Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi17g376 . . . . . . . . Cmo13g01087 . . . . . . Cpe20g00102 . . . . . . . . . . . . . . . . . . . Lsi02g00157 Csa01g00642 Chy12g01460 Cme12g01900 . . . Bda14g00907 . Bpe15g00551 Bma03g00881 . Sed08g2159 . . Cma13g01046 Cma18g00027 Car13g00879 . . . Bhi08g01036 Tan05g2299 Cmetu12g1793 Lac10g0209 Hepe07g2420 . . Cla04g01116 Cam04g1169 Cec01g1680 Cco01g1728 Clacu04g1197 Cmu04g1176 Cre01g1475 . . . .
Vvi17g377 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g378 . Blo16g00145 . . . Bpe13g00336 Bma06g00006 . Cmo13g01088 . . . . . . Cpe20g00101 . . . . . . . . . . . . . . . . . . . . Csa01g00641 Chy12g01461 Cme12g01901 . . . . . . . . . . . Cma13g01047 . Car13g00880 . . . Bhi08g01037 . . . . . . Cla04g01117 Cam04g1170 Cec01g1681 Cco01g1729 Clacu04g1198 Cmu04g1177 . . . . .
Vvi17g379 . . Bda06g00496 . . . . Bma12g00945 . . Cma10g00258 . Car10g00243 . . . . Bhi02g00015 . . . . . . Cla06g01495 Cam06g1649 Cec06g1709 Cco06g1707 Clacu06g1615 Cmu06g1564 Cre06g2376 . . Cone13ag0006 Cone19ag0005 . . . . . Blo15g00357 . . Bpe07g00737 . . Bma08g00253 . Cmo10g00275 . . . . . . Cpe18g00737 . . . . . . . . . . . . . . Lsi06g01359 Csa01g00353 Chy02g02390 Cme02g01775
Vvi17g380 . Blo16g00146 Bda06g00497 . . Bpe13g00335 Bma06g00007 Bma12g00946 Cmo13g01089 . Cma10g00259 . Car10g00244 . Sed08g0327 Cpe20g00100 . Bhi02g00016 Tan09g1959 Cmetu02g0820 . Hepe09g0317 . . Cla06g01496 Cam06g1650 Cec06g1710 Cco06g1708 Clacu06g1616 Cmu06g1565 Cre06g2377 . . Cone13ag0007 Cone19ag0006 Lsi02g00156 Csa01g00640 Chy12g01462 Cme12g01902 . Blo15g00356 Bda11g01789 . Bpe07g00738 Bpe15g00552 Bma03g00880 . Sed14g0142 Cmo10g00277 . Cma13g01048 . Car13g00881 . . Cpe18g00736 Bhi08g01038 Tan05g2301 Cmetu08g1010 Lac10g0205 Hepe07g2422 . . Cla04g01118 Cam04g1171 Cec01g1682 Cco01g1730 Clacu04g1199 Cmu04g1178 Cre01g1476 Lsi06g01360 Csa01g00352 Chy02g02391 Cme02g01776
Vvi17g381 . Blo16g00147 . Bda15g00650 Bpe12g00503 . . . . . Cma10g00260 . Car10g00245 . Sed08g0326 . . Bhi02g00018 Tan09g1961 Cmetu02g0654 . . . . Cla06g01497 Cam06g1651 Cec06g1711 Cco06g1709 Clacu06g1617 Cmu06g1566 Cre06g2378 . . Cone13ag0008 Cone19ag0007 . . . . . . . Bda14g00905 . Bpe15g00553 Bma03g00879 . . Cmo10g00278 . . . . . . . . . . . . . . . . . . . . . Lsi06g01361 Csa01g00351 Chy02g02392 Cme02g01777
Vvi17g382 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g383 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g384 . . . . . . . . . . . . . . . . Cpe04g01420 Bhi02g00019 Tan09g1962 . . Hepe09g0315 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi06g01363 . Chy02g02393 .
Vvi17g385 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7075644 7079243 + Bda023745.1 Bda06g00496 496
6 7080408 7081181 - Bda023746.1 Bda06g00497 497
11 52826062 52832623 + Bda008714.1 Bda11g01789 1789
14 7036190 7038851 + Bda027685.1 Bda14g00905 905
14 7041790 7044748 - Bda027687.1 Bda14g00907 907
15 9955655 9957936 + Bda012497.1 Bda15g00650 650
2 330056 334748 + XM_039023196.1 Bhi02g00015 15
2 337356 339097 - XM_039023197.1 Bhi02g00016 16
2 339243 342737 - XM_039023198.1 Bhi02g00018 18
2 390413 401352 + XM_039022943.1 Bhi02g00019 19
8 33827602 33828280 + XM_039037576.1 Bhi08g01036 1036
8 33828948 33835495 - XM_039039412.1 Bhi08g01037 1037
8 33926915 33929429 - XM_039040093.1 Bhi08g01038 1038
15 4563656 4564417 + BLOR06750 Blo15g00356 356
15 4571992 4575043 - BLOR06751 Blo15g00357 357
16 3232204 3236146 - BLOR07393 Blo16g00145 145
16 3244972 3245337 - BLOR07394 Blo16g00146 146
16 3246930 3249127 - BLOR07395 Blo16g00147 147
3 8582910 8587609 + Bma017197.1 Bma03g00879 879
3 8588710 8589495 + Bma017198.1 Bma03g00880 880
3 8622619 8623189 - Bma017200.1 Bma03g00881 881
6 207829 211774 - Bma022607.1 Bma06g00006 6
6 215755 216324 - Bma022608.1 Bma06g00007 7
8 3228300 3228722 - Bma027270.1 Bma08g00253 253
12 41352191 41355441 + Bma008287.1 Bma12g00945 945
12 41356431 41357204 - Bma008288.1 Bma12g00946 946
7 13914763 13918249 + Bpe021581.1 Bpe07g00737 737
7 13919459 13920232 - Bpe021582.1 Bpe07g00738 738
12 10867718 10872634 - Bpe005766.1 Bpe12g00503 503
13 11215128 11215907 + Bpe006462.1 Bpe13g00335 335
13 11222247 11226130 + Bpe006463.1 Bpe13g00336 336
15 16589733 16592587 + Bpe001486.2 Bpe15g00551 551
15 16593334 16594119 - Bpe001487.1 Bpe15g00552 552
15 16595219 16597886 - Bpe001488.1 Bpe15g00553 553
4 25755348 25755970 + CaPI482276_04g011690.1 Cam04g1169 1169
4 25757276 25762455 - CaPI482276_04g011700.1 Cam04g1170 1170
4 25767445 25768833 - CaPI482276_04g011710.1 Cam04g1171 1171
6 27922725 27926871 + CaPI482276_06g016490.1 Cam06g1649 1649
6 27930218 27931015 - CaPI482276_06g016500.1 Cam06g1650 1650
6 27931917 27935715 - CaPI482276_06g016510.1 Cam06g1651 1651
10 1156025 1160024 + Carg17900-RA Car10g00243 243
10 1162923 1163717 - Carg17899-RA Car10g00244 244
10 1164343 1167585 - Carg17898-RA Car10g00245 245
13 9268310 9269195 + Carg04793-RA Car13g00879 879
13 9269409 9274524 - Carg04792-RA Car13g00880 880
13 9275750 9276532 - Carg04791-RA Car13g00881 881
1 30010716 30011333 + CcPI632755_01g017280.1 Cco01g1728 1728
1 30012581 30017787 - CcPI632755_01g017290.1 Cco01g1729 1729
1 30023443 30024282 - CcPI632755_01g017300.1 Cco01g1730 1730
6 27618002 27622797 + CcPI632755_06g017070.1 Cco06g1707 1707
6 27626126 27626923 - CcPI632755_06g017080.1 Cco06g1708 1708
6 27627850 27631564 - CcPI632755_06g017090.1 Cco06g1709 1709
1 31435443 31436066 + CePI673135_01g016800.1 Cec01g1680 1680
1 31437286 31442290 - CePI673135_01g016810.1 Cec01g1681 1681
1 31448015 31448854 - CePI673135_01g016820.1 Cec01g1682 1682
6 30670025 30674791 + CePI673135_06g017090.1 Cec06g1709 1709
6 30678135 30678932 - CePI673135_06g017100.1 Cec06g1710 1710
6 30679842 30683472 - CePI673135_06g017110.1 Cec06g1711 1711
2 27693635 27697554 + Chy2G046570.1 Chy02g02390 2390
2 27700927 27701727 - Chy2G046580.1 Chy02g02391 2391
2 27702604 27706275 - Chy2G046590.1 Chy02g02392 2392
2 27711536 27721869 + Chy2G046600.1 Chy02g02393 2393
12 18561881 18562528 + Chy12G220600.1 Chy12g01460 1460
12 18563296 18567935 - Chy12G220610.1 Chy12g01461 1461
12 18571937 18572758 - Chy12G220620.1 Chy12g01462 1462
4 26143152 26143773 + ClG42_04g0119700.10 Clacu04g1197 1197
4 26145036 26150194 - ClG42_04g0119800.10 Clacu04g1198 1198
4 26155712 26156551 - ClG42_04g0119900.10 Clacu04g1199 1199
6 26974164 26978312 + ClG42_06g0161500.10 Clacu06g1615 1615
6 26981688 26982485 - ClG42_06g0161600.10 Clacu06g1616 1616
6 26983386 26986331 - ClG42_06g0161700.10 Clacu06g1617 1617
4 26369594 26370232 + ClCG04G011350.1 Cla04g01116 1116
4 26371353 26376653 - ClCG04G011360.2 Cla04g01117 1117
4 26382171 26383010 - ClCG04G011370.1 Cla04g01118 1118
6 28501233 28505898 + ClCG06G015110.1 Cla06g01495 1495
6 28509697 28510786 - ClCG06G015120.2 Cla06g01496 1496
6 28511397 28515542 - ClCG06G015130.2 Cla06g01497 1497
10 1147864 1151680 + CmaCh10G002580.1 Cma10g00258 258
10 1154937 1155737 - CmaCh10G002590.1 Cma10g00259 259
10 1156363 1159837 - CmaCh10G002600.1 Cma10g00260 260
13 7973924 7974685 + CmaCh13G010460.1 Cma13g01046 1046
13 7975283 7980409 - CmaCh13G010470.1 Cma13g01047 1047
13 7981602 7982390 - CmaCh13G010480.1 Cma13g01048 1048
18 104630 105199 + CmaCh18G000270.1 Cma18g00027 27
2 24628738 24633549 + MELO3C017278.2.1 Cme02g01775 1775
2 24636167 24637371 - MELO3C017277.2.1 Cme02g01776 1776
2 24637859 24641616 - MELO3C017276.2.1 Cme02g01777 1777
12 25137341 25138305 + MELO3C002068.2.1 Cme12g01900 1900
12 25138729 25143315 - MELO3C002067.2.1 Cme12g01901 1901
12 25146840 25148083 - MELO3C002066.2.1 Cme12g01902 1902
2 22971665 22974788 - PI0005811.1 Cmetu02g0654 654
2 22969999 22970799 - PI0010240.1 Cmetu02g0820 820
8 7691608 7692697 + PI0019494.1 Cmetu08g1010 1010
12 1070528 1071290 - PI0011654.1 Cmetu12g1793 1793
10 1228859 1232703 + CmoCh10G002750.1 Cmo10g00275 275
10 1235696 1236490 - CmoCh10G002770.1 Cmo10g00277 277
10 1237091 1240049 - CmoCh10G002780.1 Cmo10g00278 278
13 8985209 8985839 + CmoCh13G010870.1 Cmo13g01087 1087
13 8986171 8991732 - CmoCh13G010880.1 Cmo13g01088 1088
13 8992855 8993637 - CmoCh13G010890.1 Cmo13g01089 1089
4 26324926 26325547 + CmPI595203_04g011760.1 Cmu04g1176 1176
4 26326812 26331970 - CmPI595203_04g011770.1 Cmu04g1177 1177
4 26337480 26338319 - CmPI595203_04g011780.1 Cmu04g1178 1178
6 26876849 26880997 + CmPI595203_06g015640.1 Cmu06g1564 1564
6 26884363 26885160 - CmPI595203_06g015650.1 Cmu06g1565 1565
6 26886063 26889019 - CmPI595203_06g015660.1 Cmu06g1566 1566
13 23641 24594 + Conep13aG0000600.1 Cone13ag0006 6
13 25778 26867 - Conep13aG0000700.1 Cone13ag0007 7
13 27839 29747 - Conep13aG0000800.1 Cone13ag0008 8
19 53712 57392 + Conep19aG0000500.1 Cone19ag0005 5
19 58543 59468 - Conep19aG0000600.1 Cone19ag0006 6
19 60280 62675 - Conep19aG0000700.1 Cone19ag0007 7
4 11402890 11413537 - Cp4.1LG04g14270.1 Cpe04g01420 1420
18 7170002 7175489 + Cp4.1LG18g07250.1 Cpe18g00736 736
18 7178085 7182438 - Cp4.1LG18g07340.1 Cpe18g00737 737
20 535949 536728 + Cp4.1LG20g00930.1 Cpe20g00100 100
20 537703 542935 + Cp4.1LG20g00980.1 Cpe20g00101 101
20 543297 543924 - Cp4.1LG20g01030.1 Cpe20g00102 102
1 27973521 27974141 + CrPI670011_01g014750.1 Cre01g1475 1475
1 27975393 27987179 - CrPI670011_01g014760.1 Cre01g1476 1476
6 31687201 31691330 + CrPI670011_06g023760.1 Cre06g2376 2376
6 31694618 31695817 - CrPI670011_06g023770.1 Cre06g2377 2377
6 31696333 31699981 - CrPI670011_06g023780.1 Cre06g2378 2378
1 2186973 2190630 + CsaV3_1G003510.1 Csa01g00351 351
1 2190689 2192460 + CsaV3_1G003520.1 Csa01g00352 352
1 2194805 2199676 - CsaV3_1G003530.1 Csa01g00353 353
1 4084242 4086065 + CsaV3_1G006400.1 Csa01g00640 640
1 4089424 4094042 + CsaV3_1G006410.1 Csa01g00641 641
1 4094426 4095658 - CsaV3_1G006420.1 Csa01g00642 642
7 68580743 68582046 + Hsped.07g24200.1 Hepe07g2420 2420
7 68596738 68598871 - Hsped.07g24220.1 Hepe07g2422 2422
9 2727937 2738797 - Hsped.09g03150.1 Hepe09g0315 315
9 2749299 2750485 + Hsped.09g03170.1 Hepe09g0317 317
10 1592920 1593759 + Lag0024250.1 Lac10g0205 205
10 1626367 1627637 - Lag0024254.1 Lac10g0209 209
2 1304562 1305401 + Lsi02G001560.1 Lsi02g00156 156
2 1310933 1311656 - Lsi02G001570.1 Lsi02g00157 157
6 24161449 24166431 + Lsi06G013590.1 Lsi06g01359 1359
6 24171038 24172557 - Lsi06G013600.1 Lsi06g01360 1360
6 24173027 24175870 - Lsi06G013610.1 Lsi06g01361 1361
6 24193743 24206296 + Lsi06G013630.1 Lsi06g01363 1363
8 1960580 1965651 + Sed0024201.1 Sed08g0326 326
8 1965787 1967121 + Sed0009707.1 Sed08g0327 327
8 35527636 35529744 - Sed0027059.1 Sed08g2159 2159
14 1563061 1565043 + Sed0001449.1 Sed14g0142 142
5 74473466 74474117 + Tan0006279.1 Tan05g2299 2299
5 74487925 74488764 - Tan0011151.1 Tan05g2301 2301
9 70488438 70490157 - Tan0005099.1 Tan09g1959 1959
9 70490188 70493603 - Tan0011146.2 Tan09g1961 1961
9 70501067 70512682 + Tan0006304.1 Tan09g1962 1962
17 4521709 4522460 + Vvi17g376 Vvi17g376 376
17 4523011 4527218 + Vvi17g377 Vvi17g377 377
17 4528655 4537653 - Vvi17g378 Vvi17g378 378
17 4537832 4549604 + Vvi17g379 Vvi17g379 379
17 4552985 4554238 - Vvi17g380 Vvi17g380 380
17 4554836 4563362 - Vvi17g381 Vvi17g381 381
17 4566358 4592434 - Vvi17g382 Vvi17g382 382
17 4601341 4613394 - Vvi17g383 Vvi17g383 383
17 4641322 4645945 + Vvi17g384 Vvi17g384 384
17 4650026 4650725 - Vvi17g385 Vvi17g385 385
       

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