Table 1.
Key statistics and sequencing platforms for salmon louse assemblies available March 2021.
| Assemblies and accession details | Assembly level | Louse origin | Size (Mbps) | N50 (Kbps) | Sequencing platform (s) | Depth | Reference |
|---|---|---|---|---|---|---|---|
| UVic_Lsal_1.0 GCA_016086655.1 | Chromosome | Pacific | 668.1 | 48,457 | Oxford Nanopore, Illumina | 45X | Database only*** |
|
UStir_LSAA PRJEB43242 |
Chromosome | Atlantic |
632.5 609.3* |
5100 43,017** |
PacBio | 107** | Database only*** |
| LSalAtl2S licebase.org | Scaffold | Atlantic | 695.4 | 478 | Illumina HiSeq, 454, Sanger fosmid end | 175X | 41 |
| Atlantic female GCA_001005205.1 | Scaffold | Atlantic | 665.1 | 16 | Illumina HiSeq | 45X | Database only*** |
| Atlantic male GCA_001005235.1 | Scaffold | Atlantic | 665.3 | 13 | Illumina HiSeq | 55X | Database only*** |
| ASM18125v2 GCA_000181255.2 | Scaffold | Pacific | 790.1 | 10 | Illumina, 454 | 88X | 42 |
Depths of sequencing coverage are the values associated with the assemblies and are estimated based on assembly-indicated genome sizes (i.e. ≈700 Mbps). The ASM18125v2 assembly is quite fragmented and the authors indicate that the assembly overestimates the actual size suggested to be around 600 Mbps (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA40179). Only LSalAtl2s is extensively assessed and the predicted gene set appears to be quite complete as it contains 92.4% of the expected genes in a BUSCO analysis and maps ≈ 90% of transcriptome reads48,49.
*The UStir_LSAA assembly comprised 158 sequences in total, 15 of which were identified as chromosomes. The value denoted ‘*’ is the assembly size for these 15 chromosomes.
**Calculated based on the 632.5 Mbp assembly size.
***Data available in public repositories were included with permission from the assembly authors in adherence to the Fort Lauderdale agreement50.