Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

Abstract The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Joanna Malukiewicz, Reed A. Cartwright, Jorge A. Dergam, Claudia S. Igayara, Patricia A. Nicola, Luiz M. C. Pereira, Carlos R. Ruiz-Miranda, Anne C. Stone, Daniel L. Silva, Fernanda de Fatima Rodrigues da Silva, Arvind Varsani, Lutz Walter, Melissa A. Wilson, Dietmar Zinner, Christian Roos
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4c2240396339451e82b58be088eb004b
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:4c2240396339451e82b58be088eb004b
record_format	dspace
spelling	oai:doaj.org-article:4c2240396339451e82b58be088eb004b2021-12-02T18:53:14ZGenomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates10.1038/s41598-021-96404-62045-2322https://doaj.org/article/4c2240396339451e82b58be088eb004b2021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-96404-6https://doaj.org/toc/2045-2322Abstract The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.Joanna MalukiewiczReed A. CartwrightJorge A. DergamClaudia S. IgayaraPatricia A. NicolaLuiz M. C. PereiraCarlos R. Ruiz-MirandaAnne C. StoneDaniel L. SilvaFernanda de Fatima Rodrigues da SilvaArvind VarsaniLutz WalterMelissa A. WilsonDietmar ZinnerChristian RoosNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Joanna Malukiewicz Reed A. Cartwright Jorge A. Dergam Claudia S. Igayara Patricia A. Nicola Luiz M. C. Pereira Carlos R. Ruiz-Miranda Anne C. Stone Daniel L. Silva Fernanda de Fatima Rodrigues da Silva Arvind Varsani Lutz Walter Melissa A. Wilson Dietmar Zinner Christian Roos Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates
description	Abstract The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.
format	article
author	Joanna Malukiewicz Reed A. Cartwright Jorge A. Dergam Claudia S. Igayara Patricia A. Nicola Luiz M. C. Pereira Carlos R. Ruiz-Miranda Anne C. Stone Daniel L. Silva Fernanda de Fatima Rodrigues da Silva Arvind Varsani Lutz Walter Melissa A. Wilson Dietmar Zinner Christian Roos
author_facet	Joanna Malukiewicz Reed A. Cartwright Jorge A. Dergam Claudia S. Igayara Patricia A. Nicola Luiz M. C. Pereira Carlos R. Ruiz-Miranda Anne C. Stone Daniel L. Silva Fernanda de Fatima Rodrigues da Silva Arvind Varsani Lutz Walter Melissa A. Wilson Dietmar Zinner Christian Roos
author_sort	Joanna Malukiewicz
title	Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates
title_short	Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates
title_full	Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates
title_fullStr	Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates
title_full_unstemmed	Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates
title_sort	genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/4c2240396339451e82b58be088eb004b
work_keys_str_mv	AT joannamalukiewicz genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT reedacartwright genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT jorgeadergam genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT claudiasigayara genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT patriciaanicola genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT luizmcpereira genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT carlosrruizmiranda genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT annecstone genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT daniellsilva genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT fernandadefatimarodriguesdasilva genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT arvindvarsani genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT lutzwalter genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT melissaawilson genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT dietmarzinner genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates AT christianroos genomicskimmingandnanoporesequencinguncovercryptichybridizationinoneofworldsmostthreatenedprimates
_version_	1718377324366266368

Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

Ejemplares similares