Table 1 Comparison of A. japonicus genome assemblies in 2017, 2018 and 2023.
From: Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus
Year | 2017 | 2018 | 2023 |
|---|---|---|---|
Sequencing instrument | Illumina + PacBio (CLR) | Illumina + PacBio (CLR) | Illumina + Pacbio (CCS) |
# Reads | 128,784,478 | — | 10,588,443 |
# Bases (Gbp) | 260 (Illumina) + 64 (Pacbio) | 349 (Illumina) + 23 (Pacbio) | 56.54 (Illumina) + 43.22 (Pacbio) |
Coverage | 295 × (Illumina) + 73 × (Pacbio) | 346 × (Illumina) + 24 × (Pacbio) | 84 × (Illumina) + 64 × (Pacbio) |
Hi-C(Gbp) | — | — | 3.18 |
# Chromosomes | — | 22 | 23 |
Genome size (Mbp) | 804.9 | 952 | 671.6 |
# Contigs | 4,741 | 21,303 | 198 |
Contig N50 (Mbp) | 0.190 | 0.045 | 17.20 |
# Scaffolds | 3,281 | 7,286 | 34 |
Scaffold N50 (Mbp) | 0.486 | 0.196 | 29.65 |
Repeat rate (%) | 27.2 | 26.6 | 47.33 |
GC content (%) | 36.75 | 37.37 | 38.56 |
# Genes | 30,350 | 29,451 | 19,828 |
miRNAs | 137 | — | 1,066 |
tRNAs | 1,127 | — | 4,963 |
rRNAs | 75 | — | 3,379 |
snRNAs | 223 | — | 1,088 |
