Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum

Íria Gabriela Dias Dos Santos,Patricia Dayane Carvalho Schaker,André Brait Carneiro Fabotti,Luiz Lehmann Coutinho,Tiago Antônio De Oliveira Mendes,Amanda Maria Sena Reis,Cláudia Barros Monteiro-Vitorello,Erika Cristina Jorge,Gerluza Aparecida Borges Silva,Roberto Hirochi Herai

doi:10.1186/s12864-019-6240-x

Abstract

BackgroundThe 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.ResultsThe 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.ConclusionsThe 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.

Highlights

The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America
After birth, neonates climb into the marsupium pouch, where each attaches to one of the mother’s teats, and a complex system of lactation is established while the main organogenesis stages of development take place [1,2,3,4,5,6,7,8,9,10,11,12]
The analysis of all Ribonucleic acid (RNA)-seq samples was performed; on average, over 47.5 million raw reads per library/biological replicate were obtained for each postnatal stage (Table 1) with a 100 bp paired-end fragment length

Summary

Introduction

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. 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. Marsupials are one of the three large modern groups of mammals and are considered the closest external group to eutherian mammals (placentals) They comprise a group of 350 extant species found in the Americas, mostly in South America and Australasia [1]. Marsupial neonates are in an altricial developmental stage equivalent to E10–12 of mouse embryos or 10 weeks of human development [6]

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