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
Vvi17g236 Blo04g00842 Blo16g00123 . Bda15g00506 Bpe12g00703 Bpe13g00370 Bma06g00058 . . . Cma10g00321 Cma11g00302 Car10g00301 Car11g00276 Sed08g2632 . Cpe04g01381 Bhi02g00121 Tan09g1843 Cmetu09g0775 . Hepe09g0374 . . Cla06g01433 Cam06g1587 Cec06g1647 Cco06g1639 Clacu06g1548 Cmu06g1503 Cre06g2312 Cone2ag0750 . . . . . . . Blo13g00177 . . . . Bpe15g00520 Bma03g00908 Bma08g00007 . Cmo10g00344 Cmo11g00305 . . . . . . . . . . . . . . . . . . . . Lsi06g01300 . . .
Vvi17g237 . Blo16g00124 . . . . Bma06g00057 . . . . . . . Sed08g0388 . Cpe04g01382 Bhi02g00120 Tan09g1844 Cmetu02g1177 . Hepe09g0373 . . . . . . . . . . . . Cone19ag0325 . . . . . . . . . . Bma03g00907 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g238 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g239 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g240 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g241 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g242 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g243 Blo04g00841 . . . . Bpe13g00369 . . . . . Cma11g00301 . Car11g00275 . . . . . . . . . . Cla06g01434 Cam06g1589 Cec06g1649 Cco06g1641 Clacu06g1550 Cmu06g1505 Cre06g2314 . . . . . . . . . . . . . Bpe15g00521 . . . Cmo10g00342 Cmo11g00304 . . . . . . . . . . . . . . . . . . . . Lsi06g01301 . . .
Vvi17g244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g245 Blo04g00840 . . . . . . . Cmo13g01037 Cmo18g00046 . . . . . Cpe20g00141 . . . . . . . . . . . . . . . Cone2ag0749 . . . Lsi02g00220 Csa01g00702 Chy12g01410 Cme12g01844 . . . . . Bpe15g00522 Bma03g00906 . Sed01g1756 . . Cma13g01001 . Car13g00835 . Cpe09g01123 . Bhi08g01275 Tan05g2212 Cmetu12g2133 Lac10g0275 Hepe07g2366 . . Cla04g01061 Cam04g1104 Cec01g1618 Cco01g1665 Clacu04g1128 Cmu04g1112 Cre01g1414 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
15 8145613 8155742 - Bda012335.2 Bda15g00506 506
2 2137359 2148623 - XM_039022638.1 Bhi02g00120 120
2 2253403 2255346 + XM_039023741.1 Bhi02g00121 121
8 39169368 39173100 - XM_039037645.1 Bhi08g01275 1275
4 9121131 9136679 - BLOR13752 Blo04g00840 840
4 9150051 9156684 - BLOR13753 Blo04g00841 841
4 9171425 9180301 + BLOR13754 Blo04g00842 842
13 6711550 6720296 - BLOR05458 Blo13g00177 177
16 2789563 2791756 - BLOR07371 Blo16g00123 123
16 2794666 2796724 + BLOR07372 Blo16g00124 124
3 9020366 9023079 - Bma030997 Bma03g00906 906
3 9028481 9031967 - Bma017232.1 Bma03g00907 907
3 9039956 9041939 + Bma030998 Bma03g00908 908
6 908315 911948 - Bma022668.1 Bma06g00057 57
6 913347 924181 + Bma022669.1 Bma06g00058 58
8 171955 182743 - Bma026998.2 Bma08g00007 7
12 12573083 12584118 + Bpe005963.1 Bpe12g00703 703
13 11449568 11451764 - Bpe006495.1 Bpe13g00369 369
13 11453677 11455959 + Bpe006496.1 Bpe13g00370 370
15 16369703 16371483 - Bpe001453.1 Bpe15g00520 520
15 16374804 16376822 + Bpe001454.1 Bpe15g00521 521
15 16377485 16380108 + Bpe001455.1 Bpe15g00522 522
4 25183706 25187235 + CaPI482276_04g011040.1 Cam04g1104 1104
6 27350680 27352250 - CaPI482276_06g015870.1 Cam06g1587 1587
6 27369984 27371686 + CaPI482276_06g015890.1 Cam06g1589 1589
10 1473315 1483401 - Carg15168-RA Car10g00301 301
11 1507749 1510835 - Carg09114-RA Car11g00275 275
11 1513273 1515367 + Carg09113-RA Car11g00276 276
13 9022513 9024579 + Carg04837-RA Car13g00835 835
1 29397680 29402252 + CcPI632755_01g016650.1 Cco01g1665 1665
6 27002697 27005446 - CcPI632755_06g016390.1 Cco06g1639 1639
6 27026886 27028587 + CcPI632755_06g016410.1 Cco06g1641 1641
1 30834404 30837920 + CePI673135_01g016180.1 Cec01g1618 1618
6 30075212 30077504 - CePI673135_06g016470.1 Cec06g1647 1647
6 30094327 30096028 + CePI673135_06g016490.1 Cec06g1649 1649
12 18192493 18197522 + Chy12G220100.1 Chy12g01410 1410
4 25554806 25559714 + ClG42_04g0112800.10 Clacu04g1128 1128
6 26407048 26408618 - ClG42_06g0154800.10 Clacu06g1548 1548
6 26426022 26427724 + ClG42_06g0155000.10 Clacu06g1550 1550
4 25779753 25784750 + ClCG04G010780.1 Cla04g01061 1061
6 27904532 27906575 - ClCG06G014460.1 Cla06g01433 1433
6 27912394 27928511 + ClCG06G014470.2 Cla06g01434 1434
10 1460648 1471269 - CmaCh10G003210.1 Cma10g00321 321
11 1487830 1492457 - CmaCh11G003010.1 Cma11g00301 301
11 1493377 1496169 + CmaCh11G003020.1 Cma11g00302 302
13 7728758 7731796 + CmaCh13G010010.1 Cma13g01001 1001
12 24771170 24775020 + MELO3C002120.2.1 Cme12g01844 1844
2 22486326 22492816 + PI0025183.2 Cmetu02g1177 1177
9 20972954 20979704 - PI0015399.1 Cmetu09g0775 775
12 1457409 1461231 - PI0014178.1 Cmetu12g2133 2133
10 1543517 1547682 - CmoCh10G003420.1 Cmo10g00342 342
10 1551415 1561143 - CmoCh10G003440.1 Cmo10g00344 344
11 1468586 1473846 - CmoCh11G003040.1 Cmo11g00304 304
11 1476833 1478966 + CmoCh11G003050.1 Cmo11g00305 305
13 8722227 8724185 + CmoCh13G010370.1 Cmo13g01037 1037
18 297080 302740 - CmoCh18G000460.1 Cmo18g00046 46
4 25735920 25740828 + CmPI595203_04g011120.1 Cmu04g1112 1112
6 26310327 26311897 - CmPI595203_06g015030.1 Cmu06g1503 1503
6 26329292 26330994 + CmPI595203_06g015050.1 Cmu06g1505 1505
2 33288249 33294066 - Conep02aG0176600.1 Cone2ag0749 749
2 33305481 33307958 + Conep02aG0176700.1 Cone2ag0750 750
19 2596035 2601969 + Conep19aG0033600.1 Cone19ag0325 325
4 11194844 11197171 - Cp4.1LG04g13860.1 Cpe04g01381 1381
4 11197653 11202638 + Cp4.1LG04g13850.1 Cpe04g01382 1382
9 9646090 9650165 + Cp4.1LG09g11170.1 Cpe09g01123 1123
20 799336 802689 - Cp4.1LG20g01510.1 Cpe20g00141 141
1 27387910 27391445 + CrPI670011_01g014140.1 Cre01g1414 1414
6 31076650 31079510 - CrPI670011_06g023120.1 Cre06g2312 2312
6 31095478 31097270 + CrPI670011_06g023140.1 Cre06g2314 2314
1 4451569 4457422 - CsaV3_1G007020.1 Csa01g00702 702
7 68029835 68033173 + Hsped.07g23660.1 Hepe07g2366 2366
9 3310252 3320399 - Hsped.09g03730.1 Hepe09g0373 373
9 3329604 3331853 + Hsped.09g03740.1 Hepe09g0374 374
10 2095234 2098075 - Lag0024320.1 Lac10g0275 275
2 1839257 1843161 - Lsi02G002200.1 Lsi02g00220 220
6 23539081 23541486 - Lsi06G013000.1 Lsi06g01300 1300
6 23551893 23558860 + Lsi06G013010.1 Lsi06g01301 1301
1 12784005 12789095 - Sed0021446.2 Sed01g1756 1756
8 2339513 2344859 - Sed0027899.3 Sed08g0388 388
8 38512257 38517037 - Sed0017304.3 Sed08g2632 2632
5 73068416 73072442 + Tan0019958.4 Tan05g2212 2212
9 69783931 69786289 - Tan0012583.1 Tan09g1843 1843
9 69796715 69803470 + Tan0003875.1 Tan09g1844 1844
17 2514164 2540954 + Vvi17g236 Vvi17g236 236
17 2544595 2556819 + Vvi17g237 Vvi17g237 237
17 2561243 2561770 - Vvi17g238 Vvi17g238 238
17 2563707 2564480 - Vvi17g239 Vvi17g239 239
17 2564536 2565055 - Vvi17g240 Vvi17g240 240
17 2565055 2565658 - Vvi17g241 Vvi17g241 241
17 2565690 2576275 - Vvi17g242 Vvi17g242 242
17 2576749 2586959 + Vvi17g243 Vvi17g243 243
17 2589882 2593611 - Vvi17g244 Vvi17g244 244
17 2596173 2605689 + Vvi17g245 Vvi17g245 245
       

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