De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata)

Journal article


Ibeh, Neke, Feigin, Charles Y., Frankenberg, Stephen R., McCarthy, Davis J., Pask, Andrew J. and Gallego Romero, Irene. (2024). De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata). GigaByte. 2024, pp. 1-16. https://doi.org/10.46471/gigabyte.118
AuthorsIbeh, Neke, Feigin, Charles Y., Frankenberg, Stephen R., McCarthy, Davis J., Pask, Andrew J. and Gallego Romero, Irene
Abstract

Marsupials exhibit distinctive modes of reproduction and early development that set them apart from their eutherian counterparts and render them invaluable for comparative studies. However, marsupial genomic resources still lag far behind those of eutherian mammals. We present a series of novel genomic resources for the fat-tailed dunnart (Sminthopsis crassicaudata), a mouse-like marsupial that, due to its ease of husbandry and ex-utero development, is emerging as a laboratory model. We constructed a highly representative multi-tissue de novo transcriptome assembly of dunnart RNA-seq reads spanning 12 tissues. The transcriptome includes 2,093,982 assembled transcripts and has a mammalian transcriptome BUSCO completeness score of 93.3%, the highest amongst currently published marsupial transcriptomes. This global transcriptome, along with ab initio predictions, supported annotation of the existing dunnart genome, revealing 21,622 protein-coding genes. Altogether, these resources will enable wider use of the dunnart as a model marsupial and deepen our understanding of mammalian genome evolution.

Keywordsgenetics and genomics; bioinformatics; evolutionary biology
Year2024
JournalGigaByte
Journal citation2024, pp. 1-16
PublisherGigaScience Press
ISSN2709-4715
Digital Object Identifier (DOI)https://doi.org/10.46471/gigabyte.118
PubMed ID38746537
Scopus EID2-s2.0-85193749622
PubMed Central IDPMC11091235
Open accessPublished as ‘gold’ (paid) open access
Page range1-16
FunderAustralian Research Council (ARC)
European Union Horizon 2020
European Regional Development Fund (FEDER)
Publisher's version
License
File Access Level
Open
Output statusPublished
Publication dates
Online02 May 2024
Publication process dates
Accepted13 Apr 2024
Deposited07 Apr 2025
Grant IDDP210102645
810645
MOBEC008
Additional information

Copyright © The Author(s) 2024. Published by GigaScience Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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