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
Vvi17g176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g178 . . . . . . . . . . Cma10g00334 Cma11g00319 Car10g00317 Car11g00294 Sed08g0412 . . Bhi02g00164 Tan09g1806 Cmetu05g0436 . Hepe09g0401 . . Cla06g01410 Cam06g1563 Cec06g1623 Cco06g1615 Clacu06g1525 Cmu06g1479 Cre06g2288 . . . . . . . . . . . . . . . . . Cmo10g00362 Cmo11g00324 . . . . . . . . . . . . . . . . . . . . Lsi06g01269 Csa01g00446 Chy02g02298 Cme02g01669
Vvi17g179 Blo04g00856 . . . . . . . . . . . . . . Cpe20g00158 . . . . . . . . . . . . . . . . . . . Lsi02g00241 . . . . . . . . . . . . . . . . Car13g00819 . . . . . . . . . . . . . . . . . . . . .
Vvi17g180 . . Bda06g00824 . . . . Bma12g01248 . . . . Car10g00316 . . . . Bhi02g00155 . . . Hepe09g0400 . . Cla06g01412 Cam06g1565 Cec06g1625 Cco06g1617 Clacu06g1527 Cmu06g1481 Cre06g2290 . . . Cone19ag0357 . . . . . Blo15g00055 . . Bpe07g01052 . . . . Cmo10g00361 . . . . . . . . . . . . . . . . . . . . . Lsi06g01272 Csa01g00444 Chy02g02301 Cme02g01672
Vvi17g181 . . . . Bpe12g00652 . . . . . Cma10g00333 . Car10g00315 . Sed08g0409 . . Bhi02g00153 Tan09g1808 Cmetu02g0610 . Hepe09g0399 . . Cla06g01413 Cam06g1566 Cec06g1626 Cco06g1618 Clacu06g1528 Cmu06g1482 Cre06g2291 . . . . . . . . Blo13g00126 . . . . . . . . Cmo10g00359 . . . . . . . . . . . . . . . . . . . . . Lsi06g01273 Csa01g00443 Chy02g02303 Cme02g01674
Vvi17g182 . . . . . . . . . . . . . . . . Cpe04g01362 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00503 Bma03g00924 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g183 . . . . . Bpe13g00380 Bma06g00069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01807 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g184 . Blo16g00110 . . . . . . . Cmo18g00060 . . . . . . . . . . . . . . . . . . . . . Cone2ag0775 . . . . Csa01g00722 Chy12g01390 Cme12g01823 . . . . . . . . . . . . Cma18g00078 . . . . . . . . . . . . . . . . . . . . . .
Vvi17g185 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00180 . . . . . . . . Car18g00069 Cpe09g01109 . Bhi08g01311 . . . . . . Cla04g01036 Cam04g1078 Cec01g1592 Cco01g1641 Clacu04g1106 Cmu04g1089 Cre01g1390 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11472712 11485436 - Bda024155.1 Bda06g00824 824
11 53110413 53115100 + Bda008736.2 Bda11g01807 1807
2 2802794 2804668 + XM_039024040.1 Bhi02g00153 153
2 2806773 2832470 - XM_039022815.1 Bhi02g00155 155
2 2936780 2937540 - XM_039024061.1 Bhi02g00164 164
8 39795101 39799824 + XM_039039345.1 Bhi08g01311 1311
4 9416721 9417143 + BLOR13768 Blo04g00856 856
13 3605281 3619962 - BLOR05407 Blo13g00126 126
15 427379 445394 + BLOR06449 Blo15g00055 55
16 2592730 2596637 + BLOR07358 Blo16g00110 110
3 9554300 9556641 - Bma017248.2 Bma03g00924 924
6 1085450 1091404 + Bma022680.1 Bma06g00069 69
12 45473717 45502619 - Bma030546 Bma12g01248 1248
7 15990059 16006607 - Bpe021895.1 Bpe07g01052 1052
12 12183111 12183706 - Bpe005912.1 Bpe12g00652 652
13 11558441 11566854 + Bpe006504.1 Bpe13g00380 380
15 12539397 12541040 - Bpe001117.1 Bpe15g00180 180
15 16278085 16284007 + Bpe024567 Bpe15g00503 503
4 24957291 24961019 - CaPI482276_04g010780.1 Cam04g1078 1078
6 27114719 27115228 + CaPI482276_06g015630.1 Cam06g1563 1563
6 27132468 27153886 + CaPI482276_06g015650.1 Cam06g1565 1565
6 27154238 27155654 - CaPI482276_06g015660.1 Cam06g1566 1566
10 1544885 1545773 + Carg15182-RA Car10g00315 315
10 1545032 1562554 - Carg15183-RA Car10g00316 316
10 1564555 1565064 - Carg15184-RA Car10g00317 317
11 1606708 1607220 - Carg09095-RA Car11g00294 294
13 8931264 8932151 - Carg04853-RA Car13g00819 819
18 353887 357212 + Carg06634-RA Car18g00069 69
1 29164699 29168430 - CcPI632755_01g016410.1 Cco01g1641 1641
6 26749426 26749935 + CcPI632755_06g016150.1 Cco06g1615 1615
6 26775519 26796874 + CcPI632755_06g016170.1 Cco06g1617 1617
6 26797226 26798608 - CcPI632755_06g016180.1 Cco06g1618 1618
1 30604401 30608056 - CePI673135_01g015920.1 Cec01g1592 1592
6 29831048 29831557 + CePI673135_06g016230.1 Cec06g1623 1623
6 29849812 29871209 + CePI673135_06g016250.1 Cec06g1625 1625
6 29871561 29872979 - CePI673135_06g016260.1 Cec06g1626 1626
2 27042197 27042709 + Chy2G045650.1 Chy02g02298 2298
2 27055918 27072271 + Chy2G045680.1 Chy02g02301 2301
2 27078667 27080177 - Chy2G045700.1 Chy02g02303 2303
12 18057761 18061046 + Chy12G219900.1 Chy12g01390 1390
4 25320574 25324292 - ClG42_04g0110600.10 Clacu04g1106 1106
6 26169738 26170247 + ClG42_06g0152500.10 Clacu06g1525 1525
6 26191131 26209007 + ClG42_06g0152700.10 Clacu06g1527 1527
6 26209359 26210784 - ClG42_06g0152800.10 Clacu06g1528 1528
4 25528947 25532665 - ClCG04G010530.2 Cla04g01036 1036
6 27654072 27655015 + ClCG06G014210.2 Cla06g01410 1410
6 27672074 27697357 + ClCG06G014240.1 Cla06g01412 1412
6 27695843 27697268 - ClCG06G014250.1 Cla06g01413 1413
10 1533195 1534582 + CmaCh10G003330.1 Cma10g00333 333
10 1533339 1552948 - CmaCh10G003340.1 Cma10g00334 334
11 1583965 1584477 - CmaCh11G003190.1 Cma11g00319 319
18 338240 343033 - CmaCh18G000780.1 Cma18g00078 78
2 23859803 23860563 + MELO3C017371.2.1 Cme02g01669 1669
2 23870990 23892739 + MELO3C017366.2.1 Cme02g01672 1672
2 23898420 23900462 - MELO3C017364.2.1 Cme02g01674 1674
12 24649836 24653461 + MELO3C002139.2.1 Cme12g01823 1823
2 22314050 22317511 - PI0022051.1 Cmetu02g0610 610
5 5877796 5878444 + PI0028915.1 Cmetu05g0436 436
10 1623801 1624955 + CmoCh10G003590.1 Cmo10g00359 359
10 1638100 1642511 - CmoCh10G003610.1 Cmo10g00361 361
10 1644822 1645331 - CmoCh10G003620.1 Cmo10g00362 362
11 1571793 1572305 - CmoCh11G003240.1 Cmo11g00324 324
18 382394 387223 - CmoCh18G000600.1 Cmo18g00060 60
4 25505022 25508740 - CmPI595203_04g010890.1 Cmu04g1089 1089
6 26073083 26073592 + CmPI595203_06g014790.1 Cmu06g1479 1479
6 26091025 26109009 + CmPI595203_06g014810.1 Cmu06g1481 1481
6 26112736 26114161 - CmPI595203_06g014820.1 Cmu06g1482 1482
2 33708011 33711194 - Conep02aG0180200.1 Cone2ag0775 775
19 2952084 2968805 + Conep19aG0037000.1 Cone19ag0357 357
4 11096269 11099010 - Cp4.1LG04g13720.1 Cpe04g01362 1362
9 9562929 9566338 - Cp4.1LG09g11180.1 Cpe09g01109 1109
20 893854 896117 + Cp4.1LG20g01630.1 Cpe20g00158 158
1 27159042 27162739 - CrPI670011_01g013900.1 Cre01g1390 1390
6 30836665 30837174 + CrPI670011_06g022880.1 Cre06g2288 2288
6 30855109 30876301 + CrPI670011_06g022900.1 Cre06g2290 2290
6 30876653 30878081 - CrPI670011_06g022910.1 Cre06g2291 2291
1 2773948 2778133 + CsaV3_1G004430.1 Csa01g00443 443
1 2782345 2798659 - CsaV3_1G004440.1 Csa01g00444 444
1 2806311 2811412 - CsaV3_1G004460.1 Csa01g00446 446
1 4574249 4580172 - CsaV3_1G007220.1 Csa01g00722 722
9 3570420 3571327 + Hsped.09g03990.1 Hepe09g0399 399
9 3571504 3587640 - Hsped.09g04000.1 Hepe09g0400 400
9 3590818 3591339 - Hsped.09g04010.1 Hepe09g0401 401
2 2034817 2040857 + Lsi02G002410.1 Lsi02g00241 241
6 23280538 23281047 + Lsi06G012690.1 Lsi06g01269 1269
6 23299461 23317888 + Lsi06G012720.1 Lsi06g01272 1272
6 23317703 23319416 - Lsi06G012730.1 Lsi06g01273 1273
8 2474259 2475106 + Sed0027837.1 Sed08g0409 409
8 2497747 2502112 - Sed0016646.2 Sed08g0412 412
9 69516147 69516845 + Tan0014706.1 Tan09g1806 1806
9 69544707 69545632 - Tan0002266.1 Tan09g1808 1808
17 1679825 1685710 + Vvi17g176 Vvi17g176 176
17 1702670 1706116 + Vvi17g177 Vvi17g177 177
17 1714387 1715151 + Vvi17g178 Vvi17g178 178
17 1717076 1718118 - Vvi17g179 Vvi17g179 179
17 1736379 1773393 + Vvi17g180 Vvi17g180 180
17 1773396 1775196 - Vvi17g181 Vvi17g181 181
17 1776167 1784724 + Vvi17g182 Vvi17g182 182
17 1793567 1816622 + Vvi17g183 Vvi17g183 183
17 1818131 1823808 - Vvi17g184 Vvi17g184 184
17 1830226 1832876 + Vvi17g185 Vvi17g185 185
       

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