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. 2013 Apr 25;8(4):e56006. doi: 10.1371/journal.pone.0056006

Table 1. Male sex-determining/differentiation gene inventory.

Transcript in L. menadoensis Gene location in L. chalumnae Transcript prediction in L. chalumnae
Gene Accession Length CDS Scaffold N° exons3 Divergence4 Ka/Ks ENSEMBL accession Length CDS
AMH HF562302 13121 13122 JH126742 >5 0.046 0.000 ENSLACT00000009808 1689 16892
HF562303 10391 670
AMHR2 HF562304 693 6932 JH126659 >9 0.289 0.343 ENSLACT00000020587 921 9212
AR HF562305 2590 21332 JH126641 >8 0.165 0.000 ENSLACT00000017177 2235 12392
CYP11B - - - JH127279 - - - ENSLACT00000015536 1422 4742
DAX1 HF562306 966 786 JH128268 2 0.207 0.309 ENSLACT00000007979 786 786
DHH HF562307 926 9262 JH126563 2 0.540 0.649 ENSLACT00000021749 1275 1275
DMRT1 HF562308 2244 9982 JH127237 5 0.134 0.000 ENSLACT00000015034 798 7982
DMRT3 - - - JH127237 - - - ENSLACT00000013757 1455 1455
DMRT6 HF562309 3121 957 JH130928 4 0.129 NA ENSLACT00000003773 798 7982
FGF9 - - - JH128123 - - - Manually identified
FGF20 HF562310 370 3702 JH127134 3 0.270 NA ENSLACT00000014939 627 627
GATA-4 HF562311 1655 1200 JH128461 >6 0.064 NA ENSLACT00000007000 1209 1209
GSDF HF562312 1258 693 JH1276325 >3 0.826 0.470 - - -
PDGFα HF562313 968 594 JH126909 6 0.000 NA ENSLACT00000025036 1892 594
PDGFβ HF562314 664 4832 JH128946 >4 0.000 NA ENSLACT00000002931 630 630
PDGFRα HF562315 823 8232 JH128279 >7 0.243 NA ENSLACT00000010417 3285 32852
PDGFRβ HF562316 9951 9952 JH126585 >17 0.195 0.954 ENSLACT00000016664 3312 3312
HF562317 10551 10552
SF-1 HF562318 1686 1401 JH1265726 7 0.000 NA ENSLACT00000021404 591 5912
SOX8 HF562319 735 7352 JH126713 >3 0.000 NA ENSLACT00000019016 1434 1410
SOX9 HF562320 3306 1428 JH126581 3 0.185 0.000 ENSLACT00000021484 1908 1428
SOX10 HF562321 1403 13532 JH127309 3 0.359 0.199 ENSLACT00000005034 4571 1356
SRD5A1 HF562322 3664 786 JH129903 5 0.164 NA ENSLACT00000002047 6104 684
SRD5A2 HF562323 2711 765 JH126700 5 0.112 NA ENSLACT00000025936 2918 765
SRD5A3 HF562324 1244 945 JH127256 5 0.000 NA ENSLACT00000014423 2733 945
WT1 HF562325 2260 1257 JH126652 9 0.134 0.000 ENSLACT00000018732 1260 1257
1

Fragmented contig. 2Partial CDS. 3Number of exons from the alignment of L. menadoensis transcripts to the L. chalumnae genome. Where the transcript carries only a partial CDS, the number of exon is partial. 4Divergence between the two coelacanth sequences calculated as p-distance x100. 5The L. chalumnae GSDF gene is split between scaffold JH127632 and contig AFYH01270444. 6 The L. chalumnae SF-1 gene is split between scaffold JH126572 and contig AFYH01271535.