KR, Reed RD. Seasonal plasticity: how do butterfly wing pattern traits evolve environmental responsiveness? Curr Opin Genet Dev 2021; 69:82-87. [PMID: 33740694 DOI: 10.1016/j.gde.2021.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/28/2023]
Abstract
Phenotypic plasticity in response to environmental cues is common in butterflies, and is a major driver of butterfly wing pattern diversity. The endocrine signal ecdysone has been revealed as a major modulator of plasticity in butterflies. External cues such as day length or temperature are translated internally into variation in ecdysone titers, which in turn lead to alternate phenotypes such as seasonal wing patterns. Here we review the evidence showing that ecdysone-mediated plasticity of different wing pattern features such as wing color and eyespot size can evolve independently. Recent studies show that ecdysone regulates gene expression in Drosophila melanogaster via a chromatin remodeling mechanism. We thus propose that environmentally responsive ecdysone titers in butterflies may also function via chromatin regulation to promote different seasonal phenotypes. We present a model of ecdysone response evolution that integrates both gene regulatory architecture and organismal development, and propose a set of testable mechanistic hypotheses for how plastic response profiles of specific genes can evolve.
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Affiliation(s)
- Karin Rl van der Burg
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
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14
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Niederhuber MJ, McKay DJ. Mechanisms underlying the control of dynamic regulatory element activity and chromatin accessibility during metamorphosis. CURRENT OPINION IN INSECT SCIENCE 2021; 43:21-28. [PMID: 32979530 PMCID: PMC7985040 DOI: 10.1016/j.cois.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/25/2020] [Indexed: 05/10/2023]
Abstract
Cis-regulatory modules of metazoan genomes determine the when and where of gene expression during development. Here we discuss insights into the genetic and molecular mechanisms behind cis-regulatory module usage that have come from recent application of genomics assays to insect metamorphosis. Assays including FAIRE-seq, ATAC-seq, and CUT&RUN indicate that sequential changes in chromatin accessibility play a key role in mediating stage-specific cis-regulatory module activity and gene expression. We review the current understanding of what controls precisely coordinated changes in chromatin accessibility during metamorphosis and describe evidence that points to systemic hormone signaling as a primary signal to trigger genome-wide shifts in accessibility patterns and cis-regulatory module usage.
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Affiliation(s)
- Matthew J Niederhuber
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.
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15
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Beldade P, Monteiro A. Eco-evo-devo advances with butterfly eyespots. Curr Opin Genet Dev 2021; 69:6-13. [PMID: 33434722 DOI: 10.1016/j.gde.2020.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 01/09/2023]
Abstract
Eyespots on the wings of different nymphalid butterflies have become valued models in eco-evo-devo. They are ecologically significant, evolutionarily diverse, and developmentally tractable. Their study has provided valuable insight about the genetic and developmental basis of inter-specific diversity and intra-specific variation, as well as into other key themes in evo-evo-devo: evolutionary novelty, developmental constraints, and phenotypic plasticity. Here we provide an overview of eco-evo-devo studies of butterfly eyespots, highlighting previous reviews, and focusing on both the most recent advances and the open questions expected to be solved in the future.
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Affiliation(s)
- Patrícia Beldade
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal; CE3C: Centre for Ecology, Evolution, and Environmental Changes, Faculty of Sciences, University of Lisbon, Campo Grande C2, 1749-016 Lisboa, Portugal.
| | - Antónia Monteiro
- Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Science Division, Yale-NUS College, Singapore 138614, Singapore.
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16
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van der Burg KRL, Lewis JJ, Brack BJ, Fandino RA, Mazo-Vargas A, Reed RD. Genomic architecture of a genetically assimilated seasonal color pattern. Science 2020; 370:721-725. [DOI: 10.1126/science.aaz3017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 06/16/2020] [Accepted: 10/01/2020] [Indexed: 12/31/2022]
Affiliation(s)
| | - James J. Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Benjamin J. Brack
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Richard A. Fandino
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Anyi Mazo-Vargas
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Robert D. Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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17
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Lewis JJ, Van Belleghem SM. Mechanisms of Change: A Population-Based Perspective on the Roles of Modularity and Pleiotropy in Diversification. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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18
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Tomoyasu Y, Halfon MS. How to study enhancers in non-traditional insect models. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb212241. [PMID: 32034049 DOI: 10.1242/jeb.212241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcriptional enhancers are central to the function and evolution of genes and gene regulation. At the organismal level, enhancers play a crucial role in coordinating tissue- and context-dependent gene expression. At the population level, changes in enhancers are thought to be a major driving force that facilitates evolution of diverse traits. An amazing array of diverse traits seen in insect morphology, physiology and behavior has been the subject of research for centuries. Although enhancer studies in insects outside of Drosophila have been limited, recent advances in functional genomic approaches have begun to make such studies possible in an increasing selection of insect species. Here, instead of comprehensively reviewing currently available technologies for enhancer studies in established model organisms such as Drosophila, we focus on a subset of computational and experimental approaches that are likely applicable to non-Drosophila insects, and discuss the pros and cons of each approach. We discuss the importance of validating enhancer function and evaluate several possible validation methods, such as reporter assays and genome editing. Key points and potential pitfalls when establishing a reporter assay system in non-traditional insect models are also discussed. We close with a discussion of how to advance enhancer studies in insects, both by improving computational approaches and by expanding the genetic toolbox in various insects. Through these discussions, this Review provides a conceptual framework for studying the function and evolution of enhancers in non-traditional insect models.
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Affiliation(s)
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
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19
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Hines HM, Rahman SR. Evolutionary genetics in insect phenotypic radiations: the value of a comparative genomic approach. CURRENT OPINION IN INSECT SCIENCE 2019; 36:90-95. [PMID: 31541856 DOI: 10.1016/j.cois.2019.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Expanding genome sequencing and transgenic technologies are enabling the discovery of genes driving phenotypic diversity across insect taxa. Limitations in downstream functional genetic approaches, however, have been an obstacle for developing non-model systems for evolutionary genetics. Phenotypically diverse radiations, such as those exhibiting convergence and divergence as a result of mimicry, are ideal for evolutionary genetics as they can lead to insights using comparative genomic approaches alone. The varied and repeated instances of phenotypes in highly polymorphic systems allow assessment of whether similar loci are repeatedly targeted by selection and can inform how alleles sort across lineages. Comparative genomics of these taxa can be used to decipher components of gene regulatory networks, dissect regulatory regions, and validate genes.
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Affiliation(s)
- Heather M Hines
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
| | - Sarthok Rasique Rahman
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
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20
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Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry. Proc Natl Acad Sci U S A 2019; 116:24174-24183. [PMID: 31712408 DOI: 10.1073/pnas.1907068116] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Color pattern mimicry in Heliconius butterflies is a classic case study of complex trait adaptation via selection on a few large effect genes. Association studies have linked color pattern variation to a handful of noncoding regions, yet the presumptive cis-regulatory elements (CREs) that control color patterning remain unknown. Here we combine chromatin assays, DNA sequence associations, and genome editing to functionally characterize 5 cis-regulatory elements of the color pattern gene optix We were surprised to find that the cis-regulatory architecture of optix is characterized by pleiotropy and regulatory fragility, where deletion of individual cis-regulatory elements has broad effects on both color pattern and wing vein development. Remarkably, we found orthologous cis-regulatory elements associate with wing pattern convergence of distantly related comimics, suggesting that parallel coevolution of ancestral elements facilitated pattern mimicry. Our results support a model of color pattern evolution in Heliconius where changes to ancient, multifunctional cis-regulatory elements underlie adaptive radiation.
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