1
|
Rayner JG, Eichenberger F, Bainbridge JVA, Zhang S, Zhang X, Yusuf LH, Balenger S, Gaggiotti OE, Bailey NW. Competing adaptations maintain nonadaptive variation in a wild cricket population. Proc Natl Acad Sci U S A 2024; 121:e2317879121. [PMID: 39088392 PMCID: PMC11317585 DOI: 10.1073/pnas.2317879121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 06/08/2024] [Indexed: 08/03/2024] Open
Abstract
How emerging adaptive variants interact is an important factor in the evolution of wild populations, but the opportunity to empirically study this interaction is rare. We recently documented the emergence of an adaptive phenotype "curly-wing" in Hawaiian populations of field crickets (Teleogryllus oceanicus). Curly-wing inhibits males' ability to sing, protecting them from eavesdropping parasitoid flies (Ormia ochracea). Surprisingly, curly-wing co-occurs with similarly protective silent "flatwing" phenotypes in multiple populations, in which neither phenotype has spread to fixation. These two phenotypes are frequently coexpressed, but since either sufficiently reduces song amplitude to evade the fly, their coexpression confers no additional fitness benefit. Numerous "off-target" phenotypic changes are known to accompany flatwing, and we find that curly-wing, too, negatively impacts male courtship ability and affects mass and survival of females under lab conditions. We show through crosses and genomic and mRNA sequencing that curly-wing expression is associated with variation on a single autosome. In parallel analyses of flatwing, our results reinforce previous findings of X-linked single-locus inheritance. By combining insights into the genetic architecture of these alternative phenotypes with simulations and field observations, we show that the co-occurrence of these two adaptations impedes either from fixing, despite extreme fitness benefits, due to fitness epistasis. This co-occurrence of similar adaptive forms in the same populations might be more common than is generally considered and could be an important force inhibiting adaptive evolution in wild populations of sexually reproducing organisms.
Collapse
Affiliation(s)
- Jack G. Rayner
- Department of Biology, University of Maryland, College Park, MD20740
| | - Franca Eichenberger
- Centre for Biological Diversity, University of St Andrews, St AndrewsKY16 9TH, United Kingdom
| | | | - Shangzhe Zhang
- Centre for Biological Diversity, University of St Andrews, St AndrewsKY16 9TH, United Kingdom
| | - Xiao Zhang
- Centre for Biological Diversity, University of St Andrews, St AndrewsKY16 9TH, United Kingdom
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin300387, China
| | - Leeban H. Yusuf
- Centre for Biological Diversity, University of St Andrews, St AndrewsKY16 9TH, United Kingdom
| | - Susan Balenger
- College of Biological Sciences, University of Minnesota, St. Paul, MN55108
| | - Oscar E. Gaggiotti
- Centre for Biological Diversity, University of St Andrews, St AndrewsKY16 9TH, United Kingdom
| | - Nathan W. Bailey
- Centre for Biological Diversity, University of St Andrews, St AndrewsKY16 9TH, United Kingdom
| |
Collapse
|
2
|
Huang YH, Sun YF, Li H, Li HS, Pang H. PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era. Mol Biol Evol 2024; 41:msae150. [PMID: 39041199 PMCID: PMC11287380 DOI: 10.1093/molbev/msae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/15/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024] Open
Abstract
The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, prior to core analyses, traditional methods typically involve intricate and time-consuming procedures, including assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple sequence alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive data sets. In this study, we develop PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as a reference for phylogenetic and evolutionary analyses. Through testing with simulated data sets of species spanning the tree of life, PhyloAln demonstrates consistently robust performance compared with other reference-based tools across different data types, sequencing technologies, coverages, and species, with percent completeness and identity at least 50 percentage points higher in the alignments. Additionally, we validate the efficacy of PhyloAln in removing a minimum of 90% foreign and 70% cross-contamination issues, which are prevalent in sequencing data but often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments (completeness mostly larger than 80%, identity larger than 90%) and reconstructing robust phylogenies using real data sets of transcriptomes of ladybird beetles, plastid genes of peppers, or ultraconserved elements of turtles. With these advantages, PhyloAln is expected to facilitate phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.
Collapse
Affiliation(s)
- Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Yi-Fei Sun
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| |
Collapse
|
3
|
Sun YX, Chen MJ, Hao YN, Wang SS, Zhang CL. Canola bee pollen is an effective artificial diet additive for improving larval development of predatory coccinellids: a lesson from Harmonia axyridis. PEST MANAGEMENT SCIENCE 2024; 80:2920-2928. [PMID: 38288907 DOI: 10.1002/ps.8000] [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: 11/22/2023] [Revised: 01/08/2024] [Accepted: 01/28/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Pollen is a common plant-derived food source for predatory ladybird beetles under field conditions, yet the potential for pollen to improve the quality of artificial diets remains largely unexplored. In this study, we developed three pollen diets by incorporating varying proportions of canola bee pollen (7.5%, 15.0% and 22.5% with 2.5%, 5.0%, and 7.5% of water, respectively) into a conventional diet. The feeding efficiency of Harmonia axyridis, an omnivorous predator, was evaluated and compared on three pollen diets, a conventional nonpollen diet and pea aphids. RESULTS The larvae fed a medium or high pollen diet exhibited significantly higher survival in the 4th instar, pupa and adult stages than those fed a nonpollen diet. These larvae also developed into significantly heavier adults, and their survival rates in adulthood were comparable to those fed pea aphids. Specifically, we revealed the underlying mechanisms through which a high pollen diet enhances pupal development. Consumption of high pollen diet versus nonpollen diet resulted not only in a significant decrease in pupal glycogen content, but also an increase in adult lipid content. Both diet treatments induced similar changes in carbohydrate and glycogen content compared to the aphid diet while exhibiting different alterations in pupal protein content and adult lipid content. Furthermore, the transcriptome analysis revealed that the nutrient metabolism, immune response, and cuticle development pathways were predominantly enriched among the differentially expressed genes (DEGs). CONCLUSION Canola bee pollen offers diverse advantages in terms of rearing H. axyridis larvae with an artificial diet, which will advance the development of effective diets for predaceous coccinellids. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Yuan-Xing Sun
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Ming-Juan Chen
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Ya-Nan Hao
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Sen-Shan Wang
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Chu-Lin Zhang
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
4
|
Koshiishi Y, Wada K. Genetic structure and origin of emu populations in Japanese farms inferred from large-scale SNP genotyping based on double-digest RAD-seq. Sci Rep 2024; 14:6982. [PMID: 38523157 PMCID: PMC10961305 DOI: 10.1038/s41598-024-57032-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/13/2024] [Indexed: 03/26/2024] Open
Abstract
The emu is a novel poultry species in Japan. However, Japanese farmed emu populations have reduced genetic diversity owing to inbreeding. We have previously suggested that there are genetic resources in the Tohoku Safari Park (TSP) and Fuji/Kakegawa Kachoen Garden Park (FGP/KGP) to extend the genetic diversity of commercial emu farms based on microsatellite (SSR) and mitochondrial DNA. However, those markers provide relatively poor information. Thus, we investigated the genetic structure of farmed Japanese populations based on a large-scale genotyping system using RAD-seq and verified the usefulness of TSP and FGP/KGP as genetic resources for expanding genetic diversity. Admixture, phylogenetic, and principal component analyses based on 28,676 SNPs showed that TSP individuals were ancestors in the Okhotsk Emu Farm (OEF). FGP/KGP individuals showed a unique genetic component that differed from that of the others. We have previously reported that the mitochondrial haplotypes of FGP/KGP were shared with an isolated wild population in eastern Australia. These results suggest that FGP/KGP individuals originated from an eastern Australia isolated population different from other populations including ancestral of OEF/TSP. Our results would provide information for the development of Japanese emu farms and industry and for the conservation of genetic resources in the Australian wild emu.
Collapse
Affiliation(s)
- Yuichi Koshiishi
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya, Tokyo, 156-8502, Japan.
| | - Kenta Wada
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan.
| |
Collapse
|
5
|
Orteu A, Kucka M, Gordon IJ, Ng’iru I, van der Heijden ESM, Talavera G, Warren IA, Collins S, ffrench-Constant RH, Martins DJ, Chan YF, Jiggins CD, Martin SH. Transposable Element Insertions Are Associated with Batesian Mimicry in the Pantropical Butterfly Hypolimnas misippus. Mol Biol Evol 2024; 41:msae041. [PMID: 38401262 PMCID: PMC10924252 DOI: 10.1093/molbev/msae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three color morphs of D. chrysippus found in different regions of Africa. In this study, we examine the evolution of the M locus and identify it as an example of adaptive atavism. This phenomenon involves a morphological reversion to an ancestral character that results in an adaptive phenotype. We show that H. misippus has re-evolved an ancestral wing pattern present in other Hypolimnas species, repurposing it for Batesian mimicry of a D. chrysippus morph. Using haplotagging, a linked-read sequencing technology, and our new analytical tool, Wrath, we discover two large transposable element insertions located at the M locus and establish that these insertions are present in the dominant allele responsible for producing mimetic phenotype. By conducting a comparative analysis involving additional Hypolimnas species, we demonstrate that the dominant allele is derived. This suggests that, in the derived allele, the transposable elements disrupt a cis-regulatory element, leading to the reversion to an ancestral phenotype that is then utilized for Batesian mimicry of a distinct model, a different morph of D. chrysippus. Our findings present a compelling instance of convergent evolution and adaptive atavism, in which the same pattern element has independently evolved multiple times in Hypolimnas butterflies, repeatedly playing a role in Batesian mimicry of diverse model species.
Collapse
Affiliation(s)
- Anna Orteu
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Ian J Gordon
- Centre of Excellence in Biodiversity, University of Rwanda, Huye, Rwanda
| | - Ivy Ng’iru
- Mpala Research Centre, Nanyuki 10400, Laikipia, Kenya
- School of Biosciences, Cardiff University, Cardiff CF 10 3AX, UK
- UK Centre for Ecology and Hydrology, Wallingford OX10 8BB, UK
| | - Eva S M van der Heijden
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Catalonia, Spain
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | | | - Dino J Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
6
|
Pu DQ, Wu XL, Chen ZT, Wei SJ, Cai P, Liu HL. Chromosome-level genome assembly of the giant ladybug Megalocaria dilatata. Sci Data 2024; 11:117. [PMID: 38267446 PMCID: PMC10808094 DOI: 10.1038/s41597-024-02990-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024] Open
Abstract
The giant ladybug Megalocaria dilatata (Fabricius) is a potential biocontrol agent and a valuable model for coccinellid genomics and evolutionary biology. However, the lack of a reference genome for M. dilatata has impeded further explorations into its evolution and constrained its use in pest management. Here, we assembled and annotated a high-quality, chromosome-level genome of M. dilatata. The resulting assembly spans 772.3 Mb, with a scaffold N50 of 72.48 Mb and a GC content of 34.23%. The Hi-C data aided in anchoring the assembly onto 10 chromosomes ranging from 43.35 to 108.16 Mb. We identified 493.33 Mb of repeat sequences, accounting for 63.88% of the assembled genome. Our gene prediction identified 25,346 genes, with 81.89% annotated in public protein databases. The genome data will provide a valuable resource for studying the biology and evolution of Coccinellidae, aiding in pest control strategies and advancing research in the field.
Collapse
Affiliation(s)
- De-Qiang Pu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
| | - Xing-Long Wu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Zhi-Teng Chen
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, 212004, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Peng Cai
- Horticultural Institute, Sichuan Academy of Agricultural Sciences, Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Hong-Ling Liu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
| |
Collapse
|
7
|
Zhou J, Ng BF, Han N, Chen L, Wang Z, Li X, Zou M. Structure and mechanical properties of ladybird elytra as biological sandwich panels. J Mech Behav Biomed Mater 2023; 143:105917. [PMID: 37216753 DOI: 10.1016/j.jmbbm.2023.105917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
Abstract
The armour of the ladybird, elytra, protect the body from injury and are well-adapted to flight. However, experimental methods to decipher their mechanical performances had been challenging due to the small size, making it unclear how the elytra balance mass and strength. Here, we provide insights to the relationship between the microstructure and multifunctional properties of the elytra by means of structural characterization, mechanical analysis and finite element simulations. Micromorphology analysis on the elytron revealed the thickness ratio of the upper lamination, middle layer and lower lamination is approximately 51:139:7. The upper lamination had multiple cross fibre layers and the thickness of each fibre layer is not the same. In addition, the tensile strength, elastic modulus, fracture strain, bending stiffness and hardness of elytra were obtained through in-situ tensile and nanoindentation-bending under the influence of multiple loading conditions, which also serve as references for finite element models. The finite element model revealed that structural factors such as thickness of each layer, angle of fibre layer and trabeculae are key to affecting the mechanical properties, but the effect is different. When the thickness of upper, middle and lower layers is the same, the tensile strength provided by unit mass of the model is 52.78% lower than that provided by elytra. These findings broaden the relationship between the structural and mechanical properties of the ladybird elytra, and are expected to inspire the development of sandwich structures in biomedical engineering.
Collapse
Affiliation(s)
- Jianfei Zhou
- Key Lab of Bionic Engineering, Ministry of Education, Jilin University, Changchun, 130022, China; School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue 639798, Singapore
| | - Bing Feng Ng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue 639798, Singapore
| | - Na Han
- Key Lab of Bionic Engineering, Ministry of Education, Jilin University, Changchun, 130022, China
| | - Lining Chen
- Key Lab of Bionic Engineering, Ministry of Education, Jilin University, Changchun, 130022, China
| | - Zhaoyang Wang
- Key Lab of Bionic Engineering, Ministry of Education, Jilin University, Changchun, 130022, China
| | - Xiujuan Li
- Key Lab of Bionic Engineering, Ministry of Education, Jilin University, Changchun, 130022, China
| | - Meng Zou
- Key Lab of Bionic Engineering, Ministry of Education, Jilin University, Changchun, 130022, China.
| |
Collapse
|
8
|
Crowley LM, Barclay M, Roy HE, Brown PM. The genome sequence of the orange ladybird, Halyzia sedecimguttata (Linnaeus, 1758). Wellcome Open Res 2023; 8:186. [PMID: 37476650 PMCID: PMC10354457 DOI: 10.12688/wellcomeopenres.19369.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 07/22/2023] Open
Abstract
We present a genome assembly from an individual Halyzia sedecimguttata (the orange ladybird, Arthropoda; Insecta; Coleoptera, Coccinellidae). The genome sequence is 919.1 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 27,547 protein coding genes.
Collapse
Affiliation(s)
| | | | - Helen E. Roy
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
| | - Peter M.J. Brown
- School of Life Sciences, Anglia Ruskin University, Cambridge, England, UK
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Zhu W, Chi S, Wang Y, Li H, Wang Z, Gu S, Sun T, Xiang H, You P, Ren Y. A chromosome-level genome assembly of the Henosepilachna vigintioctomaculata provides insights into the evolution of ladybird beetles. DNA Res 2023; 30:6988042. [PMID: 36645207 PMCID: PMC9936504 DOI: 10.1093/dnares/dsad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/17/2023] Open
Abstract
The ladybird beetle Henosepilachna vigintioctomaculata is an economically significant oligophagous pest that induces damage to many Solanaceae crops. An increasing number of studies have examined the population and phenotype diversity of ladybird beetles. However, few comparative genome analyses of ladybird beetle species have been conducted. Here, we obtained a high-quality chromosome-level genome assembly of H. vigintioctomaculata using various sequencing technologies, and the chromosome-level genome assembly was ~581.63 Mb, with 11 chromosomes successfully assembled. The phylogenetic analysis showed that H. vigintioctomaculata is a more ancient lineage than the other three sequenced ladybird beetles, Harmonia axyridis, Propylea japonica, and Coccinella septempunctata. We also compared positively selected genes (PSGs), transposable elements (TEs) ratios and insertion times, and key gene families associated with environmental adaptation among these ladybird beetles. The pattern of TEs evolution of H. vigintioctomaculata differs from the other three ladybird beetles. The PSGs were associated with ladybird beetles development. However, the key gene families associated with environmental adaptation in ladybird beetles varied. Overall, the high-quality draft genome sequence of H. vigintioctomaculata provides a useful resource for studies of beetle biology, especially for the invasive biology of ladybird beetles.
Collapse
Affiliation(s)
| | | | | | | | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Songdong Gu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, China
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | | | - Yandong Ren
- To whom correspondence should be addressed. Tel. +86-029-85310266; (Y.R.)
| |
Collapse
|
10
|
Wu MM, Chen X, Xu QX, Zang LS, Wang S, Li M, Xiao D. Melanin Synthesis Pathway Interruption: CRISPR/Cas9-mediated Knockout of dopa decarboxylase (DDC) in Harmonia axyridis (Coleoptera: Coccinellidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:6694719. [PMID: 36082675 PMCID: PMC9459435 DOI: 10.1093/jisesa/ieac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 05/28/2023]
Abstract
CRISPR/Cas9 technology is a very powerful genome editing tool and has been used in many insect species for functional genomics studies through targeted gene mutagenesis. Here, we successfully established CRISPR/Cas9 research platform in Asian multi-colored ladybird beetle, Harmonia axyridis, an important natural enemy in biological control. In this study, one pivotal gene dopa decarboxylase (DDC) in melanin synthesis was targeted by CRISPR/Cas9 to generate mutants in H. axyridis by CRISPR/Cas9 technology. Our results showed that injection of single guide RNA of the DDC and Cas9 protein into preblastoderm eggs induced one insertion and four deletion (indels) mutant H. axyridis. Mutations of HaDDC gene generated 25% mutant rate with melanin missing phenotype in larva, pupa,l and adult stage. The predation ability of the fourth instar larvae has no significant difference between wild (control) and mutant H. axyridis (G0), while these mutant fourth instar larvae had longer developmental period than that of the wild type. Consequently, the total predation of the fourth instar larvae was significantly increased in H. axyridis mutants comparing with the wild type. These results indicated that the success of CRISPR/Cas9 gene editing in H. axyridis. The gene editing platform in H. axyridis would facilitate the gene function research and promote special strain of predatory ladybird beetle generation.
Collapse
Affiliation(s)
| | | | - Qing-xuan Xu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lian-sheng Zang
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering of Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Su Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Ming Li
- Corresponding author, e-mail: (M.L.), (D.X.)
| | - Da Xiao
- Corresponding author, e-mail: (M.L.), (D.X.)
| |
Collapse
|
11
|
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
|
12
|
Gibert JM. [Small scale evolution]. Biol Aujourdhui 2022; 216:41-47. [PMID: 35876520 DOI: 10.1051/jbio/2022008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Small-scale evolution or microevolution concerns evolution at the intra-specific level or between closely related species. At the intra-specific level, it allows the analysis of the evolutionary forces at work: mutation, genetic drift, migration and selection. Moreover, because of the short evolutionary time, it is easier to identify the genetic basis of observed phenotypic differences. Most studies focus on current populations but more and more analyses are performed on ancient DNA. This provides important information for tracing the history of populations and also allows the reconstruction of phenotypes of individuals that disappeared several thousand years ago. In this short review, I present studies showing how pre-zygotic or post-zygotic barriers involved in species formation are set up using the example of the geographical barrier due to the formation of the Isthmus of Panama and that of the heterochromatin divergence in Drosophilidae. I also describe the different approaches that have been used to identify the genetic basis of well known phenotypic variations: candidate gene approach (about melanism in felines), QTL mapping (variation in the number of lateral bone plates in sticklebacks), association study (pigmentation in the Asian ladybird). Finally, I illustrate the key impact of natural selection with the iconic example of the evolution of the beak of Galapagos finches, and the role of certain developmental genes in its morphological diversification.
Collapse
Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, UMR 7622, 9 quai St-Bernard 75005 Paris, France
| |
Collapse
|
13
|
Feron R, Waterhouse RM. Exploring new genomic territories with emerging model insects. CURRENT OPINION IN INSECT SCIENCE 2022; 51:100902. [PMID: 35301165 DOI: 10.1016/j.cois.2022.100902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Improvements in reference genome generation for insects and across the tree of life are extending the concept and utility of model organisms beyond traditional laboratory-tractable supermodels. Species or groups of species with comprehensive genome resources can be developed into model systems for studying a large variety of biological phenomena. Advances in sequencing and assembly technologies are supporting these emerging genome-enabled model systems by producing resources that are increasingly accurate and complete. Nevertheless, quality controls including assessing gene content completeness are required to ensure that these data can be included in expanding catalogues of high-quality references that will greatly advance understanding of insect biology and evolution.
Collapse
Affiliation(s)
- Romain Feron
- Department of Ecology and Evolution, University of Lausanne, and the Swiss Institute of Bioinformatics,1015 Lausanne, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and the Swiss Institute of Bioinformatics,1015 Lausanne, Switzerland.
| |
Collapse
|
14
|
Tian R, Chen X, Wu M, Xu Q, Wang S, Zang L, Xiao D. The Molecular Properties and Roles of Pannier in Harmonia axyridis's Metamorphosis and Melanin Synthesis. Front Physiol 2022; 13:909258. [PMID: 35592031 PMCID: PMC9110671 DOI: 10.3389/fphys.2022.909258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
The GATA transcription factor Pannier is identified as the major regulatory gene in color pattern formation in the Asian multi-colored ladybird beetle (Harmonia axyridis). however, the mechanisms of Pannier in regulating melanin synthesis and development in H. axyridis remain elusive. In this study, we identified and characterized Pannier in H. axyridis (HaPnr) and showed it to have two alternative spliced variants named HaPnr-α and HaPnr-β. Analyses of developmental stage expression patterns revealed that HaPnr, HaPnr-α and HaPnr-β were constitutively expressed throughout all developmental stages. To examine the role of HaPnr in H. axyridis development, RNA interference was performed in late larvae (the fourth instar) and early pupae (the first day of pupa stage). The transcript levels of HaPnr were effectively suppressed after the injection of double-stranded RNA of HaPnr (dsHaPnr). The fourth instar larvae injected with dsHaPnr reduced the pupation rates to only 61.50%, compared with 88.5% in the dsGFP-injected group. The un-pupated larvae gradually died after 1 week, and visually unaffected pupae emerged into abnormal adults with malformed hind wings and melanin absent from the cuticle. These abnormal adults gradually died 10 days after eclosion. However, when early pupae were injected with dsHaPnr, the normal eclosion rate was achieved at 88.41% on day 6 after the injection. In addition, these successful eclosion adults also showed an absence of melanin in the cuticle, but they could mate normally and have normal fecundity as compared with the control. We further demonstrated that the suppression of HaPnr-α or HaPnr-β individually did not affect the pupation and eclosion process. The suppression of HaPnr-α expression resulted in elytra melanin decreasing in both the conspicua and the succinea subgroup in H. axyridis. Even though the suppression of HaPnr-β expression only affected the melanin synthesis in the succinea subgroup, it significantly prolonged the time taken for melanin synthesis to occur in the conspicua subgroup in H. axyridis. These results indicate that HaPnr plays an essential role in insect development, especially during their metamorphosis, and also support our hypothesis that HaPnr could regulate melanin synthesis in H. axyridis under the combined action with its two splicing variants, HaPnr-α and HaPnr-β.
Collapse
Affiliation(s)
- Renbin Tian
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xu Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering of Ministry of Education, Guizhou University, Guiyang, China
| | - Mengmeng Wu
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qingxuan Xu
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Su Wang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Liansheng Zang
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering of Ministry of Education, Guizhou University, Guiyang, China
| | - Da Xiao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| |
Collapse
|
15
|
Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). BMC Genomics 2022; 23:90. [PMID: 35100986 PMCID: PMC8805230 DOI: 10.1186/s12864-022-08299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the genus Novius Mulsant, 1846 (= Rodolia Mulsant, 1850) (Coleoptera, Coccinellidae), play important roles in the biological control of cotton cushion scale pests, especially those belonging to Icerya. Since the best-known species, the vedalia beetle Novius cardinalis (Mulsant, 1850) was introduced into California from Australia, more than a century of successful use in classical biological control, some species of Novius have begun to exhibit some field adaptations to novel but related prey species. Despite their economic importance, relatively little is known about the underlying genetic adaptations associated with their feeding habits. Knowledge of the genome sequence of Novius is a major step towards further understanding its biology and potential applications in pest control. RESULTS We report the first high-quality genome sequence for Novius pumilus (Weise, 1892), a representative specialist of Novius. Computational Analysis of gene Family Evolution (CAFE) analysis showed that several orthogroups encoding chemosensors, digestive, and immunity-related enzymes were significantly expanded (P < 0.05) in N. pumilus compared to the published genomes of other four ladybirds. Furthermore, some of these orthogroups were under significant positive selection pressure (P < 0.05). Notably, transcriptome profiling demonstrated that many genes among the significantly expanded and positively selected orthogroups, as well as genes related to detoxification were differentially expressed, when N. pumilus feeding on the nature prey Icerya compared with the no feeding set. We speculate that these genes are vital in the Icerya adaptation of Novius species. CONCLUSIONS We report the first Novius genome thus far. In addition, we provide comprehensive transcriptomic resources for N. pumilus. The results from this study may be helpful for understanding the association of the evolution of genes related to chemosensing, digestion, detoxification and immunity with the prey adaptation of insect predators. This will provide a reference for future research and utilization of Novius in biological control programs. Moreover, understanding the possible molecular mechanisms of prey adaptation also inform mass rearing of N. pumilus and other Novius, which may benefit pest control.
Collapse
|
16
|
Recombinant inbred lines and next-generation sequencing enable rapid identification of candidate genes involved in morphological and agronomic traits in foxtail millet. Sci Rep 2022; 12:218. [PMID: 34997038 PMCID: PMC8742101 DOI: 10.1038/s41598-021-04012-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. We successfully constructed a linkage map using flexible ddRAD-seq with parents and RILs and detected major QTLs for each of three traits: leaf sheath colors, spikelet-tipped bristles (stb), and days to heading (DTH). (1) For leaf sheath colors, we identified the C gene on chromosome IV. (2) We identified a homeobox (HOX14) gene for stb on chromosome II, which shows homology with HvVrs1 in barley. (3) Finally, we identified a QTL with a large effect on DTH on chromosome II. A parent of the RILs from Taiwan and Yugu1 had a Harbinger-like TE in intron 3 of this gene. We also investigated the geographical distribution of the TE insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones.
Collapse
|
17
|
Huo SM, Zhang YY, Song ZR, Xiong XH, Hong XY. The potential pigmentation-related genes in spider mites revealed by comparative transcriptomes of the red form of Tetranychus urticae. INSECT MOLECULAR BIOLOGY 2021; 30:580-593. [PMID: 34309936 DOI: 10.1111/imb.12727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/27/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Colouration in spider mites is due to the presence of carotenoids with diverse colours, including yellows, oranges and reds. Tetranychus urticae has two main colour forms, red and green. Although a ketolase has been implicated in determining the colour, the underlying genetic basis of body colour divergence between the two forms has remained unclear. Based on a combination of comparative transcriptomes and RNA interference, we found that a gene encoding a cytochrome P450 enzyme of the CYP4 clan (CYP389B1) had remarkably high expression in adult females of the red T. urticae, as well as in hybrids obtained by crossing the red and green forms. Down-regulation of this gene by RNA interference resulted in decreased accumulation of red pigment. Up-regulation of the expressions of a scavenger receptor gene (SCARB1) and a mitochondrial glycine transporter (SLC25A38) also strongly contributed to red colour development in adult females. Suppressing the mRNA levels of these genes also resulted in reduced accumulation of red pigment in the three other spider mites with red body colour. Our results provide evidence that the body colour divergence between the two forms is caused by different expressions of pigmentation-related genes, and point to a possible role of a novel cytochrome P450 gene (CYP389B1) in regulating red-orange body colour. These findings expand the number of candidate cytochrome P450 genes involved in endogenous pigmentation and will help to understand their roles in determining colour patterns in mites and other species.
Collapse
Affiliation(s)
- S-M Huo
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Y-Y Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Z-R Song
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - X-H Xiong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - X-Y Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| |
Collapse
|
18
|
Zhang Y, Wang XX, Feng ZJ, Tian HG, Feng Y, Liu TX. Aspartate-β-alanine-NBAD pathway regulates pupal melanin pigmentation plasticity of ladybird Harmonia axyridis. INSECT SCIENCE 2021; 28:1651-1663. [PMID: 33063466 DOI: 10.1111/1744-7917.12877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/05/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Phenotypic plasticity is observed in many animal species and it is effective for them to cope with many types of environmental threats. The multicolored Asian ladybird Harmonia axyridis shows a cuticular pigmentation plasticity that can be rapidly induced by temperature changes, and in the form of changeable melanin spot patterns to adjust heat-absorbing. Here, H. axyridis with thermal stimulation were selected for determining the molecular regulations behind it. First, we confirmed the melanin level changes of H. axyridis pupa could be induced by temperature, and then screened the efficient time window for thermal sensing of H. axyridis pre-pupa; it is suggested that the late stage of pre-pupa (late stage of 4th instar larva) is the critical period to sense thermal signals and adjust its pupal melanin spot area size to adapt to upcoming thermal conditions. The Ha-ADC (aspartate decarboxylase) and Ha-ebony (NBAD synthase) of aspartate-β-alanine-NBAD pathway were then proved in regulation of cuticular melanization for pupa through RNA interference experiments; knockdown of these two genes enlarged the melanin spot size. Finally, we designed a random injection of Ha-ADC at different pre-pupal stages, to further study the regulation window during this process. Combined with all evidence observed, we suggested the spot size determination can be regulated very close to the time point of pupation, and genes of the aspartate-β-alanine-NBAD pathway play an important role at the molecular level. In brief, H. axyridis exhibits a flexible active physiological regulation through transcriptional modification to thermal changes.
Collapse
Affiliation(s)
- Yi Zhang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xing-Xing Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhu-Jun Feng
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hong-Gang Tian
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yi Feng
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tong-Xian Liu
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
19
|
Ogata N. Whole-Genome Sequence of the Trypoxylus dichotomus Japanese rhinoceros beetle. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000487. [PMID: 34723147 PMCID: PMC8553429 DOI: 10.17912/micropub.biology.000487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/06/2022]
Abstract
The draft whole-genome sequence of the Japanese rhinoceros beetle, Trypoxylus dichotomus was obtained using long-read PacBio sequence technology. The final assembled genome consisted of 739 Mbp in 2,347 contigs, with 24.5× mean coverage and a G+C content of 35.99%.
Collapse
Affiliation(s)
- Norichika Ogata
- Nihon BioData Corporation,
Correspondence to: Norichika Ogata ()
| |
Collapse
|
20
|
Xue HJ, Niu YW, Segraves KA, Nie RE, Hao YJ, Zhang LL, Cheng XC, Zhang XW, Li WZ, Chen RS, Yang XK. The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae). BMC Genomics 2021; 22:243. [PMID: 33827435 PMCID: PMC8028732 DOI: 10.1186/s12864-021-07558-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome reported thus far. RESULTS The genome is 864.8 Mb and consists of 4490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation. CONCLUSIONS The genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.
Collapse
Affiliation(s)
- Huai-Jun Xue
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yi-Wei Niu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kari A Segraves
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
- Archbold Biological Station, 123 Main Drive, Venus, FL, 33960, USA
| | - Rui-E Nie
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ya-Jing Hao
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Li Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Chao Cheng
- Biomarker Technologies Corporation, Floor 8, Shunjie Building, 12 Fuqian Road, Nanfaxin Town, Shunyi District, Beijing, 101300, China
| | - Xue-Wen Zhang
- Biomarker Technologies Corporation, Floor 8, Shunjie Building, 12 Fuqian Road, Nanfaxin Town, Shunyi District, Beijing, 101300, China
| | - Wen-Zhu Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Run-Sheng Chen
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xing-Ke Yang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
21
|
The color pattern inducing gene wingless is expressed in specific cell types of campaniform sensilla of a polka-dotted fruit fly, Drosophila guttifera. Dev Genes Evol 2021; 231:85-93. [PMID: 33774724 DOI: 10.1007/s00427-021-00674-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/15/2021] [Indexed: 12/16/2022]
Abstract
A polka-dotted fruit fly, Drosophila guttifera, has a unique pigmentation pattern on its wings and is used as a model for evo-devo studies exploring the mechanism of evolutionary gain of novel traits. In this species, a morphogen-encoding gene, wingless, is expressed in species-specific positions and induces a unique pigmentation pattern. To produce some of the pigmentation spots on wing veins, wingless is thought to be expressed in developing campaniform sensillum cells, but it was unknown which of the four cell types there express(es) wingless. Here we show that two of the cell types, dome cells and socket cells, express wingless, as indicated by in situ hybridization together with immunohistochemistry. This is a unique case in which non-neuronal SOP (sensory organ precursor) progeny cells produce Wingless as an inducer of pigmentation pattern formation. Our finding opens a path to clarifying the mechanism of evolutionary gain of a unique wingless expression pattern by analyzing gene regulation in dome cells and socket cells.
Collapse
|
22
|
Evo-devo of wing colour patterns in beetles. Curr Opin Genet Dev 2021; 69:97-102. [PMID: 33744509 DOI: 10.1016/j.gde.2021.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/24/2022]
Abstract
Insects have evolved tremendously diverse wing colour patterns that fulfil ecologically vital functions, including intraspecific sexual signalling, mimesis, mimicry, and detering predators. Beetles, which form the most species-rich order Coleoptera, have amazingly diverse wing colour patterns; however, the molecular mechanisms that give rise to these patterns remain poorly understood. Recently, the gene pannier (pnr), which encodes a transcription factor of the GATA family, was identified as an essential player in the wing patterning of the multi-coloured Asian ladybird beetle Harmonia axyridis. Here we review recent progress in understanding the molecular underpinnings of wing colour pattern formation in H. axyridis.
Collapse
|
23
|
Chen M, Mei Y, Chen X, Chen X, Xiao D, He K, Li Q, Wu M, Wang S, Zhang F, Li F. A chromosome-level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology. Mol Ecol Resour 2021; 21:1318-1332. [PMID: 33529495 DOI: 10.1111/1755-0998.13342] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/11/2022]
Abstract
The harlequin ladybird, Harmonia axyridis (Pallas), is a well-known model organism for genetic studies and is also a well-studied natural enemy used for pest control. It became an invasive species after being introduced to North America and Europe as a pest control agent. Though two genome assemblies for this insect have been previously reported, a high-quality genome assembly at the chromosome level is still not available. Here, we obtained a new chromosome-level genome assembly of H. axyridis by combining various sequencing technologies, namely Illumina short reads, PacBio long reads, 10X Genomics and Hi-C. The chromosome-level genome assembly is 423 Mb with a scaffold N50 of 45.92 Mb. Using Hi-C data 1,897 scaffolds were anchored to eight chromosomes. A total of 730,068 repeat sequences were identified, making up 51.2% of the assembled genome. After masking these repeat sequences, we annotated 22,810 protein-encoding genes. The X chromosome and Y-linked scaffolds were also identified by resequencing male and female genomes and calculating the male to female coverage ratios. Two gene families associated with environmental adaptation, odorant receptor and cytochrome P450, were analysed and showed no obvious expansion in H. axyridis. We successfully constructed a putative biosynthesis pathway of harmonine, a defence compound in the haemolymph of H. axyridis, which is a key factor for H. axyridis strong immunity. The chromosome-level genome assembly of H. axyridis is a helpful resource for studies of beetle biology and invasive biology.
Collapse
Affiliation(s)
- Mengyao Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Yang Mei
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Xu Chen
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Xi Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Da Xiao
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Qiang Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Mengmeng Wu
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Su Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Fan Zhang
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| |
Collapse
|
24
|
Li HS, Tang XF, Huang YH, Xu ZY, Chen ML, Du XY, Qiu BY, Chen PT, Zhang W, Ślipiński A, Escalona HE, Waterhouse RM, Zwick A, Pang H. Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles. BMC Biol 2021; 19:7. [PMID: 33446206 PMCID: PMC7807722 DOI: 10.1186/s12915-020-00945-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/22/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) has been documented in many herbivorous insects, conferring the ability to digest plant material and promoting their remarkable ecological diversification. Previous reports suggest HGT of antibacterial enzymes may have contributed to the insect immune response and limit bacterial growth. Carnivorous insects also display many evolutionary successful lineages, but in contrast to the plant feeders, the potential role of HGTs has been less well-studied. RESULTS Using genomic and transcriptomic data from 38 species of ladybird beetles, we identified a set of bacterial cell wall hydrolase (cwh) genes acquired by this group of beetles. Infection with Bacillus subtilis led to upregulated expression of these ladybird cwh genes, and their recombinantly produced proteins limited bacterial proliferation. Moreover, RNAi-mediated cwh knockdown led to downregulation of other antibacterial genes, indicating a role in antibacterial immune defense. cwh genes are rare in eukaryotes, but have been maintained in all tested Coccinellinae species, suggesting that this putative immune-related HGT event played a role in the evolution of this speciose subfamily of predominant predatory ladybirds. CONCLUSION Our work demonstrates that, in a manner analogous to HGT-facilitated plant feeding, enhanced immunity through HGT might have played a key role in the prey adaptation and niche expansion that promoted the diversification of carnivorous beetle lineages. We believe that this represents the first example of immune-related HGT in carnivorous insects with an association with a subsequent successful species radiation.
Collapse
Affiliation(s)
- Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xue-Fei Tang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ze-Yu Xu
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mei-Lan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- School of Environment and Life Science, Nanning Normal University, Nanning, 530001, China
| | - Xue-Yong Du
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Bo-Yuan Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Pei-Tao Chen
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Hermes E Escalona
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China.
| |
Collapse
|
25
|
Gao Q, Liu W, Wang JL, Wang XP, Zhou XM. PacBio Long-Read Sequencing Transcriptome Dataset of Adult Harmonia axyridis Under Diapause Inducing and Reproductive Inducing Photoperiod. Front Genet 2020; 11:1010. [PMID: 33061940 PMCID: PMC7518098 DOI: 10.3389/fgene.2020.01010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/07/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Qiao Gao
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wen Liu
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jia-Lu Wang
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Ping Wang
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xing-Miao Zhou
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
26
|
Satellitome Analysis in the Ladybird Beetle Hippodamia variegata (Coleoptera, Coccinellidae). Genes (Basel) 2020; 11:genes11070783. [PMID: 32668664 PMCID: PMC7397073 DOI: 10.3390/genes11070783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 12/29/2022] Open
Abstract
Hippodamia variegata is one of the most commercialized ladybirds used for the biological control of aphid pest species in many economically important crops. This species is the first Coccinellidae whose satellitome has been studied by applying new sequencing technologies and bioinformatics tools. We found that 47% of the H. variegata genome is composed of repeated sequences. We identified 30 satellite DNA (satDNA) families with a median intragenomic divergence of 5.75% and A+T content between 45.6% and 74.7%. This species shows satDNA families with highly variable sizes although the most common size is 100–200 bp. However, we highlight the existence of a satDNA family with a repeat unit of 2 kb, the largest repeat unit described in Coleoptera. PCR amplifications for fluorescence in situ hybridization (FISH) probe generation were performed for the four most abundant satDNA families. FISH with the most abundant satDNA family as a probe shows its pericentromeric location on all chromosomes. This location is coincident with the heterochromatin revealed by C-banding and DAPI staining, also analyzed in this work. Hybridization signals for other satDNA families were located only on certain bivalents and the X chromosome. These satDNAs could be very useful as chromosomal markers due to their reduced location.
Collapse
|
27
|
Sucher J, Mbengue M, Dresen A, Barascud M, Didelon M, Barbacci A, Raffaele S. Phylotranscriptomics of the Pentapetalae Reveals Frequent Regulatory Variation in Plant Local Responses to the Fungal Pathogen Sclerotinia sclerotiorum. THE PLANT CELL 2020; 32:1820-1844. [PMID: 32265317 PMCID: PMC7268813 DOI: 10.1105/tpc.19.00806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/16/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
Quantitative disease resistance (QDR) is a conserved form of plant immunity that limits infections caused by a broad range of pathogens. QDR has a complex genetic determinism. The extent to which molecular components of the QDR response vary across plant species remains elusive. The fungal pathogen Sclerotinia sclerotiorum, causal agent of white mold diseases on hundreds of plant species, triggers QDR in host populations. To document the diversity of local responses to S. sclerotiorum at the molecular level, we analyzed the complete transcriptomes of six species spanning the Pentapetalae (Phaseolus vulgaris, Ricinus communis, Arabidopsis [Arabidopsis thaliana], Helianthus annuus, Solanum lycopersicum, and Beta vulgaris) inoculated with the same strain of S. sclerotiorum About one-third of plant transcriptomes responded locally to S. sclerotiorum, including a high proportion of broadly conserved genes showing frequent regulatory divergence at the interspecific level. Evolutionary inferences suggested a trend toward the acquisition of gene induction relatively recently in several lineages. Focusing on a group of ABCG transporters, we propose that exaptation by regulatory divergence contributed to the evolution of QDR. This evolutionary scenario has implications for understanding the QDR spectrum and durability. Our work provides resources for functional studies of gene regulation and QDR molecular mechanisms across the Pentapetalae.
Collapse
Affiliation(s)
- Justine Sucher
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Malick Mbengue
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Axel Dresen
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Marielle Barascud
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Marie Didelon
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Adelin Barbacci
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| |
Collapse
|
28
|
Timmermans MJTN, Srivathsan A, Collins S, Meier R, Vogler AP. Mimicry diversification in Papilio dardanus via a genomic inversion in the regulatory region of engrailed- invected. Proc Biol Sci 2020; 287:20200443. [PMID: 32345166 DOI: 10.1098/rspb.2020.0443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Polymorphic Batesian mimics exhibit multiple protective morphs that each mimic a different noxious model. Here, we study the genomic transitions leading to the evolution of different mimetic wing patterns in the polymorphic Mocker Swallowtail Papilio dardanus. We generated a draft genome (231 Mb over 30 chromosomes) and re-sequenced individuals of three morphs. Genome-wide single nucleotide polymorphism (SNP) analysis revealed elevated linkage disequilibrium and divergence between morphs in the regulatory region of engrailed, a developmental gene previously implicated in the mimicry switch. The diverged region exhibits a discrete chromosomal inversion (of 40 kb) relative to the ancestral orientation that is associated with the cenea morph, but not with the bottom-recessive hippocoonides morph or with non-mimetic allopatric populations. The functional role of this inversion in the expression of the novel phenotype is currently unknown, but by preventing recombination, it allows the stable inheritance of divergent alleles enabling geographic spread and local coexistence of multiple adaptive morphs.
Collapse
Affiliation(s)
- Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK.,Department of Natural Sciences, Middlesex University, London, UK
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore.,Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
| |
Collapse
|
29
|
Colella JP, Tigano A, MacManes MD. A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues. Mol Ecol Resour 2020; 20:856-870. [PMID: 32153100 PMCID: PMC7496956 DOI: 10.1111/1755-0998.13155] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022]
Abstract
High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with the computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges for de novo genome assembly. Linked-read or "synthetic long-read" sequencing technologies, such as 10× Genomics, may provide a cost-effective alternative solution to assemble higher quality de novo genomes from degraded tissue samples. Here, we compare assembly quality (e.g., genome contiguity and completeness, presence of orthogroups) between four new deer mouse (Peromyscus spp.) genomes assembled using linked-read technology and four published genomes assembled from a single shotgun library. At a similar price-point, these approaches produce vastly different assemblies, with linked-read assemblies having overall higher contiguity and completeness, measured by larger N50 values and greater number of genes assembled, respectively. As a proof-of-concept, we used annotated genes from the four Peromyscus linked-read assemblies and eight additional rodent taxa to generate a phylogeny, which reconstructed the expected relationships among species with 100% support. Although not without caveats, our results suggest that linked-read sequencing approaches are a viable option to build de novo genomes from degraded tissues, which may prove particularly valuable for taxa that are extinct, rare or difficult to collect.
Collapse
Affiliation(s)
- Jocelyn P Colella
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Anna Tigano
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Matthew D MacManes
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| |
Collapse
|
30
|
Zhang Y, Wang XX, Feng ZJ, Cong HS, Chen ZS, Li YD, Yang WM, Zhang SQ, Shen LF, Tian HG, Feng Y, Liu TX. Superficially Similar Adaptation Within One Species Exhibits Similar Morphological Specialization but Different Physiological Regulations and Origins. Front Cell Dev Biol 2020; 8:300. [PMID: 32457902 PMCID: PMC7225305 DOI: 10.3389/fcell.2020.00300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/07/2020] [Indexed: 12/18/2022] Open
Abstract
Animals have developed numerous strategies to contend with environmental pressures. We observed that the same adaptation strategy may be used repeatedly by one species in response to a certain environmental challenge. The ladybird Harmonia axyridis displays thermal phenotypic plasticity at different developmental stages. It is unknown whether these superficially similar temperature-induced specializations share similar physiological mechanisms. We performed various experiments to clarify the differences and similarities between these processes. We examined changes in the numbers and sizes of melanic spots in pupae and adults, and confirmed similar patterns for both. The dopamine pathway controls pigmentation levels at both developmental stages of H. axyridis. However, the aspartate-β-alanine pathway controls spot size and number only in the pupae. An upstream regulation analysis revealed the roles of Hox genes and elytral veins in pupal and adult spot formation. Both the pupae and the adults exhibited similar morphological responses to temperatures. However, they occurred in different body parts and were regulated by different pathways. These phenotypic adaptations are indicative of an effective thermoregulatory system in H. axyridis and explains how insects contend with certain environmental pressure based on various control mechanisms.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Tong-Xian Liu
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, China
| |
Collapse
|
31
|
Orteu A, Jiggins CD. The genomics of coloration provides insights into adaptive evolution. Nat Rev Genet 2020; 21:461-475. [PMID: 32382123 DOI: 10.1038/s41576-020-0234-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 01/31/2023]
Abstract
Coloration is an easily quantifiable visual trait that has proven to be a highly tractable system for genetic analysis and for studying adaptive evolution. The application of genomic approaches to evolutionary studies of coloration is providing new insight into the genetic architectures underlying colour traits, including the importance of large-effect mutations and supergenes, the role of development in shaping genetic variation and the origins of adaptive variation, which often involves adaptive introgression. Improved knowledge of the genetic basis of traits can facilitate field studies of natural selection and sexual selection, making it possible for strong selection and its influence on the genome to be demonstrated in wild populations.
Collapse
Affiliation(s)
- Anna Orteu
- Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
| |
Collapse
|
32
|
Koshikawa S. Evolution of wing pigmentation in Drosophila: Diversity, physiological regulation, and cis-regulatory evolution. Dev Growth Differ 2020; 62:269-278. [PMID: 32171022 PMCID: PMC7384037 DOI: 10.1111/dgd.12661] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 12/20/2022]
Abstract
Fruit flies (Drosophila and its close relatives, or “drosophilids”) are a group that includes an important model organism, Drosophila melanogaster, and also very diverse species distributed worldwide. Many of these species have black or brown pigmentation patterns on their wings, and have been used as material for evo‐devo research. Pigmentation patterns are thought to have evolved rapidly compared with body plans or body shapes; hence they are advantageous model systems for studying evolutionary gains of traits and parallel evolution. Various groups of drosophilids, including genus Idiomyia (Hawaiian Drosophila), have a variety of pigmentations, ranging from simple black pigmentations around crossveins to a single antero‐distal spot and a more complex mottled pattern. Pigmentation patterns are sometimes obviously used for sexual displays; however, in some cases they may have other functions. The process of wing formation in Drosophila, the general mechanism of pigmentation formation, and the transport of substances necessary for pigmentation, including melanin precursors, through wing veins are summarized here. Lastly, the evolution of the expression of genes regulating pigmentation patterns, the role of cis‐regulatory regions, and the conditions required for the evolutionary emergence of pigmentation patterns are discussed. Future prospects for research on the evolution of wing pigmentation pattern formation in drosophilids are presented, particularly from the point of view of how they compare with other studies of the evolution of new traits.
Collapse
Affiliation(s)
- Shigeyuki Koshikawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan.,Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| |
Collapse
|
33
|
Molecular and Potential Regulatory Mechanisms of Melanin Synthesis in Harmonia axyridis. Int J Mol Sci 2020; 21:ijms21062088. [PMID: 32197465 PMCID: PMC7139685 DOI: 10.3390/ijms21062088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 12/03/2022] Open
Abstract
Melanization is a common phenomenon in insects, and melanin synthesis is a conserved physiological process that occurs in epidermal cells. Moreover, a comprehensive understanding of the mechanisms of melanin synthesis influencing insect pigmentation are well-suited for investigating phenotype variation. The Asian multi-colored (Harlequin) ladybird beetle, Harmonia axyridis, exhibits intraspecific polymorphism based on relative levels of melanization. However, the specific characteristics of melanin synthesis in H. axyridis remains elusive. In this study, we performed gene-silencing analysis of the pivotal inverting enzyme, tyrosine hydroxylase (TH), and DOPA decarboxylase (DDC) in the tyrosine metabolism pathway to investigate the molecular and regulatory mechanism of melanin synthesis in H. axyridis. Using RNAi of TH and DDC genes in fourth instar larvae, we demonstrated that dopamine melanin was the primary contributor to the overall body melanization of H. axyridis. Furthermore, our study provides the first conclusive evidence that dopamine serves as a melanin precursor for synthesis in the early pupal stage. According to transcription factor Pannier, which is essential for the formation of melanic color on the elytra in H. axyridis, we further demonstrated that suppression of HaPnr can significantly decrease expression levels of HaTH and HaDDC. These results in their entirety lead to the conclusion that transcription factor Pannier can regulate dopamine melanin synthesis in the dorsal elytral epidermis of H. axyridis.
Collapse
|
34
|
Zhang L, Li S, Luo J, Du P, Wu L, Li Y, Zhu X, Wang L, Zhang S, Cui J. Chromosome‐level genome assembly of the predatorPropylea japonicato understand its tolerance to insecticides and high temperatures. Mol Ecol Resour 2019; 20:292-307. [DOI: 10.1111/1755-0998.13100] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/19/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Lijuan Zhang
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Song Li
- Biomarker Technologies Corporation Beijing China
| | - Junyu Luo
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Pei Du
- Industrial Crops Research Institute Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang‐Huai‐Hai Plains Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement Zhengzhou China
| | - Linke Wu
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Yarong Li
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Xiangzhen Zhu
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Li Wang
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Shuai Zhang
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Jinjie Cui
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| |
Collapse
|
35
|
Chen X, Xiao D, Du X, Guo X, Zhang F, Desneux N, Zang L, Wang S. The Role of the Dopamine Melanin Pathway in the Ontogeny of Elytral Melanization in Harmonia axyridis. Front Physiol 2019; 10:1066. [PMID: 31507439 PMCID: PMC6719567 DOI: 10.3389/fphys.2019.01066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/05/2019] [Indexed: 12/03/2022] Open
Abstract
Polymorphic melanism in insects is a conspicuous phenotype which is derived from specific genotypes, and might be central to speciation processes via assortative sexual selection. At the molecular level, melanism in insects is attributed to the melanin pathway. DOPA decarboxylase (DDC) protein encoded by the DDC gene plays a central role in dopamine-melanin synthesis, the main component of melanin in insects. Although the mechanism of melanism has been elucidated in holometabolous insects, other physiological processes coupled with melanin synthesis are unknown. Herein, we identified DDC from the Asian multi-colored ladybird (Harmonia axyridis), an ideal holometabolous insect for studies of melanization due to highly variable color on their elytra. Analyses revealed that HaDDC (the DDC gene of H. axyridis) was constitutively expressed throughout all developmental stages. We performed RNAi technique to examine the melanin synthesis pathway of elytra in H. axyridis. The transcript levels of HaDDC were significantly suppressed after the injection of double-strand RNA of HaDDC (dsHaDDC) at 300 ng/individual in third instar larvae. Silencing HaDDC in third instar larvae did not result in mortality nor significantly affect pupation and eclosion. We further demonstrated that all adults of H. axyridis (forms succinea, spectabilis, and conspicua) with HaDDC silenced in third larvae showed abnormal phenotype which emerged as decreased elytra melanin. However, melanin was still observed in other parts of the adults such as head or pronotum. These results demonstrate for the first time that dopamine-derived melanin is the main contributor in elytra melanization in H. axyridis. Additionally, we provide evidence for DDC in regulating fecundity by showing that silencing of HaDDC in third instar larvae significantly reduced female egg-laying and egg hatching. As such, DDC is likely pleiotropic in respect of its role in melanin production and fecundity processes. These findings bring novel insights into melanin production in holometabolous insects, and contribute to the framework on which further studies may be conducted on the mechanism of pigment production and patterning in various types of insect coloration.
Collapse
Affiliation(s)
- Xu Chen
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China.,Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Da Xiao
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Xiaoyan Du
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Xiaojun Guo
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Fan Zhang
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Nicolas Desneux
- French National Institute for Agricultural Research, University of Côte d'Azur, Sophia Antipolis, France
| | - Liansheng Zang
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China
| | - Su Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| |
Collapse
|
36
|
Veenstra JA. Coleoptera genome and transcriptome sequences reveal numerous differences in neuropeptide signaling between species. PeerJ 2019; 7:e7144. [PMID: 31245184 PMCID: PMC6585902 DOI: 10.7717/peerj.7144] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/16/2019] [Indexed: 12/20/2022] Open
Abstract
Background Insect neuropeptides are interesting for the potential their receptors hold as plausible targets for a novel generation of pesticides. Neuropeptide genes have been identified in a number of different species belonging to a variety of insects. Results suggest significant neuropeptide variation between different orders, but much less is known of neuropeptidome variability within an insect order. I therefore compared the neuropeptidomes of a number of Coleoptera. Methodology Publicly available genome sequences, transcriptomes and the original sequence data in the form of short sequence read archives were analyzed for the presence or absence of genes coding neuropeptides as well as some neuropeptide receptors in seventeen beetle species. Results Significant differences exist between the Coleoptera analyzed here, while many neuropeptides that were previously characterized from Tribolium castaneum appear very similar in all species, some are not and others are lacking in one or more species. On the other hand, leucokinin, which was presumed to be universally absent from Coleoptera, is still present in non-Polyphaga beetles. Conclusion The variability in neuropeptidome composition between species from the same insect order may be as large as the one that exists between species from different orders.
Collapse
Affiliation(s)
- Jan A Veenstra
- INCIA UMR 5287 CNRS, University of Bordeaux, Bordeaux, Pessac, France
| |
Collapse
|
37
|
Ando T, Niimi T. Development and evolution of color patterns in ladybird beetles: A case study in Harmonia axyridis. Dev Growth Differ 2019; 61:73-84. [PMID: 30644547 DOI: 10.1111/dgd.12592] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 12/18/2022]
Abstract
Many organisms show various geometric color patterns on their bodies, and the developmental, evolutionary, genetic, and ecological bases of these patterns have been intensely studied in various organisms. Ladybird beetles display highly diverse patterns of wing (elytral) color and are one of the most attractive model organisms for studying these characteristics. In this study, we reviewed the genetic history of elytral color patterns in the Asian multicolored ladybird beetle Harmonia axyridis from the classical genetic studies led by the pupils of Thomas Hunt Morgan and Theodosius Dobzhansky to recent genomic studies that revealed that a single GATA transcription factor gene, pannier, regulates the highly diverse elytral color patterns in this species. We also reviewed and discussed the developmental and evolutionary mechanisms driven by the pannier locus in H. axyridis. In the development sections, we focused on the following two topics: (a) how the red (carotenoid) and black (melanin) pigmentation of elytra is regulated by the pannier and pigmentation genes and (b) how the diverse color patterns are formed by integrating regulatory inputs from other genes involved in wing development. In the evolution section, we subsequently focused on the highly diversified DNA sequences within the first intron of pannier that are 56-76 kb long and that were generated through recurrent multiple inversions. Furthermore, we discussed how these recurrent inversions have driven the diversification of color patterns throughout evolution.
Collapse
Affiliation(s)
- Toshiya Ando
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| |
Collapse
|
38
|
Gautier M, Yamaguchi J, Foucaud J, Loiseau A, Ausset A, Facon B, Gschloessl B, Lagnel J, Loire E, Parrinello H, Severac D, Lopez-Roques C, Donnadieu C, Manno M, Berges H, Gharbi K, Lawson-Handley L, Zang LS, Vogel H, Estoup A, Prud'homme B. The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird. Curr Biol 2018; 28:3296-3302.e7. [PMID: 30146156 PMCID: PMC6203698 DOI: 10.1016/j.cub.2018.08.023] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/25/2018] [Accepted: 08/07/2018] [Indexed: 12/02/2022]
Abstract
Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [7, 8]. In the harlequin ladybird, Harmonia axyridis, more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [9, 10]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H. axyridis. We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H. axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of ∼170 kb in the cis-regulatory regions of pannier, with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that highly variable discrete color forms can arise in natural populations through cis-regulatory allelic variation of a single gene.
Collapse
Affiliation(s)
- Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Julien Foucaud
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Aurélien Ausset
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Benoit Facon
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Bernhard Gschloessl
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Jacques Lagnel
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Etienne Loire
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Hugues Parrinello
- MGX, Biocampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Dany Severac
- MGX, Biocampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | | | | | - Maxime Manno
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Helene Berges
- INRA, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Karim Gharbi
- Edinburgh Genomics, University of Edinburgh, Edinburgh, UK
| | - Lori Lawson-Handley
- Evolutionary and Environmental Genomics Group, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - Lian-Sheng Zang
- Institute of Biological Control, Jilin Agricultural University, Changchun, China
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Arnaud Estoup
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France.
| | | |
Collapse
|