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).
The genomic position of each locus in the X. tropicalis v9 and v10 are indicated, with the chromosome or scaffold followed by a range of genomic coordinates. For each group, the number of males and females sequenced are separated by slashes, followed by whether a male-specific SNP was detected (Y) or not (N); “NV” indicates no variation in the sequences. A dash indicates that the amplification was not attempted or that Sanger sequences were not clean. For two loci from the Family 2, an asterisk indicates that 4/5 males had a male-specific SNP and in both of these amplicons, the same male individual did not have this SNP; thus variants at these loci were almost but not completely sex-linked.
| 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.