Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources

Detalhes bibliográficos
Autor(a) principal: Rodrigues, Ana Clara B.
Data de Publicação: 2016
Outros Autores: Silva, Sara E., Pina-Martins, Francisco, Loureiro, João, Castro, Mariana, Gharbi, Karim, Johnson, Kevin P., Dietrich, Christopher H., Borges, Paulo A. V., Quartau, José A., Jiggins, Chris D., Paulo, Octávio S., Seabra, Sofia G.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10316/108497
https://doi.org/10.1186/s12863-016-0455-5
Resumo: Background: Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes underlying phenotypic evolution. The meadow spittlebug, Philaenus spumarius (L.) (Hemiptera, Aphrophoridae), a widespread insect species in the Holarctic region, exhibits a striking dorsal colour/pattern balanced polymorphism. Although experimental crosses have revealed the Mendelian inheritance of this trait, its genetic basis remains unknown. In this study we aimed to identify candidate genomic regions associated with the colour balanced polymorphism in this species. Results: By using restriction site-associated DNA (RAD) sequencing we were able to obtain a set of 1,837 markers across 33 individuals to test for associations with three dorsal colour phenotypes (typicus, marginellus, and trilineatus). Single and multi-association analyses identified a total of 60 SNPs associated with dorsal colour morphs. The genome size of P. spumarius was estimated by flow cytometry, revealing a 5.3 Gb genome, amongst the largest found in insects. A partial genome assembly, representing 24% of the total size, and an 81.4 Mb transcriptome, were also obtained. From the SNPs found to be associated with colour, 35% aligned to the genome and 10% to the transcriptome. Our data suggested that major loci, consisting of multi-genomic regions, may be involved in dorsal colour variation among the three dorsal colour morphs analysed. However, no homology was found between the associated loci and candidate genes known to be responsible for coloration pattern in other insect species. The associated markers showed stronger differentiation of the trilineatus colour phenotype, which has been shown previously to be more differentiated in several life-history and physiological characteristics as well. It is possible that colour variation and these traits are linked in a complex genetic architecture. Conclusions: The loci detected to have an association with colour and the genomic and transcriptomic resources developed here constitute a basis for further research on the genetic basis of colour pattern in the meadow spittlebug P. spumarius.
id RCAP_64e98593baf9b58ce02cb5ca9d6ae5d7
oai_identifier_str oai:estudogeral.uc.pt:10316/108497
network_acronym_str RCAP
network_name_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository_id_str 7160
spelling Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resourcesAssociation studyColour polymorphismde novo genome assemblyde novo transcriptome assemblyMeadow spittlebugAnimalsGene Expression ProfilingGenetic Association StudiesGenome SizeGenomicsHemipteraInsect ProteinsPhylogenyPolymorphism, Single NucleotideSkin PigmentationQuantitative Trait LociBackground: Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes underlying phenotypic evolution. The meadow spittlebug, Philaenus spumarius (L.) (Hemiptera, Aphrophoridae), a widespread insect species in the Holarctic region, exhibits a striking dorsal colour/pattern balanced polymorphism. Although experimental crosses have revealed the Mendelian inheritance of this trait, its genetic basis remains unknown. In this study we aimed to identify candidate genomic regions associated with the colour balanced polymorphism in this species. Results: By using restriction site-associated DNA (RAD) sequencing we were able to obtain a set of 1,837 markers across 33 individuals to test for associations with three dorsal colour phenotypes (typicus, marginellus, and trilineatus). Single and multi-association analyses identified a total of 60 SNPs associated with dorsal colour morphs. The genome size of P. spumarius was estimated by flow cytometry, revealing a 5.3 Gb genome, amongst the largest found in insects. A partial genome assembly, representing 24% of the total size, and an 81.4 Mb transcriptome, were also obtained. From the SNPs found to be associated with colour, 35% aligned to the genome and 10% to the transcriptome. Our data suggested that major loci, consisting of multi-genomic regions, may be involved in dorsal colour variation among the three dorsal colour morphs analysed. However, no homology was found between the associated loci and candidate genes known to be responsible for coloration pattern in other insect species. The associated markers showed stronger differentiation of the trilineatus colour phenotype, which has been shown previously to be more differentiated in several life-history and physiological characteristics as well. It is possible that colour variation and these traits are linked in a complex genetic architecture. Conclusions: The loci detected to have an association with colour and the genomic and transcriptomic resources developed here constitute a basis for further research on the genetic basis of colour pattern in the meadow spittlebug P. spumarius.Springer Nature2016-11-15info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://hdl.handle.net/10316/108497http://hdl.handle.net/10316/108497https://doi.org/10.1186/s12863-016-0455-5eng1471-2156Rodrigues, Ana Clara B.Silva, Sara E.Pina-Martins, FranciscoLoureiro, JoãoCastro, MarianaGharbi, KarimJohnson, Kevin P.Dietrich, Christopher H.Borges, Paulo A. V.Quartau, José A.Jiggins, Chris D.Paulo, Octávio S.Seabra, Sofia G.info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-08-30T10:48:30Zoai:estudogeral.uc.pt:10316/108497Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T21:24:47.235890Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
title Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
spellingShingle Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
Rodrigues, Ana Clara B.
Association study
Colour polymorphism
de novo genome assembly
de novo transcriptome assembly
Meadow spittlebug
Animals
Gene Expression Profiling
Genetic Association Studies
Genome Size
Genomics
Hemiptera
Insect Proteins
Phylogeny
Polymorphism, Single Nucleotide
Skin Pigmentation
Quantitative Trait Loci
title_short Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
title_full Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
title_fullStr Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
title_full_unstemmed Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
title_sort Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
author Rodrigues, Ana Clara B.
author_facet Rodrigues, Ana Clara B.
Silva, Sara E.
Pina-Martins, Francisco
Loureiro, João
Castro, Mariana
Gharbi, Karim
Johnson, Kevin P.
Dietrich, Christopher H.
Borges, Paulo A. V.
Quartau, José A.
Jiggins, Chris D.
Paulo, Octávio S.
Seabra, Sofia G.
author_role author
author2 Silva, Sara E.
Pina-Martins, Francisco
Loureiro, João
Castro, Mariana
Gharbi, Karim
Johnson, Kevin P.
Dietrich, Christopher H.
Borges, Paulo A. V.
Quartau, José A.
Jiggins, Chris D.
Paulo, Octávio S.
Seabra, Sofia G.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Rodrigues, Ana Clara B.
Silva, Sara E.
Pina-Martins, Francisco
Loureiro, João
Castro, Mariana
Gharbi, Karim
Johnson, Kevin P.
Dietrich, Christopher H.
Borges, Paulo A. V.
Quartau, José A.
Jiggins, Chris D.
Paulo, Octávio S.
Seabra, Sofia G.
dc.subject.por.fl_str_mv Association study
Colour polymorphism
de novo genome assembly
de novo transcriptome assembly
Meadow spittlebug
Animals
Gene Expression Profiling
Genetic Association Studies
Genome Size
Genomics
Hemiptera
Insect Proteins
Phylogeny
Polymorphism, Single Nucleotide
Skin Pigmentation
Quantitative Trait Loci
topic Association study
Colour polymorphism
de novo genome assembly
de novo transcriptome assembly
Meadow spittlebug
Animals
Gene Expression Profiling
Genetic Association Studies
Genome Size
Genomics
Hemiptera
Insect Proteins
Phylogeny
Polymorphism, Single Nucleotide
Skin Pigmentation
Quantitative Trait Loci
description Background: Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes underlying phenotypic evolution. The meadow spittlebug, Philaenus spumarius (L.) (Hemiptera, Aphrophoridae), a widespread insect species in the Holarctic region, exhibits a striking dorsal colour/pattern balanced polymorphism. Although experimental crosses have revealed the Mendelian inheritance of this trait, its genetic basis remains unknown. In this study we aimed to identify candidate genomic regions associated with the colour balanced polymorphism in this species. Results: By using restriction site-associated DNA (RAD) sequencing we were able to obtain a set of 1,837 markers across 33 individuals to test for associations with three dorsal colour phenotypes (typicus, marginellus, and trilineatus). Single and multi-association analyses identified a total of 60 SNPs associated with dorsal colour morphs. The genome size of P. spumarius was estimated by flow cytometry, revealing a 5.3 Gb genome, amongst the largest found in insects. A partial genome assembly, representing 24% of the total size, and an 81.4 Mb transcriptome, were also obtained. From the SNPs found to be associated with colour, 35% aligned to the genome and 10% to the transcriptome. Our data suggested that major loci, consisting of multi-genomic regions, may be involved in dorsal colour variation among the three dorsal colour morphs analysed. However, no homology was found between the associated loci and candidate genes known to be responsible for coloration pattern in other insect species. The associated markers showed stronger differentiation of the trilineatus colour phenotype, which has been shown previously to be more differentiated in several life-history and physiological characteristics as well. It is possible that colour variation and these traits are linked in a complex genetic architecture. Conclusions: The loci detected to have an association with colour and the genomic and transcriptomic resources developed here constitute a basis for further research on the genetic basis of colour pattern in the meadow spittlebug P. spumarius.
publishDate 2016
dc.date.none.fl_str_mv 2016-11-15
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10316/108497
http://hdl.handle.net/10316/108497
https://doi.org/10.1186/s12863-016-0455-5
url http://hdl.handle.net/10316/108497
https://doi.org/10.1186/s12863-016-0455-5
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1471-2156
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
_version_ 1799134131456573440