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
Vvi17g686 . . . . Bpe12g00578 . . . . . . . . Car11g00115 Sed08g0166 . Cpe04g01535 Bhi02g00394 Tan09g2200 Cmetu02g0643 . Hepe09g0169 . . Cla06g01635 Cam06g1818 Cec06g1868 Cco06g1874 Clacu06g1776 Cmu06g1718 Cre06g2538 . . . Cone19ag0121 . . . . . . . . . . . Bma08g00184 . . Cmo11g00122 . . . . . . . . . . . . . . . . . . . . Lsi06g01519 Csa01g00181 Chy02g02551 Cme02g01938
Vvi17g687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g688 . Blo16g00210 . . . Bpe13g00262 Bma06g00198 . Cmo13g00932 . . . . . . Cpe20g00224 . . . . . . . . . . . . . . . . Cone16ag0128 . . Lsi02g00348 Csa01g00822 Chy12g01296 Cme12g01721 . . . . . . . . Sed01g1685 . . Cma13g00906 . Car13g00745 . . . Bhi08g01454 Tan05g2041 Cmetu12g1894 Lac10g0419 Hepe07g2251 . . Cla01g01397 Cam01g1459 Cec01g1498 . Clacu01g1483 Cmu01g1378 Cre01g1293 . . . .
Vvi17g689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g690 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g691 . Blo16g00212 . . . Bpe13g00260 Bma06g00201 . . Cmo18g00115 . . . . . . . . . . . . . . . . . . . . . Cone2ag0882 . . . Lsi02g00350 Csa01g00825 Chy12g01292 Cme12g01718 . . . . . . . . Sed08g2536 . . . Cma18g00147 . Car18g00142 Cpe09g01044 . Bhi08g01456 Tan05g2039 Cmetu12g1964 Lac10g0422 Hepe07g2249 . . Cla01g01395 Cam01g1456 Cec01g1492 . Clacu01g1480 Cmu01g1375 Cre01g1291 . . . .
Vvi17g692 . . Bda06g00578 . . . . Bma12g01024 . . Cma10g00147 . Car10g00139 . Sed12g1901 . . Bhi02g00397 Tan09g2203 Cmetu02g1301 . Hepe09g0172 . . Cla06g01639 Cam06g1822 Cec06g1871 Cco06g1877 Clacu06g1781 Cmu06g1722 Cre06g2541 Cone2ag0884 . . . . . . . . Blo15g00281 . . Bpe07g00819 . . . . Cmo10g00158 . . . . . . Cpe18g00827 . . . . . . . . . . . . . . Lsi06g01522 Csa01g00178 Chy02g02554 Cme02g01941
Vvi17g693 . . . . . . . . . Cmo18g00117 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00827 Chy12g01290 Cme12g01716 . . . . . . . . Sed01g1682 . . . Cma18g00149 . Car18g00143 . . Bhi08g01458 Tan05g2037 Cmetu12g1942 . Hepe07g2247 . . Cla01g01393 Cam01g1454 Cec01g1490 . Clacu01g1478 Cmu01g1373 Cre01g1289 . . . .
Vvi17g694 Blo04g00832 . . . Bpe12g00581 Bpe13g00259 Bma06g00202 . . . Cma10g00146 Cma11g00114 Car10g00138 Car11g00113 . . Cpe04g01537 Bhi02g00399 Tan09g2205 . . . . . Cla06g01640 Cam06g1823 Cec06g1872 Cco06g1878 Clacu06g1782 Cmu06g1723 Cre06g2542 Cone2ag0885 Cone16ag0125 Cone13ag0122 Cone19ag0124 . . . . Blo13g00044 . . . . Bpe15g00529 . Bma08g00181 . Cmo10g00154 Cmo11g00118 . . . . . . . . . . . . . . . . . . . . Lsi06g01525 Csa01g00177 Chy02g02555 Cme02g01942
Vvi17g695 . . . Bda15g00572 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8026875 8032382 + Bda023840.2 Bda06g00578 578
15 8915268 8919916 + Bda012415.1 Bda15g00572 572
2 7507497 7519074 - XM_039024202.1 Bhi02g00394 394
2 7601891 7608778 + XM_039023490.1 Bhi02g00397 397
2 7610182 7616060 + XM_039022840.1 Bhi02g00399 399
8 42612809 42616464 - XM_039039052.1 Bhi08g01454 1454
8 42829148 42831129 + XM_039039013.1 Bhi08g01456 1456
8 42837740 42840080 + XM_039039127.1 Bhi08g01458 1458
4 8833973 8843761 + BLOR13744 Blo04g00832 832
13 644833 648096 + BLOR05325 Blo13g00044 44
15 3034185 3044899 - BLOR06675 Blo15g00281 281
16 4691189 4693550 - BLOR07458 Blo16g00210 210
16 4743530 4745406 + BLOR07460 Blo16g00212 212
6 2416151 2417935 - Bma031275 Bma06g00198 198
6 2442046 2443831 + Bma022815.1 Bma06g00201 201
6 2450332 2451001 + Bma022816.1 Bma06g00202 202
8 2216093 2219397 - Bma027182.2 Bma08g00181 181
8 2244442 2250110 + Bma027186.1 Bma08g00184 184
12 42343405 42353816 + Bma008373.2 Bma12g01024 1024
7 14478129 14483593 + Bpe021664.1 Bpe07g00819 819
12 11571965 11577576 - Bpe005841.1 Bpe12g00578 578
12 11587717 11589646 + Bpe005844.1 Bpe12g00581 581
13 10548626 10549646 - Bpe006382.3 Bpe13g00259 259
13 10553327 10555183 - Bpe006383.1 Bpe13g00260 260
13 10570971 10573207 + Bpe006385.1 Bpe13g00262 262
15 16449076 16456879 + Bpe001464.1 Bpe15g00529 529
1 28117099 28118853 - CaPI482276_01g014540.1 Cam01g1454 1454
1 28132638 28135241 - CaPI482276_01g014560.1 Cam01g1456 1456
1 28167161 28172487 + CaPI482276_01g014590.1 Cam01g1459 1459
6 29238618 29250248 - CaPI482276_06g018180.1 Cam06g1818 1818
6 29277373 29277621 + CaPI482276_06g018220.1 Cam06g1822 1822
6 29277835 29283248 + CaPI482276_06g018230.1 Cam06g1823 1823
10 652509 657270 - Carg10370-RA Car10g00138 138
10 658190 663358 - Carg10371-RA Car10g00139 139
11 646407 649854 - Carg18150-RA Car11g00113 113
11 660128 666132 + Carg18152-RA Car11g00115 115
13 8495657 8498207 + Carg07695-RA Car13g00745 745
18 774140 776459 + Carg06707-RA Car18g00142 142
18 780998 782012 + Carg06708-RA Car18g00143 143
6 28957113 28965997 - CcPI632755_06g018740.1 Cco06g1874 1874
6 28984404 28993931 + CcPI632755_06g018770.1 Cco06g1877 1877
6 28994145 28999320 + CcPI632755_06g018780.1 Cco06g1878 1878
1 29550827 29552509 - CePI673135_01g014900.1 Cec01g1490 1490
1 29559803 29561659 - CePI673135_01g014920.1 Cec01g1492 1492
1 29603157 29606908 + CePI673135_01g014980.1 Cec01g1498 1498
6 32017030 32028649 - CePI673135_06g018680.1 Cec06g1868 1868
6 32045709 32052579 + CePI673135_06g018710.1 Cec06g1871 1871
6 32055383 32060792 + CePI673135_06g018720.1 Cec06g1872 1872
2 28772789 28781440 - Chy2G048180.1 Chy02g02551 2551
2 28793008 28798771 + Chy2G048210.1 Chy02g02554 2554
2 28801909 28807477 + Chy2G048220.1 Chy02g02555 2555
12 17386600 17387998 - Chy12G218900.1 Chy12g01290 1290
12 17392060 17394137 - Chy12G218920.1 Chy12g01292 1292
12 17413699 17418267 + Chy12G218960.1 Chy12g01296 1296
1 26866935 26868737 - ClG42_01g0147800.10 Clacu01g1478 1478
1 26889760 26891548 - ClG42_01g0148000.10 Clacu01g1480 1480
1 26924645 26929950 + ClG42_01g0148300.10 Clacu01g1483 1483
6 28294295 28305837 - ClG42_06g0177600.10 Clacu06g1776 1776
6 28333035 28333280 + ClG42_06g0178100.10 Clacu06g1781 1781
6 28333494 28338881 + ClG42_06g0178200.10 Clacu06g1782 1782
1 28324224 28326215 - ClCG01G014080.1 Cla01g01393 1393
1 28366347 28369989 - ClCG01G014100.2 Cla01g01395 1395
1 28405418 28408785 + ClCG01G014120.2 Cla01g01397 1397
6 29867960 29879502 - ClCG06G016690.2 Cla06g01635 1635
6 29901440 29911079 + ClCG06G016740.2 Cla06g01639 1639
6 29911293 29919093 + ClCG06G016750.2 Cla06g01640 1640
10 663476 669529 - CmaCh10G001460.1 Cma10g00146 146
10 670234 675540 - CmaCh10G001470.1 Cma10g00147 147
11 614142 618131 - CmaCh11G001140.1 Cma11g00114 114
13 7255668 7261080 + CmaCh13G009060.1 Cma13g00906 906
18 756536 759490 + CmaCh18G001470.1 Cma18g00147 147
18 762977 764145 + CmaCh18G001490.1 Cma18g00149 149
2 25719452 25728617 - MELO3C017123.2.1 Cme02g01938 1938
2 25738523 25744860 + MELO3C017118.2.1 Cme02g01941 1941
2 25746744 25752841 + MELO3C017117.2.1 Cme02g01942 1942
12 23960061 23961357 - MELO3C002243.2.1 Cme12g01716 1716
12 23964744 23967062 - MELO3C002241.2.1 Cme12g01718 1718
12 23988334 23991553 + MELO3C002238.2.1 Cme12g01721 1721
2 24051490 24060496 - PI0023410.1 Cmetu02g0643 643
2 24072025 24078987 + PI0027351.2 Cmetu02g1301 1301
12 2286263 2290886 - PI0003298.1 Cmetu12g1894 1894
12 2319022 2321108 + PI0019324.1 Cmetu12g1942 1942
12 2312387 2314714 + PI0003910.1 Cmetu12g1964 1964
10 706974 709670 - CmoCh10G001540.1 Cmo10g00154 154
10 713142 718427 - CmoCh10G001580.1 Cmo10g00158 158
11 611915 615892 - CmoCh11G001180.1 Cmo11g00118 118
11 628621 634809 + CmoCh11G001220.1 Cmo11g00122 122
13 8193974 8198738 + CmoCh13G009320.1 Cmo13g00932 932
18 816160 818542 + CmoCh18G001150.1 Cmo18g00115 115
18 823704 825231 + CmoCh18G001170.1 Cmo18g00117 117
1 27210889 27212687 - CmPI595203_01g013730.1 Cmu01g1373 1373
1 27233566 27235354 - CmPI595203_01g013750.1 Cmu01g1375 1375
1 27268451 27273756 + CmPI595203_01g013780.1 Cmu01g1378 1378
6 28197747 28209291 - CmPI595203_06g017180.1 Cmu06g1718 1718
6 28236399 28236644 + CmPI595203_06g017220.1 Cmu06g1722 1722
6 28236858 28242238 + CmPI595203_06g017230.1 Cmu06g1723 1723
2 34733399 34735676 + Conep02aG0191200.1 Cone2ag0882 882
2 34738570 34743880 + Conep02aG0191400.1 Cone2ag0884 884
2 34752469 34756572 + Conep02aG0191500.1 Cone2ag0885 885
13 717559 720204 + Conep13aG0012700.1 Cone13ag0122 122
16 706271 710267 - Conep16aG0012700.1 Cone16ag0125 125
16 728370 734178 + Conep16aG0013000.1 Cone16ag0128 128
19 676876 683473 - Conep19aG0012700.1 Cone19ag0121 121
19 690718 693651 + Conep19aG0013000.1 Cone19ag0124 124
4 12050848 12056869 - Cp4.1LG04g15370.1 Cpe04g01535 1535
4 12066980 12071399 + Cp4.1LG04g15240.1 Cpe04g01537 1537
9 9136278 9138606 - Cp4.1LG09g10370.1 Cpe09g01044 1044
18 7664707 7670800 + Cp4.1LG18g08210.1 Cpe18g00827 827
20 1280025 1285774 - Cp4.1LG20g02230.1 Cpe20g00224 224
1 26123274 26125093 - CrPI670011_01g012890.1 Cre01g1289 1289
1 26131516 26133377 - CrPI670011_01g012910.1 Cre01g1291 1291
1 26181162 26187375 + CrPI670011_01g012930.1 Cre01g1293 1293
6 33016015 33027642 - CrPI670011_06g025380.1 Cre06g2538 2538
6 33045783 33055427 + CrPI670011_06g025410.1 Cre06g2541 2541
6 33055641 33060887 + CrPI670011_06g025420.1 Cre06g2542 2542
1 1146544 1153540 - CsaV3_1G001770.1 Csa01g00177 177
1 1155049 1161916 - CsaV3_1G001780.1 Csa01g00178 178
1 1172245 1182327 + CsaV3_1G001810.1 Csa01g00181 181
1 5179304 5184814 - CsaV3_1G008220.1 Csa01g00822 822
1 5204864 5207318 + CsaV3_1G008250.1 Csa01g00825 825
1 5210806 5212803 + CsaV3_1G008270.1 Csa01g00827 827
7 66872183 66873879 - Hsped.07g22470.1 Hepe07g2247 2247
7 66881148 66883869 - Hsped.07g22490.1 Hepe07g2249 2249
7 66912294 66915185 + Hsped.07g22510.1 Hepe07g2251 2251
9 1342493 1351885 - Hsped.09g01690.1 Hepe09g0169 169
9 1366538 1369592 + Hsped.09g01720.1 Hepe09g0172 172
10 3291540 3294449 - Lag0024464.1 Lac10g0419 419
10 3317657 3319516 + Lag0024467.1 Lac10g0422 422
2 2972535 2975909 - Lsi02G003480.1 Lsi02g00348 348
2 3002352 3004262 + Lsi02G003500.1 Lsi02g00350 350
6 25607858 25616622 - Lsi06G015190.1 Lsi06g01519 1519
6 25636500 25643213 + Lsi06G015220.1 Lsi06g01522 1522
6 25649722 25652521 + Lsi06G015250.1 Lsi06g01525 1525
1 12188492 12189979 - Sed0003696.1 Sed01g1682 1682
1 12225861 12230382 + Sed0010209.2 Sed01g1685 1685
8 901825 914503 + Sed0021395.1 Sed08g0166 166
8 38052481 38054691 - Sed0013262.2 Sed08g2536 2536
12 30177973 30184701 - Sed0018463.1 Sed12g1901 1901
5 70569691 70571409 - Tan0001400.1 Tan05g2037 2037
5 70581257 70583311 - Tan0001020.1 Tan05g2039 2039
5 70666425 70671465 + Tan0001491.1 Tan05g2041 2041
9 72011572 72021091 - Tan0003455.1 Tan09g2200 2200
9 72132951 72139196 + Tan0012181.1 Tan09g2203 2203
9 72140758 72150718 + Tan0017169.2 Tan09g2205 2205
17 8646691 8660814 - Vvi17g686 Vvi17g686 686
17 8671005 8672350 + Vvi17g687 Vvi17g687 687
17 8674676 8683214 - Vvi17g688 Vvi17g688 688
17 8688130 8688720 + Vvi17g689 Vvi17g689 689
17 8691793 8697959 - Vvi17g690 Vvi17g690 690
17 8704609 8731895 + Vvi17g691 Vvi17g691 691
17 8732710 8739622 + Vvi17g692 Vvi17g692 692
17 8741560 8742409 + Vvi17g693 Vvi17g693 693
17 8760310 8768301 + Vvi17g694 Vvi17g694 694
17 8768693 8770406 + Vvi17g695 Vvi17g695 695
       

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