1
|
Shu Q, Liu GC, He JW, Hu P, Dong ZW, Zhao RP, Zhang HR, Li XY. RNAi efficiency is enhanced through knockdown of double-stranded RNA-degrading enzymes in butterfly Papilio xuthus. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22113. [PMID: 38628056 DOI: 10.1002/arch.22113] [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: 12/08/2023] [Revised: 03/27/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
The efficiency of RNA interference (RNAi) has always limited the research on the phenotype innovation of Lepidoptera insects. Previous studies have found that double-stranded RNA-degrading enzyme (dsRNase) is an important factor in RNAi efficiency, but there have been no relevant reports in butterflies (Papilionoidea). Papilio xuthus is one of the important models in butterflies with an extensive experimental application value. To explore the effect of dsRNase in the RNAi efficiency on butterflies, six dsRNase genes (PxdsRNase 1-6) were identified in P. xuthus genome, and their dsRNA-degrading activities were subsequently detected by ex vivo assays. The result shows that the dsRNA-degrading ability of gut content (<1 h) was higher than hemolymph content (>12 h). We then investigated the expression patterns of these PxdsRNase genes during different tissues and developmental stages, and related RNAi experiments were carried out. Our results show that different PxdsRNase genes had different expression levels at different developmental stages and tissues. The expression of PxdsRNase2, PxdsRNase3, and PxdsRNase6 were upregulated significantly through dsGFP injection, and PxdsRNase genes can be silenced effectively by injecting their corresponding dsRNA. RNAi-of-RNAi studies with PxEbony, which acts as a reporter gene, observed that silencing PxdsRNase genes can increase RNAi efficiency significantly. These results confirm that silencing dsRNase genes can improve RNAi efficiency in P. xuthus significantly, providing a reference for the functional study of insects such as butterflies with low RNAi efficiency.
Collapse
Affiliation(s)
- Qian Shu
- Yunnan Agricultural University College of Plant Protection, Kunming, Yunnan, China
| | - Gui-Chun Liu
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jin-Wu He
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ping Hu
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhi-Wei Dong
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ruo-Ping Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong-Rui Zhang
- Yunnan Agricultural University College of Plant Protection, Kunming, Yunnan, China
| | - Xue-Yan Li
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Li J, Wang H, Zhu J, Yang Q, Luan Y, Shi L, Molina-Mora JA, Zheng Y. De novo assembly of a chromosome-level reference genome of the ornamental butterfly Sericinus montelus based on nanopore sequencing and Hi-C analysis. Front Genet 2023; 14:1107353. [PMID: 36968580 PMCID: PMC10030965 DOI: 10.3389/fgene.2023.1107353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Sericinus montelus (Lepidoptera, Papilionidae, Parnassiinae) is a high-value ornamental swallowtail butterfly species widely distributed in Northern and Central China, Japan, Korea, and Russia. The larval stage of this species feeds exclusively on Aristolochia plants. The Aristolochia species is well known for its high levels of aristolochic acids (AAs), which have been found to be carcinogenic for numerous animals. The swallowtail butterfly is among the few that can feed on these toxic host plants. However, the genetic adaptation of S. montelus to confer new abilities for AA tolerance has not yet been well explored, largely due to the limited genomic resources of this species. This study aimed to present a chromosome-level reference genome for S. montelus using the Oxford Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C technology. The final assembly was composed of 581.44 Mb with an expected genome size of 619.27 Mb. Further, 99.98% of the bases could be anchored onto 30 chromosomes. The N50 of contigs and scaffolds was 5.74 and 19.12 Mb, respectively. Approximately 48.86% of the assembled genome was suggested to be repeat elements, and 13,720 protein-coding genes were predicted in the current assembly. The phylogenetic analysis indicated that S. montelus diverged from the common ancestor of swallowtails about 58.57-80.46 million years ago. Compared with related species, S. montelus showed a significant expansion of P450 gene family members, and positive selections on eloa, heatr1, and aph1a resulted in the AA tolerance for S. montelus larva. The de novo assembly of a high-quality reference genome for S. montelus provided a fundamental genomic tool for future research on evolution, genome genetics, and toxicology of the swallowtail butterflies.
Collapse
Affiliation(s)
- Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Grandomics Biosciences Institute, Wuhan, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | | | - Qi Yang
- Grandomics Biosciences Institute, Wuhan, China
| | - Yang Luan
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Cancer Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - José Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- *Correspondence: José Arturo Molina-Mora, ; Yuanting Zheng,
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- *Correspondence: José Arturo Molina-Mora, ; Yuanting Zheng,
| |
Collapse
|
4
|
Shipilina D, Näsvall K, Höök L, Vila R, Talavera G, Backström N. Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly. Genomics 2022; 114:110481. [PMID: 36115505 DOI: 10.1016/j.ygeno.2022.110481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/14/2023]
Abstract
Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady's unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.
Collapse
Affiliation(s)
- Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden; Swedish Collegium for Advanced Study, Thunbergsvägen 2, 75236 Uppsala, Sweden.
| | - Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Roger Vila
- The Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva, Passeig Martim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Spain
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| |
Collapse
|
5
|
Metabolite Changes in Orange Dead Leaf Butterfly Kallima inachus during Ontogeny and Diapause. Metabolites 2022; 12:metabo12090804. [PMID: 36144209 PMCID: PMC9501346 DOI: 10.3390/metabo12090804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/22/2022] Open
Abstract
Holometabolism is a form of insect development which includes four life stages: egg, larva, pupa, and imago (or adult). The developmental change of whole body in metabolite levels of holometabolous insects are usually ignored and lack study. Diapause is an alternative life-history strategy that can occur during the egg, larval, pupal, and adult stages in holometabolous insects. Kallima inachus (Lepidoptera: Nymphalidae) is a holometabolous and adult diapausing butterfly. This study was intended to analyze metabolic changes in K. inachus during ontogeny and diapause through a non-targeted UPLC-MS/MS (ultra-performance liquid chromatograph coupled with tandem mass spectrometry) based metabolomics analysis. A variety of glycerophospholipids (11), amino acid and its derivatives (16), and fatty acyls (nine) are crucial to the stage development of K. inachus. 2-Keto-6-acetamidocaproate, N-phenylacetylglycine, Cinnabarinic acid, 2-(Formylamino) benzoic acid, L-histidine, L-glutamate, and L-glutamine play a potentially important role in transition of successive stages (larva to pupa and pupa to adult). We observed adjustments associated with active metabolism, including an accumulation of glycerophospholipids and carbohydrates and a degradation of lipids, as well as amino acid and its derivatives shifts, suggesting significantly changed in energy utilization and management when entering into adult diapause. Alpha-linolenic acid metabolism and ferroptosis were first found to be associated with diapause in adults through pathway analyses. Our study lays the foundation for a systematic study of the developmental mechanism of holometabolous insects and metabolic basis of adult diapause in butterflies.
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Guan DL, Zhao L, Li Y, Xing LX, Huang H, Xu SQ. Genome assembly of Luehdorfia taibai, an endangered butterfly endemic to Qinling Moutains in China with extremely small populations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.955246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conservation genomic resources over the past decade has drastically improved, since genomes can be used to predict diverse parameters vital to conservation management. Luehdorfia taibai is an endemic butterfly only found in restricted aeras in middle-west China and is critically endangered. It was classfied as a vunerlable (VN) species in the “China species red list.” Here we generated 34.38 Gb of raw DNA sequencing reads and obtained a high-qualified draft genome assembly of L. taibai. The final genome is ~683.3 Mb, with contig N50 size of 10.19 Mb. Further, 98.6% of single-copy orthologous genes have been recovered by BUSCO. An estimated 42.34% of the genome of L. taibai consists of repetitive elements. Combined with gene prediction and transcriptome sequencing, genome annotation produced 15,968 protein-coding genes. Additionally, a nearly 1:1 orthology ratio of syntenic blocks between L. taibai and its closest genome Luehdorfia chinensis suggested that the genome structures have not changed much after speciation. The genome of L. taibai have not undergone a whole genome duplication event. Population dynamics analyses indicates that L. taibai has an extremely low heterozygosity of 0.057%, and its population size has declined dramatically over the past 10 thousand years. Our study describes a draft genome assembly of the L. taibai, the first implication of this species. We consider the globally overexploited of the host plants is not the main reason to threaten L. taibai. The genome will provide advice for the conservation to the economically important Luehdorfia lineage and this specific species.
Collapse
|
8
|
Atypical laminin spots and pull-generated microtubule-actin projections mediate Drosophila wing adhesion. Cell Rep 2021; 36:109667. [PMID: 34496252 DOI: 10.1016/j.celrep.2021.109667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 06/11/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
During Drosophila metamorphosis, dorsal and ventral wing surfaces adhere, separate, and reappose in a paradoxical process involving cell-matrix adhesion, matrix production and degradation, and long cellular projections. The identity of the intervening matrix, the logic behind the adhesion-reapposition cycle, and the role of projections are unknown. We find that laminin matrix spots devoid of other main basement membrane components mediate wing adhesion. Through live imaging, we show that long microtubule-actin cables grow from those adhesion spots because of hydrostatic pressure that pushes wing surfaces apart. Formation of cables resistant to pressure requires spectraplakin, Patronin, septins, and Sdb, a SAXO1/2 microtubule stabilizer expressed under control of wing intervein-selector SRF. Silkworms and dead-leaf butterflies display similar dorso-ventral projections and expression of Sdb in intervein SRF-like patterns. Our study supports the morphogenetic importance of atypical basement-membrane-related matrices and dissects matrix-cytoskeleton coordination in a process of great evolutionary significance.
Collapse
|
9
|
Zhang Y, Teng D, Lu W, Liu M, Zeng H, Cao L, Southcott L, Potdar S, Westerman E, Zhu AJ, Zhang W. A widely diverged locus involved in locomotor adaptation in Heliconius butterflies. SCIENCE ADVANCES 2021; 7:eabh2340. [PMID: 34348900 PMCID: PMC8336958 DOI: 10.1126/sciadv.abh2340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/17/2021] [Indexed: 12/30/2023]
Abstract
Heliconius butterflies have undergone adaptive radiation and therefore serve as an excellent system for exploring the continuum of speciation and adaptive evolution. However, there is a long-lasting paradox between their convergent mimetic wing patterns and rapid divergence in speciation. Here, we characterize a locus that consistently displays high divergence among Heliconius butterflies and acts as an introgression hotspot. We further show that this locus contains multiple genes related to locomotion and conserved in Lepidoptera. In light of these findings, we consider that locomotion traits may be under selection, and if these are heritable traits that are selected for, then they might act as species barriers.
Collapse
Affiliation(s)
- Yubo Zhang
- State Key Laboratory of Protein and Plant Gene Research, 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
| | - Wei Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Min Liu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hua Zeng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Lei Cao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Laura Southcott
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
| | - Sushant Potdar
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Erica Westerman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Alan Jian Zhu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
10
|
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.
Collapse
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
| | | |
Collapse
|
11
|
Peng Y, Li H, Liu Z, Zhang C, Li K, Gong Y, Geng L, Su J, Guan X, Liu L, Zhou R, Zhao Z, Guo J, Liang Q, Li X. Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology. Mol Ecol Resour 2021; 21:2093-2108. [PMID: 33829635 DOI: 10.1111/1755-0998.13397] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.
Collapse
Affiliation(s)
- Yongdong Peng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhengzhu Liu
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Chuansheng Zhang
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Keqiang Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Mathematics and Information Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuanfang Gong
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Liying Geng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jingjing Su
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, China
| | - Xuemin Guan
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Lei Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai-an, China
| | - Ruihong Zhou
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Ziya Zhao
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jianxu Guo
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Xianglong Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| |
Collapse
|
12
|
Seixas FA, Edelman NB, Mallet J. Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus. Genome Biol Evol 2021; 13:6207971. [PMID: 33792688 PMCID: PMC8290116 DOI: 10.1093/gbe/evab069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Heliconius butterflies (Lepidoptera: Nymphalidae) are a group of 48 neotropical species widely studied in evolutionary research. Despite the wealth of genomic data generated in past years, chromosomal level genome assemblies currently exist for only two species, Heliconius melpomene and Heliconius erato, each a representative of one of the two major clades of the genus. Here, we use these reference genomes to improve the contiguity of previously published draft genome assemblies of 16 Heliconius species. Using a reference-assisted scaffolding approach, we place and order the scaffolds of these genomes onto chromosomes, resulting in 95.7-99.9% of their genomes anchored to chromosomes. Genome sizes are somewhat variable among species (270-422 Mb) and in one small group of species (Heliconius hecale, Heliconius elevatus, and Heliconius pardalinus) expansions in genome size are driven mainly by repetitive sequences that map to four small regions in the H. melpomene reference genome. Genes from these repeat regions show an increase in exon copy number, an absence of internal stop codons, evidence of constraint on nonsynonymous changes, and increased expression, all of which suggest that at least some of the extra copies are functional. Finally, we conducted a systematic search for inversions and identified five moderately large inversions fixed between the two major Heliconius clades. We infer that one of these inversions was transferred by introgression between the lineages leading to the erato/sara and burneyi/doris clades. These reference-guided assemblies represent a major improvement in Heliconius genomic resources that enable further genetic and evolutionary discoveries in this genus.
Collapse
Affiliation(s)
- Fernando A Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut, USA
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
13
|
Chen J, Wang Z, Liu C, Chen Z, Tang X, Wu Q, Zhang S, Song G, Cong S, Chen Q, Zhao Z. Mimicking Nature's Butterflies: Electrochromic Devices with Dual-Sided Differential Colorations. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007314. [PMID: 33634919 DOI: 10.1002/adma.202007314] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/24/2021] [Indexed: 05/24/2023]
Abstract
Some butterfly species such as the orange oakleaf (Kallima inachus) have strikingly different colors on the dorsal (front) sides of their wings compared to those on the ventral (back) sides of their wings, which helps camouflage the butterflies from predators and attract potential mates. However, few human-made materials, devices, and technologies can mimic such differential coloring for a long time. Here, a new type of Janus-structured two-sided electrochromic device is developed that, upon application of different voltages, exhibits a coloration state on one side that is distinctly different from that on the other side. This is achieved by inserting an optically thin (4-8 nm) metallic layer with a complex refractive index, such as a layer composed of tungsten, titanium, copper or silver, into typical electrochromic structures.
Collapse
Affiliation(s)
- Jian Chen
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Zhen Wang
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Chenglong Liu
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Zhigang Chen
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Xueqing Tang
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Qi Wu
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Shu Zhang
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Ge Song
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Shan Cong
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- Key Laboratory of Multifunctional Nanomaterials and Smart Systems, Chinese Academy of Sciences (CAS), Suzhou, 215123, China
- Division of Nanomaterials, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Nanchang, 330200, China
| | - Qin Chen
- Institute of Nanophotonics, Jinan University, Guangzhou, 511443, China
| | - Zhigang Zhao
- Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- Key Laboratory of Multifunctional Nanomaterials and Smart Systems, Chinese Academy of Sciences (CAS), Suzhou, 215123, China
- Division of Nanomaterials, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Nanchang, 330200, China
| |
Collapse
|
14
|
Butterfly Conservation in China: From Science to Action. INSECTS 2020; 11:insects11100661. [PMID: 32992975 PMCID: PMC7600441 DOI: 10.3390/insects11100661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/20/2020] [Accepted: 09/22/2020] [Indexed: 12/26/2022]
Abstract
About 10% of the Earth's butterfly species inhabit the highly diverse ecosystems of China. Important for the ecological, economic, and cultural services they provide, many butterfly species experience threats from land use shifts and climate change. China has recently adopted policies to protect the nation's biodiversity resources. This essay examines the current management of butterflies in China and suggests various easily implementable actions that could improve these conservation efforts. Our recommendations are based on the observations of a transdisciplinary group of entomologists and environmental policy specialists. Our analysis draws on other successful examples around the world that China may wish to consider. China needs to modify its scientific methodologies behind butterfly conservation management: revising the criteria for listing protected species, focusing on umbrella species for broader protection, identifying high priority areas and refugia for conservation, among others. Rural and urban land uses that provide heterogeneous habitats, as well as butterfly host and nectar plants, must be promoted. Butterfly ranching and farming may also provide opportunities for sustainable community development. Many possibilities exist for incorporating observations of citizen scientists into butterfly data collection at broad spatial and temporal scales. Our recommendations further the ten Priority Areas of China's National Biodiversity Conservation Strategy and Action Plan (2011-2030).
Collapse
|