Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum
Abstract Background The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, le...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-11-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-6240-x |
| _version_ | 1818437004609716224 |
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| author | Íria Gabriela Dias dos Santos Tiago Antônio de Oliveira Mendes Gerluza Aparecida Borges Silva Amanda Maria Sena Reis Cláudia Barros Monteiro-Vitorello Patricia Dayane Carvalho Schaker Roberto Hirochi Herai André Brait Carneiro Fabotti Luiz Lehmann Coutinho Erika Cristina Jorge |
| author_facet | Íria Gabriela Dias dos Santos Tiago Antônio de Oliveira Mendes Gerluza Aparecida Borges Silva Amanda Maria Sena Reis Cláudia Barros Monteiro-Vitorello Patricia Dayane Carvalho Schaker Roberto Hirochi Herai André Brait Carneiro Fabotti Luiz Lehmann Coutinho Erika Cristina Jorge |
| author_sort | Íria Gabriela Dias dos Santos |
| collection | DOAJ |
| description | Abstract Background The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also contribute to the understanding of the molecular mechanisms that govern the different stages of organogenesis. Opossum joeys are born after only 13 days, and the final stages of organogenesis occur when the neonates are inside the pouch, depending on lactation. As neither the genome of this opossum species nor its transcriptome has been completely sequenced, the use of D. albiventris as an animal model is limited. In this work, we sequenced the D. albiventris transcriptome by RNA-seq to obtain the first catalogue of differentially expressed (DE) genes and gene ontology (GO) annotations during the neonatal stages of marsupial development. Results The D. albiventris transcriptome was obtained from whole neonates harvested at birth (P0), at 5 days of age (P5) and at 10 days of age (P10). The de novo assembly of these transcripts generated 85,338 transcripts. Approximately 30% of these transcripts could be mapped against the amino acid sequences of M. domestica, the evolutionarily closest relative of D. albiventris to be sequenced thus far. Among the expressed transcripts, 2077 were found to be DE between P0 and P5, 13,780 between P0 and P10, and 1453 between P5 and P10. The enriched GO terms were mainly related to the immune system, blood tissue development and differentiation, vision, hearing, digestion, the CNS and limb development. Conclusions The elucidation of opossum transcriptomes provides an out-group for better understanding the distinct characteristics associated with the evolution of mammalian species. This study provides the first transcriptome sequences and catalogue of genes for a marsupial species at different neonatal stages, allowing the study of the mechanisms involved in organogenesis. |
| first_indexed | 2024-12-14T17:17:47Z |
| format | Article |
| id | doaj.art-302ad4a8c16a4fa1b2e6abbbf4a25cf5 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T17:17:47Z |
| publishDate | 2019-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-302ad4a8c16a4fa1b2e6abbbf4a25cf52022-12-21T22:53:24ZengBMCBMC Genomics1471-21642019-11-0120112010.1186/s12864-019-6240-xDidelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossumÍria Gabriela Dias dos Santos0Tiago Antônio de Oliveira Mendes1Gerluza Aparecida Borges Silva2Amanda Maria Sena Reis3Cláudia Barros Monteiro-Vitorello4Patricia Dayane Carvalho Schaker5Roberto Hirochi Herai6André Brait Carneiro Fabotti7Luiz Lehmann Coutinho8Erika Cristina Jorge9Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisDepartamento de Bioquímica e Biologia Molecular, Universidade Federal de ViçosaDepartamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisDepartamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisDepartamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São PauloDepartamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São PauloGraduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR)Centro Federal de Educação Tecnológica de Minas GeraisDepartamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São PauloDepartamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisAbstract Background The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also contribute to the understanding of the molecular mechanisms that govern the different stages of organogenesis. Opossum joeys are born after only 13 days, and the final stages of organogenesis occur when the neonates are inside the pouch, depending on lactation. As neither the genome of this opossum species nor its transcriptome has been completely sequenced, the use of D. albiventris as an animal model is limited. In this work, we sequenced the D. albiventris transcriptome by RNA-seq to obtain the first catalogue of differentially expressed (DE) genes and gene ontology (GO) annotations during the neonatal stages of marsupial development. Results The D. albiventris transcriptome was obtained from whole neonates harvested at birth (P0), at 5 days of age (P5) and at 10 days of age (P10). The de novo assembly of these transcripts generated 85,338 transcripts. Approximately 30% of these transcripts could be mapped against the amino acid sequences of M. domestica, the evolutionarily closest relative of D. albiventris to be sequenced thus far. Among the expressed transcripts, 2077 were found to be DE between P0 and P5, 13,780 between P0 and P10, and 1453 between P5 and P10. The enriched GO terms were mainly related to the immune system, blood tissue development and differentiation, vision, hearing, digestion, the CNS and limb development. Conclusions The elucidation of opossum transcriptomes provides an out-group for better understanding the distinct characteristics associated with the evolution of mammalian species. This study provides the first transcriptome sequences and catalogue of genes for a marsupial species at different neonatal stages, allowing the study of the mechanisms involved in organogenesis.http://link.springer.com/article/10.1186/s12864-019-6240-xDidelphis albiventrisWhite-eared opossumRNA-seqTranscriptomeNewbornPostnatal |
| spellingShingle | Íria Gabriela Dias dos Santos Tiago Antônio de Oliveira Mendes Gerluza Aparecida Borges Silva Amanda Maria Sena Reis Cláudia Barros Monteiro-Vitorello Patricia Dayane Carvalho Schaker Roberto Hirochi Herai André Brait Carneiro Fabotti Luiz Lehmann Coutinho Erika Cristina Jorge Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum BMC Genomics Didelphis albiventris White-eared opossum RNA-seq Transcriptome Newborn Postnatal |
| title | Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum |
| title_full | Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum |
| title_fullStr | Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum |
| title_full_unstemmed | Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum |
| title_short | Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum |
| title_sort | didelphis albiventris an overview of unprecedented transcriptome sequencing of the white eared opossum |
| topic | Didelphis albiventris White-eared opossum RNA-seq Transcriptome Newborn Postnatal |
| url | http://link.springer.com/article/10.1186/s12864-019-6240-x |
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