Table 1. Results of the Sanger sequencing survey of 18 amplified regions (Locus) for seven groups of X. tropicalis: a lab cross and wild individuals from west Ghana (Family1, GWwild) or east Ghana (Family2, GEwild) that were used for the RRGS data (but not the RNAseq data), and captive strains at the National Xenopus Resource from Ivory Coast (IC) and Nigeria (Nigerian and Superman).
Locus | v9 | v10 | Family1 | GWwild | Family2 | GEwild | IC | Nigerian | Superman | Notes |
---|---|---|---|---|---|---|---|---|---|---|
- | scaffold_486: 109006-109688 | Chr7: 590989-591647 | – | 3/2/N | – | 2/1/N | – | – | – | |
- | scaffold_1093: 25288-26168 | Chr7: 2401099-2401979 | – | 3/2/N | – | 4/1/N | – | – | – | |
vwa2 | scaffold_132: 209950-210334 | Chr7: 3988998-3989381 | – | 1/1/Y | – | 2/0/NV | – | – | – | a |
bag3 | scaffold_83: 134640-135403 | Chr7: 6350671-6351443 | – | – | – | 2/1/N | – | – | – | |
LOC108644867 | scaffold_130: 572284-572814 | Chr7: 7445611-7446140 | – | 3/2/NV | – | – | – | – | – | |
phc1 | scaffold_130:760304-761055 | Chr7: 7992897-7992184 | – | 2/2/N | – | 1/1/NV | – | – | – | |
LOC100488897 | scaffold_130: 643554-643884 | Chr7: 8109808-8110138 | 2/2/N | 5/5/N | 5/7/Y | 5/1/N | – | – | – | |
aicda | Chr7: 665453-665920 | Chr7: 9026686-9027153 | – | 4/3/N | – | 3/1/N | – | – | – | |
LOC116406517 | Chr7: 901880-902194 | Chr7: 9256905-9257219 | 2/2/NV | – | 5/7/N* | 1/1/Y | – | – | – | |
LOC100127624 | Chr7: 1364981-1365454 | Chr7: 9677066-9677539 | – | 4/3/N | – | 3/1/N | – | – | – | |
grp162 | Chr7: 1386997-1387487 | Chr7: 9698865-9699356 | – | 4/3/N | – | 3/1/N | – | – | – | |
LOC116412229 | Chr7:1928340-1928761 | Chr7: 10256773-10257194 | 2/2/N | 4/5/N | 5/7/N* | 3/1/Y | 3/5/N | 5/7/Y | 10/7/Y | b |
LOC116412144 | Chr7: 2045411-2045931 | Chr7: 10389186-10389706 | – | 4/3/N | – | 3/1/N | – | – | – | |
prkg1 | Chr7: 5207535-5208256 | Chr7: 13469130-13469851 | – | – | 5/7/N | 1/1/Y | – | – | – |
a: This is possibly an allele-specific amplification in some populations; no amplification occurred in several male and female individuals, and in the Ghana west population, one male sequence differed from one female sequence by 1 homozygous nucleotide; sequences from two Ghana east males were invariant and identical to the Ghana west male.
b: The same SNP was present in Superman and Nigerian males, but a different SNP was present in Ghana east males. The male-linked allele in Superman and Nigerian males amplified weakly, but consistently.