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
Authors | Ibeh, Neke, Feigin, Charles Y., Frankenberg, Stephen R., McCarthy, Davis J., Pask, Andrew J. and Gallego Romero, Irene |
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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. |
Keywords | genetics and genomics; bioinformatics; evolutionary biology |
Year | 2024 |
Journal | GigaByte |
Journal citation | 2024, pp. 1-16 |
Publisher | GigaScience Press |
ISSN | 2709-4715 |
Digital Object Identifier (DOI) | https://doi.org/10.46471/gigabyte.118 |
PubMed ID | 38746537 |
Scopus EID | 2-s2.0-85193749622 |
PubMed Central ID | PMC11091235 |
Open access | Published as ‘gold’ (paid) open access |
Page range | 1-16 |
Funder | Australian Research Council (ARC) |
European Union Horizon 2020 | |
European Regional Development Fund (FEDER) | |
Publisher's version | License File Access Level Open |
Output status | Published |
Publication dates | |
Online | 02 May 2024 |
Publication process dates | |
Accepted | 13 Apr 2024 |
Deposited | 07 Apr 2025 |
Grant ID | DP210102645 |
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. |
https://acuresearchbank.acu.edu.au/item/91954/de-novo-transcriptome-assembly-and-genome-annotation-of-the-fat-tailed-dunnart-sminthopsis-crassicaudata
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Publisher's version
OA_Ibeh_2024_De_novo_transcriptome_assembly_and_genome.pdf | |
License: CC BY 4.0 | |
File access level: Open |
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