Table 6 Classification of repetitive sequences and ncRNAs in the A. japonicus genome.
From: Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus
Type | Denovo + Repbase | TE Proteins | Combined TEs | ||||
|---|---|---|---|---|---|---|---|
Length(bp) | % in Genome | Length(bp) | % in Genome | Length(bp) | % in Genome | ||
DNA | 24,861,559 | 3.70 | 517,042 | 0.08 | 25,141,601 | 3.74 | |
LINE | 16,671,289 | 2.48 | 5,258,345 | 0.78 | 19,744,382 | 2.94 | |
SINE | 159,644 | 0.02 | 0 | 0 | 159,644 | 0.02 | |
LTR | 181,153,677 | 26.97 | 4,991,945 | 0.74 | 181,560,277 | 27.03 | |
Unknown | 78,711,126 | 11.72 | 0 | 0 | 78,711,126 | 11.72 | |
Total | 287,263,851 | 42.77 | 10,766,642 | 1.60 | 288,599,322 | 42.97 | |
Type | Copy number | Total length(bp) | % of genome | ||||
miRNA | 1,066 | 117,207 | 0.017451 | ||||
tRNA | 4,963 | 367,482 | 0.054714 | ||||
rRNA | rRNA | 3,379 | 421,316 | 0.062729 | |||
18 S | 558 | 130,190 | 0.019384 | ||||
28 S | 703 | 168,303 | 0.025058 | ||||
5.8 S | 86 | 7,311 | 0.001089 | ||||
5 S | 2,032 | 115,512 | 0.017198 | ||||
snRNA | snRNA | 1,088 | 142,445 | 0.021208 | |||
CD-box | 70 | 10,703 | 0.001594 | ||||
HACA-box | 12 | 2,126 | 0.000317 | ||||
splicing | 996 | 127,438 | 0.018974 | ||||
scaRNA | 4 | 661 | 0.000098 | ||||
Unknown | 6 | 1,517 | 0.00022 | ||||
