Description
- Assembly Name: US_GU_Lsax_2.0
- Assembly Type: Haploid
- Assembly Level: Chromosome
- Genome Representation: Full
- Accession: GCA_037325665.1
Assembly Statistics
| Statistic | Value |
|---|---|
| Assembly length (Mbp) | 1254.85 |
| GC % | 42.35 |
| Contig # | 10770 |
| Contig N50 (Mbp) | 0.27 |
| Contig L50 | 1289 |
| Contig N90 (Mbp) | 0.05 |
| Contig L90 | 5317 |
| Scaffold # | 4070 |
| Scaffold N50 (Mbp) | 67.52 |
| Scaffold L50 | 8 |
| Scaffold N90 (Mbp) | 44.90 |
| Scaffold L90 | 17 |
| Scaffolds >= 10 kb | 2924 |
| BUSCO % (mollusca_odb10), genome | C:79.2 [S:77.7, D:1.5], F:4.9, M:15.9, n:5295 |
Annotation Statistics
| Statistic | Value |
|---|---|
| Gene # | 25144 |
| Transcript # | 29761 |
| Avg exons per transcript | 7.2 |
| Avg gene length (bp) | 12995 |
| Avg transcript length (bp) | 14810 |
| Avg exon length (bp) | 218 |
| Avg intron length (bp) | 2145 |
| BUSCO % (mollusca_odb10), predicted proteins | C:82.2 [S:62.5, D:19.7], F:1.2, M:16.6, n:5295 |
Notes: Assembly statistics were calculated for the primary genome assembly GCA_037325665.1 (GCA_037325665.1_US_GU_Lsax_2.0_genomic.fna.gz) using Quast (v5.2.0; Mikheenko et al. 2018). Busco statistics (Manni et al., 2021) were taken from Supplemental Table S1 in De Jode et al. (2024). Annotation statistics were calculated for GCA_037325665.1_US_GU_Lsax_2.0_genomic.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: mollusca_odb10). See also the official BUSCO manual.
Publication(s)
The data for Littorina saxatilis displayed in the genome portal comes from:
De Jode, A., Faria, R., Formenti, G., Sims, Y., Smith, T. P., Tracey, A., Wood, J. M. D., Zagrodzka, Z. B., Johannesson, K., Butlin, R. K., & Leder, E. H. (2024). Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis. Genome Biology and Evolution, 16(4), evae076. https://doi.org/10.1093/gbe/evae076The 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 (De Jode et al. 2024) acknowledge funding by:
- The European Research Council (grant agreement number 693030),
- The Swedish Research Council VR (grant agreement numbers 2018-03695, 2020-05385, and 2021-04191)
- The European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie (grant agreement number 706376)
- The Fundação para a Ciência e a Tecnologia (2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021)
Page last updated: 15/10/2024