Table 1 Squam3 SINE in scaled reptiles. Major subfamilies are described by the proportion and estimated number of full-length copies, the mean sequence similarity, and the tail repeat unit. Certain parameters of genome assemblies are given in the left columns (the level column indicates the chromosome-, scaffold-, and contig-levels levels of assembly: â—•, â—‘, and â—”, respectively)
Family | Species | Squam3 SINE | Genome assembly | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
subfamily | copies | lengthw/o tail, nt | similarity | tail | level | ‘N’ | N50 | Reference | ||||
Squamata | Gekkota | Gekkonidae | Gekko japonicus | 3A (21%) | 54,829 | 224 | 60% | (TAAA)n | â—‘ | 4% | 707,733 | [14] |
3B (10%) | 26,109 | 238 | 75% | (CTT)n | ||||||||
3B3 (69%) | 180,151 | 271 | 81% | (CTT)n | ||||||||
Paroedura picta | 3A (12%) | 17,761 | 221 | 57% | (TAAA)n | â—‘ | 9% | 4,106,116 | [15] | |||
3B (19%) | 28,122 | 238 | 61% | (CTT)n | ||||||||
3B3 (57%) | 84,367 | 267 | 74% | (CTT)n | ||||||||
Eublepharidae | Eublepharis macularius | 3A (50%) | 68,299 | 224 | 60% | (TAAA)n | â—” | 2% | 663,762 | [16] | ||
3B (50%) | 63,045 | 239 | 85% | (GTT)n | ||||||||
Lacertoidea | Lacertidae | Darevskia valentini | 3A (48%) | 25,848 | 218 | 63% | (TAAA)n | â—” | 16% | 658,539 | [17] | |
3B (52%) | 28,003 | 238 | 91% | (CTT)n | ||||||||
Lacerta agilis | 3A (16%) | 17,446 | 219 | 62% | (TAAA)n | â—• | 0% | 86,565,987 | [18] | |||
3B (84%) | 91,590 | 238 | 92% | (CTT)n | ||||||||
Lacerta bilineata | 3A (39%) | 24,123 | 219 | 63% | (TAAA)n | â—” | 0% | 368,212 | [19] | |||
3B (61%) | 37,732 | 238 | 75% | (CTT)n | ||||||||
Lacerta viridis | 3A (39%) | 24,836 | 219 | 61% | (TAAA)n | â—” | 0% | 662,519 | ||||
3B (61%) | 38,847 | 238 | 94% | (CTT)n | ||||||||
Podarcis muralis | 3A (35%) | 16,967 | 220 | 61% | (TAAA)n | â—• | 0% | 92,398,148 | [20] | |||
3B (65%) | 31,440 | 238 | 88% | (CTT)n | ||||||||
Zootica vivipara | 3A (38%) | 10,036 | 220 | 61% | (TAAA)n | â—• | 3% | 92,810,032 | [21] | |||
3B (62%) | 16,374 | 238 | 89% | (CTY)n | ||||||||
Teiidae | Salvator merianae | 3A (53%) | 4892 | 221 | 54% | (TAAA)n | â—‘ | 2% | 55,382,274 | [22] | ||
3B (47%) | 4338 | 234 | 85% | (CTT)n | ||||||||
Serpentes | Colubridae | Pantherophis guttatus | 3C | 12,936 | 226 | 64% | (TAAA)n | â—‘ | 5% | 16,790,024 | [23] | |
Pantherophis obsoletus | 3C | 12,961 | 226 | 63% | (TAAA)n | â—‘ | 3% | 14,519,768 | [24] | |||
Ptyas mucosa | 3C | 19,524 | 226 | 63% | (TAAA)n | â—‘ | 3% | 15,963,960 | [25] | |||
Thamnophis elegans | 3C | 16,934 | 226 | 64% | (TAAA)n | â—• | 0% | 440,193 | [26] | |||
Thamnophis sirtalis | 3C | 12,410 | 226 | 63% | (TAAA)n | â—‘ | 21% | 647,592 | [27] | |||
Thermophis baileyi | 3C | 15,914 | 228 | 65% | (TAAA)n | â—‘ | 8% | 2,413,955 | [28] | |||
Elapidae | Emydocephalus ijimae | 3C | 15,782 | 226 | 62% | (TAAA)n | â—‘ | 0% | 18,937 | [29] | ||
Hydrophis cyanocinctus | 3C | 15,094 | 226 | 64% | (TAAA)n | â—‘ | 4% | 7437 | [30] | |||
Hydrophis hardwickii | 3C | 15,782 | 228 | 62% | (TAAA)n | â—‘ | 4% | 5391 | [31] | |||
Hydrophis melanocephalus | 3C | 14,271 | 226 | 63% | (TAAA)n | â—‘ | 11% | 59,810 | [29] | |||
Laticauda colubrina | 3C | 19,118 | 226 | 63% | (TAAA)n | â—‘ | 13% | 3,139,541 | ||||
Laticauda laticaudata | 3C | 27,835 | 226 | 61% | (TAAA)n | â—‘ | 0% | 39,330 | ||||
Naja naja | 3C | 10,813 | 226 | 64% | (TAAA)n | â—• | 6% | 224,088,900 | [32] | |||
Notechis scutatus | 3C | 27,122 | 226 | 63% | (TAAA)n | â—‘ | 5% | 5,997,050 | [33] | |||
Ophiophagus hannah | 3C | 11,613 | 226 | 63% | (TAAA)n | â—‘ | 13% | 241,519 | [34] | |||
Pseudonaja textilis | 3C | 17,187 | 226 | 65% | (TAAA)n | â—‘ | 2% | 14,685,528 | [35] | |||
Pythonidae | Python bivittatus | 3A (43%) | 9349 | 221 | 58% | (TAAA)n | â—‘ | 4% | 213,970 | [36] | ||
3C (57%) | 12,393 | 237 | 75% | (A)n | ||||||||
Viperidae | Crotalus horridus | 3C | 15,006 | 226 | 63% | (TAAA)n | â—‘ | 12% | 23,829 | [37] | ||
Crotalus pyrrhus | 3C | 15,556 | 226 | 64% | (TAAA)n | â—‘ | 0% | 5299 | [38] | |||
Crotalus viridis viridis | 3C | 18,694 | 226 | 63% | (TAAA)n | â—• | 6% | 179,897,795 | [39] | |||
Protobothrops flavoviridis | 3C | 20,667 | 226 | 64% | (TAAA)n | â—‘ | 3% | 467,050 | [40] | |||
Protobothrops mucrosquamatus | 3C | 20,184 | 228 | 64% | (TAAA)n | â—‘ | 8% | 424,052 | [41] | |||
Vipera berus berus | 3C | 19,964 | 226 | 64% | (TAAA)n | â—‘ | 14% | 126,452 | [42] | |||
Shinisauria | Shinisauridae | Shinisaurus crocodilurus | 3A | 165,288 | 225 | 58% | (TAAA)n | â—‘ | 8% | 1,469,749 | [43] | |
Anguimorpha | Anguidae | Dopasia gracilis | 3A | 35,118 | 225 | 71% | (TAAA)n | â—‘ | 3% | 1,273,270 | [44] | |
Varanoidea | Varanidae | Varanus komodoensis | 3A | 108,651 | 229 | 66% | (TAAA)n | â—‘ | 1% | 23,831,982 | [45] | |
Iguania | Agamidae | Pogona vitticeps | 3A | 4542 | 221 | 53% | (TAAA)n | â—‘ | 4% | 2,290,546 | [46] | |
Dactyloidae | Anolis carolinensis | 3A | 457 | 217 | 54% | (TAA)n | â—• | 5% | 150,641,573 | [47] | ||
Rhynchocephalia | Sphenodon punctatus | ─ | ─ | ─ | ─ | ─ | ◑ | 10% | 3,052,611 | [12] | ||
Testudines | Trachemys scripta elegans | ─ | ─ | ─ | ─ | ─ | ◕ | 1% | 147,425,149 | [48] | ||
Crocodilia | Crocodylus porosus | ─ | ─ | ─ | ─ | ─ | ◑ | 5% | 84,437,661 | [49] | ||
Aves | Gallus gallus | ─ | ─ | ─ | ─ | ─ | ◕ | 1% | 91,315,245 | [50] | ||