Description
- Assembly Name: Parnassius_mnemosyne_n_2023_11
- Assembly Type: Haploid
- Assembly Level: Scaffold
- Genome Representation: Full
- Accession: GCA_963668995.1
Assembly Statistics
| Statistic | Value |
|---|---|
| Assembly length (Mbp) | 1494.39 |
| GC % | 38.04 |
| Contig # | 285 |
| Contig N50 (Mbp) | 23.93 |
| Contig L50 | 22 |
| Contig N90 (Mbp) | 4.73 |
| Contig L90 | 82 |
| Scaffold # | 169 |
| Scaffold N50 (Mbp) | 49.64 |
| Scaffold L50 | 13 |
| Scaffold N90 (Mbp) | 34.77 |
| Scaffold L90 | 27 |
| Scaffolds >= 10 kb | 168 |
| BUSCO % (lepidoptera_odb10) | C:99 [S:97.8, D:1.2], F:0.2, M:0.8, n:5286 |
Annotation Statistics
| Statistic | Value |
|---|---|
| Gene # | 22852 |
| Transcript # | 27376 |
| Average exons per transcript | 4.7 |
| Avg. gene length (bp) | 16898 |
| Avg. transcript length (bp) | 16026 |
| Avg. exon length (bp) | 343 |
| Avg. intron length (bp) | 3916 |
Notes: Assembly statistics were calculated for the primary genome assembly GCA_963668995.1 (CAVLGL01.fasta.gz) using Quast (v5.2.0; Mikheenko et al. 2018). This did not include the mitochondrial assembly (OZ075093.1). Busco statistics (Manni et al., 2021) were taken from Höglund et al. (2024) and communication with the authors. Annotation statistics were calculated for pmne_functional_edit1.gff.gz using AGAT (v1.4.1; Dainat, 2024).
BUSCO notation: C: Complete; S: Single-copy; D: Duplicated; F: Fragmented; M: Missing; n: Total BUSCO genes included in the dataset (here: lepidoptera_odb10). See also the official BUSCO manual.
Publication(s)
The data for Parnassius mnemosyne displayed in the genome portal comes from:
Höglund, J., Dias, G., Olsen, R. A., Soares, A., Bunikis, I., Talla, V., & Backström, N. (2024). A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern. Genome Biology and Evolution, 16(2), evae031. https://doi.org/10.1093/gbe/evae031The tools used by to calculate the statistics shown on top of this page are described in:
Dainat J. (2024). AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format. (Version v1.4.1). Zenodo. https://www.doi.org/10.5281/zenodo.3552717
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021). BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution, 38(10), 4647–4654. https://doi.org/10.1093/molbev/msab199
Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D., & Gurevich, A. (2018). Versatile genome assembly evaluation with QUAST-LG. Bioinformatics, 34(13), i142–i150. https://doi.org/10.1093/bioinformatics/bty266
Funding
The study in which the genome data was generated (Höglund et al. 2024) was funded by:
- Swedish Research Council (Grant number 2019-04791)
- NBIS/SciLifeLab long-term bioinformatics support
- Swedish Rescue Program for P. mnemosyne through the local administrative board (Länsstyrelsen) of Blekinge
Page last updated: 22/10/2024