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Fat tailed dunnart transcriptome reference files

Published on by IRENE GALLEGO ROMERO

Files associated with the fat tailed dunnart (Sminthopsis crassicaudata) transcriptome from Ibeh et al, bioRxiv, 2023.


Marsupials exhibit highly specialized patterns of reproduction and development, making them uniquely valuable for comparative genomics studies with their sister lineage, eutherian (also known as placental) mammals. However, marsupial genomic resources still lag far behind those of eutherian mammals, limiting our insight into mammalian diversity. Here, 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 \textit{ex-utero} development, is emerging as a laboratory model. To enable wider use, we have generated a multi-tissue \textit{de novo} transcriptome assembly of dunnart RNA-seq reads spanning 15 tissues. This highly representative transcriptome is comprised of 2,093,982 assembled transcripts, with a mean transcript length of 830 bp. The transcriptome mammalian BUSCO completeness score of 93% is the highest amongst all other published marsupial transcriptomes. Additionally, we report an improved fat-tailed dunnart genome assembly which is 3.23 Gb long, organized into 1,848 scaffolds, with a scaffold N50 of 72.64 Mb. The genome annotation, supported by assembled transcripts and ab initio predictions, revealed 21,622 protein-coding genes. Altogether, these resources will contribute greatly towards characterizing marsupial biology and mammalian genome evolution.


For additional info or help with contents, please contact Neke Ibeh: oibeh@student.unimelb.edu.au



CONTENTS


Dunnart_asm_12-2021_sm.fa

- The draft genome assembly of the fat-tailed dunnart. We employed a hybrid approach, which integrated ONT and PacBio long-read data with Illumina paired-end short reads.


Dunnart_asm_12-2021_sm_BUSCO_summary.txt

- BUSCO (v5.2.2) summary statistics for the draft genome assembly.


Dunnart_trinity_k29_output.Trinity.fasta

- Trinity (v2.13.2) de novo multi-tissue transcriptome assembly. We used a total of 24 dunnart RNA-seq samples, originating from the liver, testis, prostate, ovary, oviduct, uterus, eye, whole neonate, allantois, amnion, distal yolk sac, proximal yolk sac, and endometrium.


Dunnart_trinity_k29_BUSCO_summary.txt

- BUSCO (v5.2.2) summary statistics for the transcriptome assembly.


Dunnart_trinity_k29_BUSCO_fulltable.tsv

- BUSCO (v5.2.2) full output table for the transcriptome assembly.


Dunnart_trinity_k29_BUSCO_missinglist.tsv

- BUSCO (v5.2.2) list of missing IDs for the transcriptome assembly.


transcriptome_evaluation.txt

- Code and parameters used for filtering the transcriptome, evaluating transcriptome quality, ORF prediction, and transcriptome functional annotation.


reads_mapped_toTranscriptome.bam

- Alignment file of the RNA-seq reads mapped back to the reconstructed transcriptome.


DUN.CDS.fasta

- Dunnart coding sequence fasta file.


DUN.protein.fasta

- Dunnart protein fasta file.


maker_bopts.ctl

- MAKER control file specifying the parameters for the evidence aligners.


maker_opts.ctl

- MAKER control file specifying the parameters for the decision making process during gene building.


Sminthopsis_crassicaudata_1.gtf

- De novo annotation of the fat-tailed dunnart genome. Annotation of the dunnart genome was conducted using a combination of ab initio gene prediction algorithms and homology-based methods.


repeatmasker.gff3

- RepeatMasker output (for genome annotation) in gff format.


iprscan.xml

- InterProScan annotation output.


dbCAN_annotations.txt

- dbCAN annotation output.


eggNOG_and_KOG_annotations.txt

- eggNOG and KOG annotation output.


merops_annotations.txt

- MEROPS annotation output.


GO_distribution_seqs.csv

- Gene Ontology annotation distributions for Molecular Function (MF), Biological Process (BP), and Cellular Component (CC). Top 20 terms are listed for each category.


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Funding

Developing the dunnart as a marsupial model for conservation researchAustralian Research CouncilFind out more...

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