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Standard methods and good practices in Apis honey bee omics research

2025Journal article Open access
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datacite.subject.fosCiências Agrárias::Ciência Animal e dos Laticínios
datacite.subject.sdg03:Saúde de Qualidade
datacite.subject.sdg15:Proteger a Vida Terrestre
dc.contributor.authorTecher, Maeva A.
dc.contributor.authorChakrabarti, Priyadarshini
dc.contributor.authorCaesar, Lílian
dc.contributor.authorEynard, Sonia E.
dc.contributor.authorFarrell, M. Catherine
dc.contributor.authorFoster, Leonard J.
dc.contributor.authorGorrochategui-Ortega, June
dc.contributor.authorHenriques, Dora
dc.contributor.authorLi-Byarlay, Hongmei
dc.contributor.authorMorré, Jeffrey T.
dc.contributor.authorNewton, Irene L. G.
dc.contributor.authorParejo, Melanie
dc.contributor.authorPinto, Maria Alice
dc.contributor.authorVignal, Alain
dc.contributor.authorZarraonaindia, Iratxe
dc.contributor.authorMcAfee, Alison
dc.date.accessioned2025-06-13T15:22:27Z
dc.date.available2025-06-13T15:22:27Z
dc.date.issued2025
dc.description.abstractIn the past decades, COLOSS members have joined forces multiple times to develop and condense standard methods related to research on honey bees, their pests, pathogens, and colony products. This led to the publication of four open-access BEEBOOK volumes that have been utilized by researchers worldwide. Among the chapters, “Standard methods for molecular research in Apis mellifera,” written by Evans and collaborators in 2013, has been a cornerstone for the standardization of honey bee molecular studies. However, since sequencing technologies and analyzing algorithms have made tremendous progress, many described methods require updating. In parallel, other Apis species’ genomes have now been sequenced, thus opening new research avenues in a comparative framework. In this chapter, we add to the methods previously covered by Evans et al. in 2013 and provide updated methodology where necessary, including worked examples and bioinformatic analysis pipe-lines. We also cover topics which were not previously covered in depth, such as sequencing ancient samples, population genomics, proteomics, and sampling honey bee colony products for microbiome studies, among others. Our hope is for this to become a lasting resource for honey bee scientists as the field continues to advance.eng
dc.description.abstractEn las últimas décadas, los miembros de COLOSS han unido sus fuerzas en múltiples ocasiones para desarrollar y condensar métodos estándar relacionados con la investigación de las abejas melíferas, sus plagas, patógenos y productos apícolas. Esto ha dado lugar a la publicación de cuatro volúmenes BEEBOOK de acceso libre que han sido utilizados por investigadores de todo el mundo. Entre los capítulos, «Métodos estándar para la investigación molecular en Apis mellifera», escrito por Evans y colaboradores en 2013, ha sido una piedra angular para la estandarización de los estudios moleculares de las abejas melíferas. Sin embargo, dado que las tecnologías de secuenciación y los algoritmos de análisis han avanzado enormemente, muchos de los métodos descritos requieren una actualización. Paralelamente, se han secuenciado los genomas de otras especies de Apis, lo que abre nuevas vías de investigación en un marco comparativo. En este capítulo, revisamos los métodos previamente cubiertos por Evans et al. en 2013 y proporcionamos metodología actualizada cuando es necesario, incluyendo ejemplos trabajados y pipelines de análisis bioinformático. También cubrimos temas que antes no se trataban en profundidad, como la secuenciación de muestras antiguas, la genómica de poblaciones, la proteómica y el muestreo de productos de colonias de abejas melíferas para estudios del microbioma, entre otros. El marco de este trabajo también está disponible en forma de wiki que puede actualizarse en tiempo real a medida que se produzcan futuros avances tecnológicos. Esperamos que se convierta en un recurso duradero para los científicos de las abejas melíferas, a medida que el campo siga evolucionando.spa
dc.description.abstract在过去的几十年中, COLOSS成员多次联合开发和凝练与蜜蜂 、蜜蜂病害和蜂产 品等研究相 关的标 准方法。出版了 四本可免费浏览的BEEBOOK, 供世界各地的研究人员使 用。其中 埃文斯及合作者于 2013年撰写的一个章节"意 大利蜜蜂 分子研究的标准方 法"一直是蜜蜂 分子研究标准化的基石。然而, 由于测序技术和分析算法取得了巨大的进步, 许多描述的 方法需要更新。与 此同时, 蜜蜂属其它物种的基因组也已完成测序, 从而在比较框架下开 辟了新的研究 途径。在本章中, 我们将重温埃文斯等人在 2013 年 介绍的方法, 并在必要 时提供更新的方法, 包括工作实例和生物信息学分析管 道。我们也涵盖了 以前没 有深入 探讨的主题, 如古代样本测序、种群基因组学、蛋白质组学、微生物组研究中的蜂产品采样 等。本文的框架也可以通过维基站点获得, 并随 未来技术的进步 而实时更新。我们 希望随着该领域的不断发展, 将其做成蜜蜂科学家的一个持久性资源。cmn
dc.description.sponsorshipThe COLOSS (Prevention of honey bee (COlony LOSSes) Association aims to explain and prevent massive honey bee colony losses. It was originally funded through the COST (European Cooperation in Science and Technology) Action FA0803. The COLOSS Association is now supported by the Ricola Foundation – Nature & Culture. M.A.T.’s postdoctoral research was supported by a fellow-ship from the Japan Society for Promotion of Science (JSPS) [P19723] and by the BPRI funded by the NSF-BII award [2021795]. Am was supported by a L’Oréal-UNESCO For Women in Science Fellowship and a Project Apis m.grant. Financial support was granted to H.L.-B. by the USDA NIFA Evans-Allen funds [NI171445XXXXG004, NI201445XXXXG018-0001], a NSF-RIA award [1900793], a USDA NIFA AFRI grant [2020-67014-31557], and USDA SARE Grants [ONC19-062 and LNC21-459]. P.C.’s research was funded by the United States Department of Agriculture—Agriculture and Food Research Initiative (USDA-AFRI) and a grant from Project Apis m. D.H. was supported by the project MEDIBEES—Monitoring the Mediterranean honey bee subspecies and their resilience to climate change for the improvement of sustainable agro-ecosystems. MEDIBEES is part of the PRIMA program supported by the European Union. D.H. and M.A.P were supported by national funds from Fundação para a Ciência e a Tecnologia (FCT)/MCTES (PIDDAC) to CIMO [UIDB/00690/2020 and UIDP/00690/2020] and SusTEC [LA/P/0007/2021]. J.G. is supported by a predoctoral grant from the Department of Agriculture, Fisheries and Food of the Basque Government. J.G.’s, M.P.’s and I.Z.’s work was sup-ported by the Government of the Basque Country (Research Group IT1571-22). I.L.G.N. and L.C.’s work was supported by an NSF DBI grant [2022049] and NSF IOS grant [2005306].
dc.identifier.citationTecher, Maeva A.; Chakrabarti, Priyadarshini; Caesar, Lílian; Eynard, Sonia E.; Farrell, M. Catherine; Foster, Leonard J.; Gorrochategui-Ortega, June; Henriques, Dora; Li-Byarlay, Hongmei; Morré, Jeffrey T.; Newton, Irene L. G.; Parejo, Melanie; Pinto, Maria Alice; Vignal, Alain; Zarraonaindia, Iratxe; McAfee, Alison. (2025). Standard methods and good practices in Apis honey bee omics research. Journal of Apicultural Research. ISSN 0021-8839. 64:2, p. 307-402
dc.identifier.doi10.1080/00218839.2025.2455852
dc.identifier.eissn2078-6913
dc.identifier.issn0021-8839
dc.identifier.urihttp://hdl.handle.net/10198/34602
dc.language.isoeng
dc.peerreviewedyes
dc.publisherTaylor and Francis
dc.relationMountain Research Center
dc.relationMountain Research Center
dc.relation.ispartofJournal of Apicultural Research
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectCOLOSS
dc.subjectBEEBOOK
dc.subjectApis
dc.subjectHoney bee
dc.subjectOmics
dc.subjectStandard methods
dc.subjectProtocol
dc.titleStandard methods and good practices in Apis honey bee omics researcheng
dc.title.alternativeMétodos Estándar Y Buenas Prácticas En La Investigación Ómica De Las Abejas Del Género Apisspa
dc.title.alternative蜜蜂组学研究的标准方法和良好做法cmn
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleMountain Research Center
oaire.awardTitleMountain Research Center
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F00690%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F00690%2F2020/PT
oaire.citation.endPage402
oaire.citation.issue2
oaire.citation.startPage307
oaire.citation.titleJournal of Apicultural Research
oaire.citation.volume64
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
person.familyNameHenriques
person.familyNamePinto
person.givenNameDora
person.givenNameMaria Alice
person.identifier.ciencia-id291F-986F-07DA
person.identifier.ciencia-idF814-A1D0-8318
person.identifier.orcid0000-0001-7530-682X
person.identifier.orcid0000-0001-9663-8399
person.identifier.scopus-author-id55761737300
person.identifier.scopus-author-id8085507800
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
relation.isAuthorOfPublicationd2abd09f-a90c-4cfb-9a60-7fc32f56184d
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