Table 1 Predicted orthology relationships by sequence comparison of all Hox genes reported to date in different lamprey species to infer the condition of the LCA of lampreys
PG | Lamprey Hox Gene | Petromyzon marinus | Lethenteron japonicum | Lampetra planeri | GenBank Acc. No | |||
|---|---|---|---|---|---|---|---|---|
Pendleton et al.[59] | Irvine et al.[63] | Smith et al.[67] | Sharman et al.[64] | |||||
1 | Hox1α | Pm27-a | LpHox1A (5 nt different: syn) | L14893; AF044797 | ||||
Hox1β | Pm6-b* | 1w | 1B | Pm2Hox1w (5 nt, 3 aa different; 3 nt del.) | LjHox1w | LpHox1B (Identical) | L14902; AF434665; AB286671; AF044798 | |
Hox1y | Pm87-c | PmHox1 (1 nt, 1 aa different) | L14908; ENSPMAT00000011284 (Ensembl) | |||||
Hox1δ | Pm62-d* | LpHox1C (4 nt different: syn) | L14904; AF044799 | |||||
2 | Hox2α | Pm6-e | E2 | Pm1Hox2 | L14890; AF410908; JQ706314 | |||
Hox2β | LjHox2 (5 nt different from E2) | LpHox2A (Identical to LjHox2) | AY497314; AF044800 | |||||
3*** | Hox3α | 3 | Pm1Hox3 | LjHox3d | AF410909; AB125270; JQ706315 | |||
Hox3β | LpHox3A | AF044801 | ||||||
4 | Hox4α | Pm33-n** | 4w | Pm1Hox4w | LjHox4w (1nt different from 4w) | LpHox4-7B (1 nt different from 4w) | L14896; AF434666; AB125269; AF044803; JQ706316 | |
Hox4β | Pm2Hox4 | JQ706323 | ||||||
Hox4γ | Pm2-i | 4x | LjHox4x | LpHox4-7E (3 nt, 1 aa different) | L14891; AY056469; AB125278; AF044806 | |||
Hox4δ | Pm99-g | 4y | G4 | L14912; AF410911 | ||||
Hox4ϵ | Pm88-h | L14909 | ||||||
5-7*** | Hox5α | N5 | Pm1Hox5 (1nt, 1aa different) | AF410915; JQ706317 | ||||
Hox6α | Pm33-n** | 6w (1nt different: syn) | N6 | Pm1Hox6 | LjHox6w (4nt different from N6/Hox6: syn) | L14896; AF071235; AF410916; AB125275; JQ706318 | ||
Hox7α | N7 | Pm1Hox7 | AF410917; JQ706319 | |||||
Hox5β | Pm63-l | 51 | L5/6 | Pm2Hox5 | L14905; AF410914; JQ706324 | |||
Hox7β | Pm4-k | 83 | K6/7 | Pm2Hox7 | LjHox6/7m (3 nt different from K6/7: syn) | LpHox4-7C (1 nt different from LjHox6/7m: syn) | L14897; AF410913; AB125272; AF044804 | |
Hox5-7γ | Pm22-f | 31 | F5/6/7 | PmHox7 | LpHox4-7D (3 nt different: syn) | L14892; AF410910; AF044805; ENSPMAT00000011116 (Ensembl) | ||
Hox5-7δ | Pm54.T7m | L14899 | ||||||
Hox5-7ϵ | Pm66-j | 5w | J5/6/7 | LjHox5w (1 nt different: syn) | LpHox4-7A (Identical to LjHox5w) | L14906; AF071234; AF410912; AB125277; AF044802 | ||
Hox5-7ζ | Pm74-o | LjHox5i (2 nt different) | L14907; AB125276 | |||||
Hox5-7η | Pm50-p | L14898 | ||||||
8 | Hox8α | Pm57-q | Q8 | Pm1Hox8Q (4 nt, 1 aa different; 6 nt del.) | LjHoxQ8 (4nt different from Hox8: syn) | L14901; AH005896; AB125274; JQ706320 | ||
Hox8β | Q8a | Pm2Hox8Qb | AF035589; JQ706325 | |||||
Hox8γ | Pm60-r | R8 | PmHox8 (2 nt different: syn) | LpHox8A (3 nt different: syn) | L14903; AF035588; AF044807; ENSPMAT00000005057 (Ensembl) | |||
Hox8δ | LjHox8p (7 nt, 2 aa different from Q8a) | AB125273 | ||||||
9 | Hox9α | Pm28-v | 9y | V9 | Pm1Hox9 (6 nt, 2 aa different) | L14889; AF410919; JQ706321 | ||
Hox9β | Pm29-t | 9w | T9 | Pm2Hox9 (1 nt different: syn) | LjHox9r (5 nt different from T9: syn) | LpHox9B (4 nt different from T9: syn) | L14894; AF410918; AB125271; AF044810; JQ706326 | |
Hox9γ | Pm94-u | 9x | LpHox9C (3 nt different: syn) | L14910; AF044811 | ||||
Hox9δ | Pm98-s | PmHox9 (Scaffold_6175) | LpHox9A (2 nt different: syn) | L14911; AF044809; ENSPMAT00000011060 | ||||
Hox9ϵ | PmHox9 (Scaffold_16685) | ENSPMAT00000011449 (Ensembl) | ||||||
10 | Hox10α | W10b | LjHox10s (5 nt different from W10b: syn) | AF410921; AB286673 | ||||
Hox10β | P3-w | 10w | W10a | Pm2Hoxa10b | LjHoxW10a (4nt different from W10a: syn) | LpHox10B (2 nt different from W10a: syn) | L14895; AF410920; AB286672; AF044813 | |
Hox10γ | Pm56-x | X10 | L14900; AF410922 | |||||
Hox10δ | LpHox10A (5 nt, 1 aa different from X10) | AF044812 | ||||||
11 | Hox11α | *** | Z11a | Pm1Hox11 (1nt, 1aa different) | AF410924; JQ706322 | |||
Hox11β | Pm2Hox11a | ENSPMAT00000010946 (Ensembl) | ||||||
Hox11γ | *** | 11w | Y11 | AF410923 | ||||
Hox11δ | Z11b | AF410925 | ||||||
Hox11ϵ | LjHox11t | AB286674 | ||||||
13 | Hox13α | LjHox13α | LpHox13A | AB293597; AF044814 | ||||
Hox13β | PmHox13β | LjHox13β | AB293598; ENSPMAT00000000840 (Ensembl) | |||||
14 | Hox14α | LjHox14α | AB293599 | |||||