High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)

Autores
Goncalves, Alejandra Lorena; García, María Victoria; Chancerel, Emilie; Lepais, Olivier; Heuertz, Myriam
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background and aims – Anadenanthera colubrina is a Neotropical native forest tree species with significant ecological importance in Seasonally Dry Tropical Forests. Developing genetic markers for this species is relevant for conservation, breeding, and evolutionary studies. Previously available genetic markers for A. colubrina consisted of a few microsatellites. Next-generation sequencing (NGS) strategies allow simple and cost-effective development of new SSR loci from lowcoverage whole genome shotgun sequencing. The main aim was to develop microsatellite markers for sequence-based high-throughput genotyping (SSRseq) in the species and to characterize their information content against traditional capillary electrophoresis-based microsatellite data by estimating the amount of molecularly accessible size homoplasy of each locus. Additionally, the reliability of these markers for population genetic analysis was assessed by genotyping two age classes (reproductively mature trees and seedlings) in a typical location in Argentina. Key results – Sixty primer pairs targeting microsatellites were designed, of which 25 were validated with allelic error rates < 3% and genotype missingness < 20%. A significantly higher number of alleles per locus and heterozygosity was detected for SSRseq considering sequence polymorphisms compared to analysing the same data based on sequence size (length) only. Size homoplasy, calculated as the proportion of mismatches between datasets relative to the number of alleles differing in length, averaged 97.85% over all SSR loci. High levels of population genetic diversity were detected in adults and seedlings from Paranaense forests, exceeding those reported in previous studies of A. colubrina using traditional SSRs. The generated datasets increase the resolution of capillary-based microsatellite genotyping, allowing for more accurate inference of eco-evolutionary processes in non-model tree species.
Fil: Goncalves, Alejandra Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; Argentina
Fil: García, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; Argentina
Fil: Chancerel, Emilie. Institut National de la Recherche Agronomique; Francia. Université de Bordeaux; Francia
Fil: Lepais, Olivier. Université de Bordeaux; Francia. Institut National de la Recherche Agronomique; Francia
Fil: Heuertz, Myriam. Institut National de la Recherche Agronomique; Francia. Université de Bordeaux; Francia
Materia
GENOTYPING
MULTIPLEX PCR
NEXT-GENERATION SEQUENCING
NUCLEAR MICROSATELLITES
SIZE HOMOPLASY
SSRSEQ
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/282859
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)Goncalves, Alejandra LorenaGarcía, María VictoriaChancerel, EmilieLepais, OlivierHeuertz, MyriamGENOTYPINGMULTIPLEX PCRNEXT-GENERATION SEQUENCINGNUCLEAR MICROSATELLITESSIZE HOMOPLASYSSRSEQhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background and aims – Anadenanthera colubrina is a Neotropical native forest tree species with significant ecological importance in Seasonally Dry Tropical Forests. Developing genetic markers for this species is relevant for conservation, breeding, and evolutionary studies. Previously available genetic markers for A. colubrina consisted of a few microsatellites. Next-generation sequencing (NGS) strategies allow simple and cost-effective development of new SSR loci from lowcoverage whole genome shotgun sequencing. The main aim was to develop microsatellite markers for sequence-based high-throughput genotyping (SSRseq) in the species and to characterize their information content against traditional capillary electrophoresis-based microsatellite data by estimating the amount of molecularly accessible size homoplasy of each locus. Additionally, the reliability of these markers for population genetic analysis was assessed by genotyping two age classes (reproductively mature trees and seedlings) in a typical location in Argentina. Key results – Sixty primer pairs targeting microsatellites were designed, of which 25 were validated with allelic error rates < 3% and genotype missingness < 20%. A significantly higher number of alleles per locus and heterozygosity was detected for SSRseq considering sequence polymorphisms compared to analysing the same data based on sequence size (length) only. Size homoplasy, calculated as the proportion of mismatches between datasets relative to the number of alleles differing in length, averaged 97.85% over all SSR loci. High levels of population genetic diversity were detected in adults and seedlings from Paranaense forests, exceeding those reported in previous studies of A. colubrina using traditional SSRs. The generated datasets increase the resolution of capillary-based microsatellite genotyping, allowing for more accurate inference of eco-evolutionary processes in non-model tree species.Fil: Goncalves, Alejandra Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; ArgentinaFil: García, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; ArgentinaFil: Chancerel, Emilie. Institut National de la Recherche Agronomique; Francia. Université de Bordeaux; FranciaFil: Lepais, Olivier. Université de Bordeaux; Francia. Institut National de la Recherche Agronomique; FranciaFil: Heuertz, Myriam. Institut National de la Recherche Agronomique; Francia. Université de Bordeaux; FranciaThe Royal Botanical Society of Belgium2025-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/282859Goncalves, Alejandra Lorena; García, María Victoria; Chancerel, Emilie; Lepais, Olivier; Heuertz, Myriam; High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae); The Royal Botanical Society of Belgium; Plant Ecology and Evolution; 158; 1; 1-2025; 43-522032-39132032-3921CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://plecevo.eu/article/138834/info:eu-repo/semantics/altIdentifier/doi/10.5091/plecevo.138834info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-08-25T14:39:47Zoai:ri.conicet.gov.ar:11336/282859instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982026-08-25 14:39:47.965CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)
title High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)
spellingShingle High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)
Goncalves, Alejandra Lorena
GENOTYPING
MULTIPLEX PCR
NEXT-GENERATION SEQUENCING
NUCLEAR MICROSATELLITES
SIZE HOMOPLASY
SSRSEQ
title_short High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)
title_full High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)
title_fullStr High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)
title_full_unstemmed High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)
title_sort High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)
dc.creator.none.fl_str_mv Goncalves, Alejandra Lorena
García, María Victoria
Chancerel, Emilie
Lepais, Olivier
Heuertz, Myriam
author Goncalves, Alejandra Lorena
author_facet Goncalves, Alejandra Lorena
García, María Victoria
Chancerel, Emilie
Lepais, Olivier
Heuertz, Myriam
author_role author
author2 García, María Victoria
Chancerel, Emilie
Lepais, Olivier
Heuertz, Myriam
author2_role author
author
author
author
dc.subject.none.fl_str_mv GENOTYPING
MULTIPLEX PCR
NEXT-GENERATION SEQUENCING
NUCLEAR MICROSATELLITES
SIZE HOMOPLASY
SSRSEQ
topic GENOTYPING
MULTIPLEX PCR
NEXT-GENERATION SEQUENCING
NUCLEAR MICROSATELLITES
SIZE HOMOPLASY
SSRSEQ
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background and aims – Anadenanthera colubrina is a Neotropical native forest tree species with significant ecological importance in Seasonally Dry Tropical Forests. Developing genetic markers for this species is relevant for conservation, breeding, and evolutionary studies. Previously available genetic markers for A. colubrina consisted of a few microsatellites. Next-generation sequencing (NGS) strategies allow simple and cost-effective development of new SSR loci from lowcoverage whole genome shotgun sequencing. The main aim was to develop microsatellite markers for sequence-based high-throughput genotyping (SSRseq) in the species and to characterize their information content against traditional capillary electrophoresis-based microsatellite data by estimating the amount of molecularly accessible size homoplasy of each locus. Additionally, the reliability of these markers for population genetic analysis was assessed by genotyping two age classes (reproductively mature trees and seedlings) in a typical location in Argentina. Key results – Sixty primer pairs targeting microsatellites were designed, of which 25 were validated with allelic error rates < 3% and genotype missingness < 20%. A significantly higher number of alleles per locus and heterozygosity was detected for SSRseq considering sequence polymorphisms compared to analysing the same data based on sequence size (length) only. Size homoplasy, calculated as the proportion of mismatches between datasets relative to the number of alleles differing in length, averaged 97.85% over all SSR loci. High levels of population genetic diversity were detected in adults and seedlings from Paranaense forests, exceeding those reported in previous studies of A. colubrina using traditional SSRs. The generated datasets increase the resolution of capillary-based microsatellite genotyping, allowing for more accurate inference of eco-evolutionary processes in non-model tree species.
Fil: Goncalves, Alejandra Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; Argentina
Fil: García, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; Argentina
Fil: Chancerel, Emilie. Institut National de la Recherche Agronomique; Francia. Université de Bordeaux; Francia
Fil: Lepais, Olivier. Université de Bordeaux; Francia. Institut National de la Recherche Agronomique; Francia
Fil: Heuertz, Myriam. Institut National de la Recherche Agronomique; Francia. Université de Bordeaux; Francia
description Background and aims – Anadenanthera colubrina is a Neotropical native forest tree species with significant ecological importance in Seasonally Dry Tropical Forests. Developing genetic markers for this species is relevant for conservation, breeding, and evolutionary studies. Previously available genetic markers for A. colubrina consisted of a few microsatellites. Next-generation sequencing (NGS) strategies allow simple and cost-effective development of new SSR loci from lowcoverage whole genome shotgun sequencing. The main aim was to develop microsatellite markers for sequence-based high-throughput genotyping (SSRseq) in the species and to characterize their information content against traditional capillary electrophoresis-based microsatellite data by estimating the amount of molecularly accessible size homoplasy of each locus. Additionally, the reliability of these markers for population genetic analysis was assessed by genotyping two age classes (reproductively mature trees and seedlings) in a typical location in Argentina. Key results – Sixty primer pairs targeting microsatellites were designed, of which 25 were validated with allelic error rates < 3% and genotype missingness < 20%. A significantly higher number of alleles per locus and heterozygosity was detected for SSRseq considering sequence polymorphisms compared to analysing the same data based on sequence size (length) only. Size homoplasy, calculated as the proportion of mismatches between datasets relative to the number of alleles differing in length, averaged 97.85% over all SSR loci. High levels of population genetic diversity were detected in adults and seedlings from Paranaense forests, exceeding those reported in previous studies of A. colubrina using traditional SSRs. The generated datasets increase the resolution of capillary-based microsatellite genotyping, allowing for more accurate inference of eco-evolutionary processes in non-model tree species.
publishDate 2025
dc.date.none.fl_str_mv 2025-01
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/282859
Goncalves, Alejandra Lorena; García, María Victoria; Chancerel, Emilie; Lepais, Olivier; Heuertz, Myriam; High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae); The Royal Botanical Society of Belgium; Plant Ecology and Evolution; 158; 1; 1-2025; 43-52
2032-3913
2032-3921
CONICET Digital
CONICET
url http://hdl.handle.net/11336/282859
identifier_str_mv Goncalves, Alejandra Lorena; García, María Victoria; Chancerel, Emilie; Lepais, Olivier; Heuertz, Myriam; High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae); The Royal Botanical Society of Belgium; Plant Ecology and Evolution; 158; 1; 1-2025; 43-52
2032-3913
2032-3921
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://plecevo.eu/article/138834/
info:eu-repo/semantics/altIdentifier/doi/10.5091/plecevo.138834
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv The Royal Botanical Society of Belgium
publisher.none.fl_str_mv The Royal Botanical Society of Belgium
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1874774412165644288
score 13.24418

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