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Trissi N, Troczka BJ, Ozsanlav-Harris L, Singh KS, Mallott M, Aishwarya V, O'Reilly A, Bass C, Wilding CS. Differential regulation of the Tor gene homolog drives the red/green pigmentation phenotype in the aphid Myzuspersicae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 153:103896. [PMID: 36587809 DOI: 10.1016/j.ibmb.2022.103896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
In some aphid species, intraspecific variation in body colour is caused by differential carotenoid content: whilst green aphids contain only yellow carotenoids (β-, γ-, and β,γ-carotenes), red aphids additionally possess red carotenoids (torulene and 3,4-didehydrolycopene). Unusually, within animals who typically obtain carotenoids from their diet, ancestral horizontal gene transfer of carotenoid biosynthetic genes from fungi (followed by gene duplication), have imbued aphids with the intrinsic gene repertoire necessary to biosynthesise carotenoids. In the pea aphid, Acyrthosiphon pisum a lycopene (phytoene) desaturase gene (Tor) underpins the red/green phenotype, with this locus present in heterozygous form in red individuals but absent in green aphids, resulting in them being unable to convert lycopene into the red compounds 3,4-didehydrolycopene and torulene. The green peach aphid, Myzus persicae, separated from the pea aphid for ≈45MY also exists as distinct colour variable morphs, with both red and green individuals present. Here, we examined genomic data for both red and green morphs of M. persicae and identified an enlarged (compared to A. pisum) repertoire of 16 carotenoid biosynthetic genes (11 carotenoid desaturases and five carotenoid cyclase/synthase genes). From these, we identify the homolog of A. pisum Tor (here called carotene desaturase 2 or CDE-2) and show through 3D modelling that this homolog can accommodate the torulene precursor lycopene and, through RNA knockdown feeding experiments, demonstrate that disabling CDE-2 expression in red M. persicae clones results in green-coloured offspring. Unlike in A. pisum, we show that functional CDE-2 is present in the genomes of both red and green aphids. However, expression differences between the two colour morphs (350-700 fold CDE-2 overexpression in red clones), potentially driven by variants identified in upstream putative regulatory elements, underpin this phenotype. Thus, whilst aphids have a common origin of their carotenoid biosynthetic pathway, two aphid species separated for over 40MY have evolved very different drivers of intraspecific colour variation.
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Affiliation(s)
- Nasser Trissi
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Bartlomiej J Troczka
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Luke Ozsanlav-Harris
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Kumar Saurabh Singh
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Mark Mallott
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | | | - Andrias O'Reilly
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK.
| | - Craig S Wilding
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK.
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Carotenoids of dragonflies, from the perspective of comparative biochemical and chemical ecological studies. BIOCHEM SYST ECOL 2020. [DOI: 10.1016/j.bse.2020.104001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Julca I, Marcet-Houben M, Cruz F, Vargas-Chavez C, Johnston JS, Gómez-Garrido J, Frias L, Corvelo A, Loska D, Cámara F, Gut M, Alioto T, Latorre A, Gabaldón T. Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha. Mol Biol Evol 2020; 37:730-756. [PMID: 31702774 PMCID: PMC7038657 DOI: 10.1093/molbev/msz261] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106-227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.
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Affiliation(s)
- Irene Julca
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Carlos Vargas-Chavez
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, Valencia, Spain
| | | | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Leonor Frias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - André Corvelo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- New York Genome Center, New York, NY
| | - Damian Loska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francisco Cámara
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Department of Experimental and Health Sciences, Barcelona, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Department of Experimental and Health Sciences, Barcelona, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, Valencia, Spain
- Joint Unit in Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO) and University of Valencia, Valencia, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Department of Experimental and Health Sciences, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Li Y, Park H, Smith TE, Moran NA. Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly. Mol Biol Evol 2020; 36:2143-2156. [PMID: 31173104 PMCID: PMC6759078 DOI: 10.1093/molbev/msz138] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome structural variations, including duplications, deletions, insertions, and inversions, are central in the evolution of eukaryotic genomes. However, structural variations present challenges for high-quality genome assembly, hampering efforts to understand the evolution of gene families and genome architecture. An example is the genome of the pea aphid (Acyrthosiphon pisum) for which the current assembly is composed of thousands of short scaffolds, many of which are known to be misassembled. Here, we present an improved version of the A. pisum genome based on the use of two long-range proximity ligation methods. The new assembly contains four long scaffolds (40-170 Mb), corresponding to the three autosomes and the X chromosome of A. pisum, and encompassing 86% of the new assembly. Assembly accuracy is supported by several quality assessments. Using this assembly, we identify the chromosomal locations and relative ages of duplication events, and the locations of horizontally acquired genes. The improved assembly illuminates the mode of gene family evolution by providing proximity information between paralogs. By estimating nucleotide polymorphism and coverage depth from resequencing data, we determined that many short scaffolds not assembling to chromosomes represent hemizygous regions, which are especially frequent on the highly repetitive X chromosome. Aligning the X-linked aphicarus region, responsible for male wing dimorphism, to the new assembly revealed a 50-kb deletion that cosegregates with the winged male phenotype in some clones. These results show that long-range scaffolding methods can substantially improve assemblies of repetitive genomes and facilitate study of gene family evolution and structural variation.
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Affiliation(s)
- Yiyuan Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Hyunjin Park
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Thomas E Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
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Nardelli A, Vecchi M, Mandrioli M, Manicardi GC. The Evolutionary History and Functional Divergence of Trehalase ( treh) Genes in Insects. Front Physiol 2019; 10:62. [PMID: 30828300 PMCID: PMC6384254 DOI: 10.3389/fphys.2019.00062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/21/2019] [Indexed: 01/04/2023] Open
Abstract
Trehalases (treh) have been found in different organisms, such as bacteria, fungi, yeast, nematodes, insects, vertebrates, and plants. Their biochemical properties are extremely variable and not yet fully understood. Gene expression patterns have shown differences among insect species suggesting a potential functional diversification of trehalase enzymes during their evolution. A second gene family encoding for enzymes with hypothetical trehalase activity has been repeatedly annotated in insect genome as acid trehalases/acid trehalase-like (ath), but its functional role is still not clear. The currently available large amount of genomic data from many insect species may enable a better understanding of the evolutionary history, phylogenetic relationships and possible roles of trehalase encoding genes in this taxon. The aim of the present study is to infer the evolutionary history of trehalases and acid trehalase genes in insects and analyze the trehalase functional divergence during their evolution, combining phylogenetic and genomic synteny/colinearity analyses.
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Affiliation(s)
- Andrea Nardelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Matteo Vecchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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A small set of differentially expressed genes was associated with two color morphs in natural populations of the pea aphid Acyrthosiphon pisum. Gene 2018; 651:23-32. [DOI: 10.1016/j.gene.2018.01.079] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/09/2018] [Accepted: 01/23/2018] [Indexed: 12/11/2022]
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Avalos J, Pardo-Medina J, Parra-Rivero O, Ruger-Herreros M, Rodríguez-Ortiz R, Hornero-Méndez D, Limón MC. Carotenoid Biosynthesis in Fusarium. J Fungi (Basel) 2017; 3:E39. [PMID: 29371556 PMCID: PMC5715946 DOI: 10.3390/jof3030039] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 01/06/2023] Open
Abstract
Many fungi of the genus Fusarium stand out for the complexity of their secondary metabolism. Individual species may differ in their metabolic capacities, but they usually share the ability to synthesize carotenoids, a family of hydrophobic terpenoid pigments widely distributed in nature. Early studies on carotenoid biosynthesis in Fusariumaquaeductuum have been recently extended in Fusarium fujikuroi and Fusarium oxysporum, well-known biotechnological and phytopathogenic models, respectively. The major Fusarium carotenoid is neurosporaxanthin, a carboxylic xanthophyll synthesized from geranylgeranyl pyrophosphate through the activity of four enzymes, encoded by the genes carRA, carB, carT and carD. These fungi produce also minor amounts of β-carotene, which may be cleaved by the CarX oxygenase to produce retinal, the rhodopsin's chromophore. The genes needed to produce retinal are organized in a gene cluster with a rhodopsin gene, while other carotenoid genes are not linked. In the investigated Fusarium species, the synthesis of carotenoids is induced by light through the transcriptional induction of the structural genes. In some species, deep-pigmented mutants with up-regulated expression of these genes are affected in the regulatory gene carS. The molecular mechanisms underlying the control by light and by the CarS protein are currently under investigation.
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Affiliation(s)
- Javier Avalos
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain.
| | - Javier Pardo-Medina
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain.
| | - Obdulia Parra-Rivero
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain.
| | - Macarena Ruger-Herreros
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain.
| | - Roberto Rodríguez-Ortiz
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain.
- Present Address: CONACYT-Instituto de Neurobiología-UNAM, Juriquilla, Querétaro 076230, Mexico.
| | - Dámaso Hornero-Méndez
- Departamento de Fitoquímica de los Alimentos, Instituto de la Grasa, CSIC, Campus Universidad Pablo de Olavide, 41013 Sevilla, Spain.
| | - María Carmen Limón
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain.
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