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
Vvi17g216 . . . . . . Bma06g00065 . . . . . . Car11g00283 Sed14g1022 . Cpe04g01374 Bhi02g00132 Tan09g1830 Cmetu04g0229 . Hepe09g0382 . . Cla06g01425 Cam06g1579 Cec06g1639 Cco06g1631 . Cmu06g1495 Cre06g2304 Cone2ag0759 . . . . . . . . . . . . . . . . . Cmo11g00313 . . . . . . . . . . . . . . . . . . . . . Csa01g00428 Chy02g02316 Cme02g01689
Vvi17g217 . . . . . . . . . . . . . Car11g00282 . . . Bhi02g00131 . . . Hepe09g0381 . . . . . . . . . . . . Cone19ag0329 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g218 . . . . . . . . . . Cma10g00325 Cma11g00306 Car10g00307 . Sed08g0399 . Cpe04g01375 Bhi02g00130 Tan09g1831 Cmetu05g0278 . . . . Cla06g01426 Cam06g1580 Cec06g1640 Cco06g1632 Clacu06g1541 Cmu06g1496 Cre06g2305 . . . . . . . . . . . . . . . . . Cmo10g00350 Cmo11g00312 . . . . . . . . . . . . . . . . . . . . Lsi06g01293 Csa01g00427 Chy02g02317 Cme02g01690
Vvi17g219 . . . . . . . . Cmo13g01031 Cmo18g00052 . . . . . Cpe20g00147 . . . . . . . . . . . . . . . . . . . Lsi02g00227 Csa01g00709 Chy12g01402 Cme12g01835 . . . . . Bpe15g00511 . . Sed08g2753 . . Cma13g00996 Cma18g00069 Car13g00829 Car18g00060 Cpe09g01117 . Bhi08g01287 Tan05g2197 . Lac10g0285 Hepe07g2358 . . Cla04g01052 Cam04g1095 Cec01g1610 Cco01g1656 Clacu04g1121 Cmu04g1105 Cre01g1404 . . . .
Vvi17g220 . . . . . . . . . Cmo18g00051 . . . . . Cpe20g00146 . . . . . . . . . . . . . . . . . . . . Csa01g00708 Chy12g01403 Cme12g01836 . . . . . . . . Sed01g1762 . . . Cma18g00068 Car13g00830 Car18g00059 Cpe09g01118 . Bhi08g01285 Tan05g2199 Cmetu12g1628 Lac10g0284 Hepe07g2359 . . Cla04g01053 Cam04g1096 Cec01g1611 Cco01g1657 Clacu04g1122 Cmu04g1106 Cre01g1405 . . . .
Vvi17g221 . . . . . . . . Cmo13g01032 Cmo18g00050 . . . . . Cpe20g00145 . . . . . . . . . . . . . . . . . . . Lsi02g00226 Csa01g00707 Chy12g01404 Cme12g01838 . . . . . . . . . . . . Cma18g00067 Car13g00831 Car18g00058 . . Bhi08g01284 . . . . . . Cla04g01054 . . . . . . . . . .
Vvi17g222 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g223 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g224 Blo04g00844 . . . . . . . Cmo13g01034 Cmo18g00049 Cma10g00324 Cma11g00304 Car10g00306 Car11g00281 . Cpe20g00144 Cpe04g01376 Bhi02g00129 . . . . . . Cla06g01427 Cam06g1581 Cec06g1641 Cco06g1633 Clacu06g1542 Cmu06g1497 Cre06g2306 Cone2ag0757 . . . Lsi02g00224 Csa01g00706 Chy12g01405 Cme12g01839 . . . . . Bpe15g00516 . . . Cmo10g00349 Cmo11g00311 Cma13g00998 . Car13g00832 . Cpe09g01119 . Bhi08g01282 . . . . . . Cla04g01055 Cam04g1098 Cec01g1613 Cco01g1658 Clacu04g1123 Cmu04g1107 Cre01g1407 Lsi06g01294 Csa01g00426 Chy02g02318 Cme02g01691
Vvi17g225 . . . . . . . . . . . . . Car11g00280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme02g01692
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
2 2426475 2432648 - XM_039022948.1 Bhi02g00129 129
2 2438437 2446742 - XM_039023173.1 Bhi02g00130 130
2 2439266 2446744 - XM_039023175.1 Bhi02g00131 131
2 2451697 2456578 - XM_039024300.1 Bhi02g00132 132
8 39282533 39287008 - XM_039037749.1 Bhi08g01282 1282
8 39301042 39319857 + XM_039038290.1 Bhi08g01284 1284
8 39320188 39321558 + XM_039038291.1 Bhi08g01285 1285
8 39330813 39335126 + XM_039038986.1 Bhi08g01287 1287
4 9210814 9216081 - BLOR13756 Blo04g00844 844
6 1046161 1048516 + Bma022676.1 Bma06g00065 65
15 16328674 16331160 + Bpe001444.1 Bpe15g00511 511
15 16352507 16357843 + Bpe001449.1 Bpe15g00516 516
4 25103640 25108753 - CaPI482276_04g010950.1 Cam04g1095 1095
4 25110448 25111572 - CaPI482276_04g010960.1 Cam04g1096 1096
4 25137837 25142582 + CaPI482276_04g010980.1 Cam04g1098 1098
6 27279822 27287592 + CaPI482276_06g015790.1 Cam06g1579 1579
6 27287679 27294426 + CaPI482276_06g015800.1 Cam06g1580 1580
6 27299321 27304948 + CaPI482276_06g015810.1 Cam06g1581 1581
10 1502928 1507882 - Carg15173-RA Car10g00306 306
10 1509958 1514884 - Carg15174-RA Car10g00307 307
11 1531924 1533486 + Carg09109-RA Car11g00280 280
11 1535991 1540767 - Carg09108-RA Car11g00281 281
11 1543326 1550183 - Carg09107-RA Car11g00282 282
11 1550970 1552521 - Carg09106-RA Car11g00283 283
13 8987234 8990975 - Carg04843-RA Car13g00829 829
13 8991387 8992623 - Carg04842-RA Car13g00830 830
13 8993799 9003762 - Carg04841-RA Car13g00831 831
13 9009266 9013372 + Carg04840-RA Car13g00832 832
18 291307 300332 + Carg06623-RA Car18g00058 58
18 301234 303237 + Carg06624-RA Car18g00059 59
18 305357 308550 + Carg06625-RA Car18g00060 60
1 29317814 29322923 - CcPI632755_01g016560.1 Cco01g1656 1656
1 29324585 29340013 - CcPI632755_01g016570.1 Cco01g1657 1657
1 29351806 29356537 + CcPI632755_01g016580.1 Cco01g1658 1658
6 26930667 26935889 + CcPI632755_06g016310.1 Cco06g1631 1631
6 26938547 26945325 + CcPI632755_06g016320.1 Cco06g1632 1632
6 26950374 26955996 + CcPI632755_06g016330.1 Cco06g1633 1633
1 30753678 30758747 - CePI673135_01g016100.1 Cec01g1610 1610
1 30760414 30761721 - CePI673135_01g016110.1 Cec01g1611 1611
1 30787732 30792665 + CePI673135_01g016130.1 Cec01g1613 1613
6 30002333 30007631 + CePI673135_06g016390.1 Cec06g1639 1639
6 30010324 30017081 + CePI673135_06g016400.1 Cec06g1640 1640
6 30022023 30027659 + CePI673135_06g016410.1 Cec06g1641 1641
2 27181153 27184182 + Chy2G045830.1 Chy02g02316 2316
2 27185504 27191564 + Chy2G045840.1 Chy02g02317 2317
2 27194904 27200088 + Chy2G045850.1 Chy02g02318 2318
12 18144433 18147682 - Chy12G220020.1 Chy12g01402 1402
12 18149166 18150357 - Chy12G220030.1 Chy12g01403 1403
12 18151135 18161988 - Chy12G220040.1 Chy12g01404 1404
12 18170850 18174169 + Chy12G220050.1 Chy12g01405 1405
4 25475248 25480411 - ClG42_04g0112100.10 Clacu04g1121 1121
4 25482086 25497455 - ClG42_04g0112200.10 Clacu04g1122 1122
4 25509285 25514004 + ClG42_04g0112300.10 Clacu04g1123 1123
6 26336845 26351476 + ClG42_06g0154100.10 Clacu06g1541 1541
6 26356467 26362081 + ClG42_06g0154200.10 Clacu06g1542 1542
4 25698941 25702813 - ClCG04G010690.2 Cla04g01052 1052
4 25704230 25705537 - ClCG04G010700.1 Cla04g01053 1053
4 25706443 25720727 - ClCG04G010710.2 Cla04g01054 1054
4 25731887 25736955 + ClCG04G010720.1 Cla04g01055 1055
6 27834119 27839409 + ClCG06G014380.2 Cla06g01425 1425
6 27841870 27848968 + ClCG06G014390.1 Cla06g01426 1426
6 27853411 27859633 + ClCG06G014400.2 Cla06g01427 1427
10 1489796 1496172 - CmaCh10G003240.1 Cma10g00324 324
10 1496311 1503870 - CmaCh10G003250.1 Cma10g00325 325
11 1510304 1520726 - CmaCh11G003040.1 Cma11g00304 304
11 1520886 1531524 - CmaCh11G003060.1 Cma11g00306 306
13 7694080 7707917 - CmaCh13G009960.1 Cma13g00996 996
13 7716467 7720767 + CmaCh13G009980.1 Cma13g00998 998
18 280844 289030 + CmaCh18G000670.1 Cma18g00067 67
18 290057 291891 + CmaCh18G000680.1 Cma18g00068 68
18 292522 297092 + CmaCh18G000690.1 Cma18g00069 69
2 23999562 24002517 + MELO3C017352.2.1 Cme02g01689 1689
2 24003887 24010299 + MELO3C017351.2.1 Cme02g01690 1690
2 24013113 24018968 + MELO3C017350.2.1 Cme02g01691 1691
2 24019248 24023485 - MELO3C029742.2.1 Cme02g01692 1692
12 24726587 24730634 - MELO3C002127.2.1 Cme12g01835 1835
12 24731067 24732680 - MELO3C002126.2.1 Cme12g01836 1836
12 24732892 24744365 - MELO3C002125.2.1 Cme12g01838 1838
12 24749678 24754160 + MELO3C002124.2.1 Cme12g01839 1839
4 33276143 33279456 + PI0028263.1 Cmetu04g0229 229
5 565889 576880 - PI0024923.1 Cmetu05g0278 278
12 1504743 1506427 + PI0002453.1 Cmetu12g1628 1628
10 1579520 1586723 - CmoCh10G003490.1 Cmo10g00349 349
10 1587763 1592910 - CmoCh10G003500.1 Cmo10g00350 350
11 1499676 1504386 - CmoCh11G003110.1 Cmo11g00311 311
11 1506265 1513443 - CmoCh11G003120.1 Cmo11g00312 312
11 1514238 1515872 - CmoCh11G003130.1 Cmo11g00313 313
13 8686443 8690464 - CmoCh13G010310.1 Cmo13g01031 1031
13 8690749 8703269 - CmoCh13G010320.1 Cmo13g01032 1032
13 8708506 8712786 + CmoCh13G010340.1 Cmo13g01034 1034
18 316757 322380 - CmoCh18G000490.1 Cmo18g00049 49
18 323440 332879 + CmoCh18G000500.1 Cmo18g00050 50
18 333438 335304 + CmoCh18G000510.1 Cmo18g00051 51
18 335956 340552 + CmoCh18G000520.1 Cmo18g00052 52
4 25656002 25661164 - CmPI595203_04g011050.1 Cmu04g1105 1105
4 25662839 25678203 - CmPI595203_04g011060.1 Cmu04g1106 1106
4 25690069 25694788 + CmPI595203_04g011070.1 Cmu04g1107 1107
6 26240055 26245367 + CmPI595203_06g014950.1 Cmu06g1495 1495
6 26248006 26254752 + CmPI595203_06g014960.1 Cmu06g1496 1496
6 26259740 26265354 + CmPI595203_06g014970.1 Cmu06g1497 1497
2 33377398 33383287 + Conep02aG0177400.1 Cone2ag0757 757
2 33396825 33400397 - Conep02aG0177600.1 Cone2ag0759 759
19 2621025 2623987 + Conep19aG0033800.1 Cone19ag0327 327
19 2640506 2657209 + Conep19aG0034000.1 Cone19ag0329 329
4 11157112 11158713 + Cp4.1LG04g13580.1 Cpe04g01374 1374
4 11159530 11166988 + Cp4.1LG04g13670.1 Cpe04g01375 1375
4 11169248 11175288 + Cp4.1LG04g13790.1 Cpe04g01376 1376
9 9611922 9616118 - Cp4.1LG09g11220.1 Cpe09g01117 1117
9 9616810 9628663 - Cp4.1LG09g11200.1 Cpe09g01118 1118
9 9629950 9635641 + Cp4.1LG09g11140.1 Cpe09g01119 1119
20 812233 816354 - Cp4.1LG20g01560.1 Cpe20g00144 144
20 821271 831537 + Cp4.1LG20g01420.1 Cpe20g00145 145
20 832131 833346 + Cp4.1LG20g01390.1 Cpe20g00146 146
20 834090 837511 + Cp4.1LG20g01450.1 Cpe20g00147 147
1 27308687 27313794 - CrPI670011_01g014040.1 Cre01g1404 1404
1 27315501 27317953 - CrPI670011_01g014050.1 Cre01g1405 1405
1 27341812 27346539 + CrPI670011_01g014070.1 Cre01g1407 1407
6 31004510 31009795 + CrPI670011_06g023040.1 Cre06g2304 2304
6 31012502 31019243 + CrPI670011_06g023050.1 Cre06g2305 2305
6 31024317 31029940 + CrPI670011_06g023060.1 Cre06g2306 2306
1 2662730 2668666 - CsaV3_1G004260.1 Csa01g00426 426
1 2671328 2677922 - CsaV3_1G004270.1 Csa01g00427 427
1 2678463 2681734 - CsaV3_1G004280.1 Csa01g00428 428
1 4473313 4477513 - CsaV3_1G007060.1 Csa01g00706 706
1 4485111 4496170 + CsaV3_1G007070.1 Csa01g00707 707
1 4496946 4498042 + CsaV3_1G007080.1 Csa01g00708 708
1 4498999 4503384 + CsaV3_1G007090.1 Csa01g00709 709
7 67948484 67954516 - Hsped.07g23580.1 Hepe07g2358 2358
7 67956059 67957910 - Hsped.07g23590.1 Hepe07g2359 2359
9 3390573 3400026 - Hsped.09g03810.1 Hepe09g0381 381
9 3401689 3406615 - Hsped.09g03820.1 Hepe09g0382 382
10 2158425 2159567 + Lag0024329.1 Lac10g0284 284
10 2161129 2164063 + Lag0024330.1 Lac10g0285 285
2 1876829 1889589 - Lsi02G002240.1 Lsi02g00224 224
2 1899950 1915214 + Lsi02G002260.1 Lsi02g00226 226
2 1915472 1923093 + Lsi02G002270.1 Lsi02g00227 227
6 23477649 23487102 + Lsi06G012930.1 Lsi06g01293 1293
6 23491733 23498139 + Lsi06G012940.1 Lsi06g01294 1294
1 12851364 12853949 + Sed0027930.1 Sed01g1762 1762
8 2404731 2413633 - Sed0002019.1 Sed08g0399 399
8 39196574 39201602 + Sed0027092.2 Sed08g2753 2753
14 19823744 19826214 - Sed0016047.1 Sed14g1022 1022
5 72937778 72942988 - Tan0001361.1 Tan05g2197 2197
5 72946444 72947773 - Tan0006854.1 Tan05g2199 2199
9 69704582 69709138 + Tan0022072.1 Tan09g1830 1830
9 69711210 69719371 + Tan0010928.1 Tan09g1831 1831
17 2282058 2286605 + Vvi17g216 Vvi17g216 216
17 2288087 2297728 + Vvi17g217 Vvi17g217 217
17 2298242 2304096 + Vvi17g218 Vvi17g218 218
17 2304466 2316230 - Vvi17g219 Vvi17g219 219
17 2319874 2321429 - Vvi17g220 Vvi17g220 220
17 2321686 2342403 - Vvi17g221 Vvi17g221 221
17 2349563 2352147 - Vvi17g222 Vvi17g222 222
17 2360666 2363479 + Vvi17g223 Vvi17g223 223
17 2368189 2377747 + Vvi17g224 Vvi17g224 224
17 2379237 2381736 - Vvi17g225 Vvi17g225 225
       

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