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
Vvi2g242 . . . . . Bpe07g00211 Bma07g01022 . Cmo06g00587 Cmo16g01278 . . . . . Cpe14g01018 . . . . . . . . Cla10g00083 Cam10g0080 Cec10g0083 Cco10g0087 Clacu10g0081 Cmu10g0928 Cre10g0343 . . . . Lsi07g01109 . . Cme06g02389 Blo03g00803 . . . Bpe08g00900 . . . . . . Cma06g00583 Cma16g01232 Car06g00517 Car16g01160 Cpe08g00916 . . . . . . . . . . . . . . . . . . .
Vvi2g243 . . . . . . Bma07g01025 Bma14g00101 . . Cma02g00943 Cma15g01315 Car02g00691 Car15g01183 . . Cpe05g00771 . . . . . . . . . . . . . . . Cone12ag0589 . . . Csa05g00165 Chy09g01333 . Blo03g00802 Blo19g00137 Bda07g00152 Bda09g00638 Bpe08g00902 Bpe11g00370 . . . Cmo02g00951 Cmo15g01380 . . . . . . Bhi12g00085 . . . . . Lcy12g1519 Cla01g00146 Cam01g0151 Cec01g0147 Cco01g0153 Clacu01g0146 Cmu01g0146 Cre09g2360 Lsi09g00137 . . Cme09g01881
Vvi2g244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00163 Chy09g01334 . Blo03g00801 . . . . Bpe11g00371 . . . . . . . . . . . Bhi12g00084 . . . . . Lcy12g1518 Cla01g00145 Cam01g0150 Cec01g0146 Cco01g0152 Clacu01g0145 Cmu01g0145 Cre09g2361 Lsi09g00136 . . Cme09g01882
Vvi2g245 . . . . . . . . Cmo06g00586 . . . . . . . . . . . . . . . Cla10g00082 Cam10g0079 Cec10g0082 Cco10g0086 Clacu10g0080 Cmu10g0927 Cre10g0342 . . . . . . . Cme06g02388 . . . . . . . . . . . Cma06g00582 . Car06g00516 . Cpe08g00917 . . . . . . . . . . . . . . . . . . .
Vvi2g246 . . . Bda08g00468 . . Bma07g01027 . . Cmo16g01136 . Cma15g01366 Car02g00658 . . Cpe14g01019 . . . . . . . . Cla10g00081 Cam10g0078 Cec10g0081 Cco10g0085 Clacu10g0079 Cmu10g0926 . . . . . Lsi07g01108 . . Cme06g02387 . . . Bda09g00637 Bpe08g00903 . . . . . . . . . Car16g01161 . . . . . . . . . . . . . . . . . . . .
Vvi2g247 . . . . . . . . Cmo06g00585 Cmo16g01281 . . . . . Cpe14g01020 . . . . . . . . Cla10g00080 Cam10g0077 Cec10g0080 Cco10g0084 Clacu10g0078 Cmu10g0925 Cre10g0341 . . . . Lsi07g01107 . . Cme06g02386 . . . . . . . . . . . Cma06g00581 Cma16g01233 Car06g00515 Car16g01162 Cpe08g00918 . . . . . . . . . . . . . . . . . . .
Vvi2g248 . . . . . . . . . . . Cma15g01316 Car02g00692 Car15g01184 . . Cpe05g00770 . . . . . . . . . . . . . . . . . . . Csa05g00162 Chy09g01335 . . Blo19g00136 . Bda09g00636 Bpe08g00904 . . . . . Cmo15g01381 . . . . . . Bhi12g00298 . . . . . Lcy12g1621 Cla01g00144 Cam01g0149 Cec01g0145 Cco01g0151 Clacu01g0144 Cmu01g0144 Cre09g2362 Lsi09g00135 . . Cme09g01883
Vvi2g249 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g01956 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g251 . . . . . . Bma07g01030 Bma14g00100 . . . Cma15g01318 . Car15g01185 . . . . . . . . . . . . . . . . . . . . . . Csa05g00161 Chy09g01336 . Blo03g00800 . Bda07g00154 . . Bpe11g00372 . . . . Cmo15g01382 . . . . . . Bhi12g00082 . . Lac11g1913 Hepe06g1434 . Lcy12g1515 Cla01g00143 Cam01g0148 Cec01g0144 Cco01g0150 Clacu01g0143 Cmu01g0143 Cre09g2363 Lsi09g00134 . . Cme09g01884
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 1891680 1894238 - Bda025219.1 Bda07g00152 152
7 1904110 1905048 + Bda025221.1 Bda07g00154 154
7 36949833 36951102 - Bda028935.1 Bda07g01956 1956
8 4886105 4889068 - Bda024920.1 Bda08g00468 468
9 9373802 9374719 - Bda031267.1 Bda09g00636 636
9 9396405 9399041 - Bda031268.1 Bda09g00637 637
9 9426913 9429255 + Bda031269.1 Bda09g00638 638
12 2542865 2544605 - XM_039019685.1 Bhi12g00082 82
12 2719045 2734329 + XM_039051346.1 Bhi12g00084 84
12 2743120 2748875 + XM_039050807.1 Bhi12g00085 85
12 8628042 8631754 - XM_039051225.1 Bhi12g00298 298
3 33206779 33207723 - BLOR11981 Blo03g00800 800
3 33209751 33211525 - BLOR11982 Blo03g00801 801
3 33219581 33221848 + BLOR11983 Blo03g00802 802
3 33254700 33256019 - BLOR11984 Blo03g00803 803
19 4079157 4080071 - BLOR09479 Blo19g00136 136
19 4197133 4199343 + BLOR09480 Blo19g00137 137
7 40965753 40966628 + Bma026208.1 Bma07g01022 1022
7 41357532 41359903 - Bma026214.1 Bma07g01025 1025
7 41451300 41452690 + Bma026216.1 Bma07g01027 1027
7 41558366 41559307 + Bma026219.1 Bma07g01030 1030
14 1376318 1377259 - Bma010506.1 Bma14g00100 100
14 1391854 1394382 + Bma010507.1 Bma14g00101 101
7 1471440 1473149 - Bpe021022.1 Bpe07g00211 211
8 11410234 11411100 + Bpe023023.1 Bpe08g00900 900
8 11437703 11440088 - Bpe023025.1 Bpe08g00902 902
8 11479177 11481992 + Bpe023027.2 Bpe08g00903 903
8 11486309 11487223 + Bpe023028.1 Bpe08g00904 904
11 2812006 2814362 - Bpe003744.1 Bpe11g00370 370
11 2818525 2820274 + Bpe003745.1 Bpe11g00371 371
11 2822691 2823629 + Bpe003746.1 Bpe11g00372 372
1 1845848 1847119 - CaPI482276_01g001480.1 Cam01g0148 148
1 1851376 1854000 - CaPI482276_01g001490.1 Cam01g0149 149
1 1866779 1871502 + CaPI482276_01g001500.1 Cam01g0150 150
1 1880077 1885829 + CaPI482276_01g001510.1 Cam01g0151 151
10 2340183 2341502 - CaPI482276_10g000770.1 Cam10g0077 77
10 2342921 2345498 - CaPI482276_10g000780.1 Cam10g0078 78
10 2350007 2354642 - CaPI482276_10g000790.1 Cam10g0079 79
10 2356530 2358543 - CaPI482276_10g000800.1 Cam10g0080 80
2 4938987 4941759 + Carg08565-RA Car02g00658 658
2 5126548 5128370 - Carg08532-RA Car02g00691 691
2 5134116 5134879 + Carg08531-RA Car02g00692 692
6 2890989 2892308 - Carg16267-RA Car06g00515 515
6 2892945 2896955 - Carg16268-RA Car06g00516 516
6 2898535 2899984 - Carg16269-RA Car06g00517 517
15 9227612 9230911 - Carg21307-RA Car15g01183 1183
15 9239142 9241644 + Carg21308-RA Car15g01184 1184
15 9243449 9245099 + Carg21309-RA Car15g01185 1185
16 9904348 9906493 + Carg19481-RA Car16g01160 1160
16 9911990 9915057 + Carg19480-RA Car16g01161 1161
16 9915514 9916821 + Carg19479-RA Car16g01162 1162
1 1410221 1411506 - CcPI632755_01g001500.1 Cco01g0150 150
1 1415922 1418505 - CcPI632755_01g001510.1 Cco01g0151 151
1 1434565 1439364 + CcPI632755_01g001520.1 Cco01g0152 152
1 1448072 1453794 + CcPI632755_01g001530.1 Cco01g0153 153
10 752219 753538 - CcPI632755_10g000840.1 Cco10g0084 84
10 755020 757650 - CcPI632755_10g000850.1 Cco10g0085 85
10 762141 766798 - CcPI632755_10g000860.1 Cco10g0086 86
10 768670 770683 - CcPI632755_10g000870.1 Cco10g0087 87
1 1417469 1418791 - CePI673135_01g001440.1 Cec01g0144 144
1 1423068 1425610 - CePI673135_01g001450.1 Cec01g0145 145
1 1435470 1440320 + CePI673135_01g001460.1 Cec01g0146 146
1 1449114 1454900 + CePI673135_01g001470.1 Cec01g0147 147
10 771507 772826 - CePI673135_10g000800.1 Cec10g0080 80
10 774226 776826 - CePI673135_10g000810.1 Cec10g0081 81
10 780014 786033 - CePI673135_10g000820.1 Cec10g0082 82
10 787961 790007 - CePI673135_10g000830.1 Cec10g0083 83
9 15188060 15192233 - Chy9G170490.1 Chy09g01333 1333
9 15198698 15202041 - Chy9G170500.1 Chy09g01334 1334
9 15210155 15211954 + Chy9G170510.1 Chy09g01335 1335
9 15214733 15215949 + Chy9G170520.1 Chy09g01336 1336
1 1459087 1460381 - ClG42_01g0014300.10 Clacu01g0143 143
1 1464411 1467012 - ClG42_01g0014400.10 Clacu01g0144 144
1 1479855 1484546 + ClG42_01g0014500.10 Clacu01g0145 145
1 1493340 1499099 + ClG42_01g0014600.10 Clacu01g0146 146
10 1074249 1075568 - ClG42_10g0007800.10 Clacu10g0078 78
10 1076949 1079529 - ClG42_10g0007900.10 Clacu10g0079 79
10 1083502 1088124 - ClG42_10g0008000.10 Clacu10g0080 80
10 1089995 1092011 - ClG42_10g0008100.10 Clacu10g0081 81
1 1453657 1454951 - ClCG01G001470.2 Cla01g00143 143
1 1458234 1460835 - ClCG01G001480.2 Cla01g00144 144
1 1473675 1480964 + ClCG01G001490.1 Cla01g00145 145
1 1487160 1492916 + ClCG01G001500.2 Cla01g00146 146
10 792295 793614 - ClCG10G000770.1 Cla10g00080 80
10 794886 797575 - ClCG10G000780.1 Cla10g00081 81
10 801410 806170 - ClCG10G000790.2 Cla10g00082 82
10 808041 810057 - ClCG10G000800.1 Cla10g00083 83
2 5596349 5598578 - CmaCh02G009430.1 Cma02g00943 943
6 2794801 2796114 - CmaCh06G005810.1 Cma06g00581 581
6 2797434 2801272 - CmaCh06G005820.1 Cma06g00582 582
6 2802550 2804226 - CmaCh06G005830.1 Cma06g00583 583
15 8270288 8273832 - CmaCh15G013150.1 Cma15g01315 1315
15 8282333 8284326 + CmaCh15G013160.1 Cma15g01316 1316
15 8285753 8287678 + CmaCh15G013180.1 Cma15g01318 1318
15 8553233 8557567 + CmaCh15G013660.1 Cma15g01366 1366
16 9341338 9343774 + CmaCh16G012320.1 Cma16g01232 1232
16 9348957 9354190 + CmaCh16G012330.1 Cma16g01233 1233
6 31032694 31034562 - MELO3C013769.2.1 Cme06g02386 2386
6 31036064 31039143 - MELO3C013770.2.1 Cme06g02387 2387
6 31042705 31046286 - MELO3C013771.2.1 Cme06g02388 2388
6 31048084 31050356 - MELO3C013772.2.1 Cme06g02389 2389
9 22941579 22944436 - MELO3C005787.2.1 Cme09g01881 1881
9 22954988 22958341 - MELO3C005788.2.1 Cme09g01882 1882
9 22964828 22967662 + MELO3C005789.2.1 Cme09g01883 1883
9 22969747 22971125 + MELO3C005790.2.1 Cme09g01884 1884
2 5818406 5820685 - CmoCh02G009510.1 Cmo02g00951 951
6 2874128 2875444 - CmoCh06G005850.1 Cmo06g00585 585
6 2876342 2880898 - CmoCh06G005860.1 Cmo06g00586 586
6 2882458 2888474 - CmoCh06G005870.1 Cmo06g00587 587
15 9393396 9396944 - CmoCh15G013800.1 Cmo15g01380 1380
15 9405419 9407900 + CmoCh15G013810.1 Cmo15g01381 1381
15 9409631 9411633 + CmoCh15G013820.1 Cmo15g01382 1382
16 8084990 8088330 + CmoCh16G011360.1 Cmo16g01136 1136
16 9130029 9132186 + CmoCh16G012780.1 Cmo16g01278 1278
16 9141640 9142947 + CmoCh16G012810.1 Cmo16g01281 1281
1 1412604 1413897 - CmPI595203_01g001430.1 Cmu01g0143 143
1 1417921 1420523 - CmPI595203_01g001440.1 Cmu01g0144 144
1 1433424 1438149 + CmPI595203_01g001450.1 Cmu01g0145 145
1 1446951 1452709 + CmPI595203_01g001460.1 Cmu01g0146 146
10 1225795 1227114 - CmPI595203_10g009250.1 Cmu10g0925 925
10 1228495 1231075 - CmPI595203_10g009260.1 Cmu10g0926 926
10 1235048 1239670 - CmPI595203_10g009270.1 Cmu10g0927 927
10 1241543 1243556 - CmPI595203_10g009280.1 Cmu10g0928 928
12 5097739 5101597 - Conep12aG0061000.1 Cone12ag0589 589
5 4778009 4778503 - Cp4.1LG05g07740.1 Cpe05g00770 770
5 4783119 4785758 + Cp4.1LG05g07640.1 Cpe05g00771 771
8 7224831 7226382 + Cp4.1LG08g09170.1 Cpe08g00916 916
8 7227816 7232383 + Cp4.1LG08g09190.1 Cpe08g00917 917
8 7233067 7234380 + Cp4.1LG08g09150.1 Cpe08g00918 918
14 8600402 8602494 + Cp4.1LG14g10180.1 Cpe14g01018 1018
14 8607284 8610757 + Cp4.1LG14g10190.1 Cpe14g01019 1019
14 8612160 8613467 + Cp4.1LG14g10140.1 Cpe14g01020 1020
9 42856309 42862106 - CrPI670011_09g023600.1 Cre09g2360 2360
9 42870686 42875567 - CrPI670011_09g023610.1 Cre09g2361 2361
9 42888363 42890798 + CrPI670011_09g023620.1 Cre09g2362 2362
9 42895413 42896717 + CrPI670011_09g023630.1 Cre09g2363 2363
10 2194654 2195973 - CrPI670011_10g003410.1 Cre10g0341 341
10 2197371 2208982 - CrPI670011_10g003420.1 Cre10g0342 342
10 2210859 2212901 - CrPI670011_10g003430.1 Cre10g0343 343
5 926271 928167 - CsaV3_5G001610.1 Csa05g00161 161
5 930043 932845 - CsaV3_5G001620.1 Csa05g00162 162
5 939300 941957 + CsaV3_5G001630.1 Csa05g00163 163
5 949031 953908 + CsaV3_5G001650.1 Csa05g00165 165
6 64844660 64846243 - Hsped.06g14340.1 Hepe06g1434 1434
11 34505747 34506965 - Lag0032551.1 Lac11g1913 1913
12 34855200 34856777 - Maker00029429 Lcy12g1515 1515
12 34930610 34934720 + Maker00029332 Lcy12g1518 1518
12 34946292 34950467 + Maker00029291 Lcy12g1519 1519
12 36508051 36511668 + Maker00029174 Lcy12g1621 1621
7 16458240 16459559 - Lsi07G011070.1 Lsi07g01107 1107
7 16460755 16474355 - Lsi07G011080.1 Lsi07g01108 1108
7 16476647 16478548 - Lsi07G011090.1 Lsi07g01109 1109
9 1347889 1349500 - Lsi09G001340.1 Lsi09g00134 134
9 1354791 1357758 - Lsi09G001350.1 Lsi09g00135 135
9 1368793 1378568 + Lsi09G001360.1 Lsi09g00136 136
9 1388484 1394236 + Lsi09G001370.1 Lsi09g00137 137
2 2286156 2287242 + Vvi2g242 Vvi2g242 242
2 2293458 2296287 - Vvi2g243 Vvi2g243 243
2 2305370 2307052 + Vvi2g244 Vvi2g244 244
2 2309711 2311891 + Vvi2g245 Vvi2g245 245
2 2313231 2315418 + Vvi2g246 Vvi2g246 246
2 2321150 2322831 + Vvi2g247 Vvi2g247 247
2 2326793 2327833 + Vvi2g248 Vvi2g248 248
2 2331026 2335451 + Vvi2g249 Vvi2g249 249
2 2335461 2337426 - Vvi2g250 Vvi2g250 250
2 2339994 2341130 + Vvi2g251 Vvi2g251 251
       

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