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] | Amores et al. [60] / Force et al. [62] | Irvine et al. [63] | Smith et al. [67] | Takio et al. [65],[66] / Kuraku et al. [44] | 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 | |||||
* Just 2 nucleotides between Pm6-b and Pm62-d, but non-synonymous: probably two different genes. They also have Lampetra counterparts.
** Clone n of Pendleton et al.[59] corresponded to two different genes in Force et al.[62]: Hox4w and Hox6w.
*** Clone 139 and Hox11 clones mentioned in [63] as personal communication by W.J. Bailey, and Hox3y and Hox5x from [62], are not taken into account for lacking a published sequence.
Note: LpHox8B (AF044808) sequence from reference [64] contains two undetermined nucleotides, N, and could be orthologue of any other Hox8 gene previously identified.
Note 2: In the case of Pm2Hox1w the whole coding sequence is available to compare, and that is why is more polymorphic than other cases, whith shorter sequences to align.
Genes for which there are linkage data are shown in bold. Bold α and β genes belong to Pm1Hox and Pm2Hox clusters, respectively. See [67] and [68].
nt, nucleotides; aa, amino acids; syn, synonymous; del, deletion.