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.

Pascual-Anaya et al.

Pascual-Anaya et al. BMC Developmental Biology 2013 13:26   doi:10.1186/1471-213X-13-26

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