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
Vvi17g536 . . Bda06g00548 . . . . Bma12g00999 . . . Cma11g00149 . Car11g00146 Sed08g0208 . . Bhi02g00331 Tan09g2132 Cmetu02g0840 . Hepe09g0126 . . . . . . . . . . . Cone13ag0076 . . . . . . . . . Bpe07g00786 . . . . . Cmo11g00158 . . . . . . . . . . . . . . . . . . . . . Csa01g00227 Chy02g02505 Cme02g01891
Vvi17g537 Blo04g00768 . Bda06g00547 Bda15g00599 Bpe12g00551 . . Bma12g00998 Cmo13g01176 . Cma10g00186 . Car10g00176 Car11g00147 Sed08g0209 Cpe20g00029 . Bhi02g00330 Tan09g2130 Cmetu02g1507 . Hepe09g0125 . . Cla06g01596 Cam06g1770 Cec06g1822 Cco06g1829 Clacu06g1733 Cmu06g1677 Cre06g2493 . . . Cone19ag0075 Lsi02g00060 Csa01g00533 Chy12g01554 Cme12g02008 Blo13g00013 Blo15g00307 . Bda14g00846 Bpe07g00785 Bpe15g00605 . Bma08g00216 . Cmo10g00203 Cmo11g00159 Cma13g01122 . Car13g00957 . . Cpe18g00799 . . . . . . . Cla04g01209 Cam04g1275 Cec01g1783 Cco01g1830 Clacu04g1303 Cmu04g1279 Cre01g1570 Lsi06g01472 Csa01g00228 Chy02g02504 Cme02g01890
Vvi17g538 . . . Bda15g00573 Bpe12g00550 . . . Cmo13g01178 . . . . . . Cpe20g00027 . . . . . . . . . . . . . . . . . Cone13ag0075 Cone19ag0074 Lsi02g00064 Csa01g00536 Chy12g01551 Cme12g02005 Blo13g00012 . . . . . . Bma08g00217 . . . Cma13g01124 . Car13g00959 . . . . . . . . . . Cla04g01206 Cam04g1272 Cec01g1780 Cco01g1827 Clacu04g1300 Cmu04g1276 Cre01g1567 . . . .
Vvi17g539 Blo04g00769 . . . . Bpe13g00286 . . Cmo13g01179 . . . . . . Cpe20g00025 . . . . . . . . . . . . . . . . . . . Lsi02g00066 Csa01g00538 Chy12g01550 Cme12g02004 . . . Bda14g00848 . Bpe15g00603 . . . . . . . Car13g00960 . . . . . . . . . . Cla04g01205 Cam04g1271 Cec01g1779 Cco01g1826 Clacu04g1299 Cmu04g1275 Cre01g1565 . . . .
Vvi17g540 . Blo16g00188 . . . Bpe13g00287 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g541 . . . . . Bpe13g00288 . . Cmo13g01180 . . . . . . Cpe20g00023 . . . . . . . . . . . . . . . . Cone16ag0162 . . Lsi02g00067 . . . . . . . . . . . . . . Cma13g01126 . Car13g00961 . . . . . . . . . . . . . . . . . . . . .
Vvi17g542 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g544 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g545 . Blo16g00187 . . . Bpe13g00289 Bma06g00176 . Cmo13g01182 . . . . . . Cpe20g00022 . . . . . . . . . . . . . . . . . . . . Csa01g00539 Chy12g01549 . . . . . . . . . . . . Cma13g01128 . Car13g00963 . . . . . . . . . . Cla04g01204 . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7746366 7747511 + Bda023805.1 Bda06g00547 547
6 7750637 7753193 + Bda023806.1 Bda06g00548 548
14 6520571 6521590 - Bda027619.1 Bda14g00846 846
14 6532342 6533466 - Bda027621.1 Bda14g00848 848
15 8930096 8933683 + Bda012416.1 Bda15g00573 573
15 9200301 9201461 - Bda012443.1 Bda15g00599 599
2 6136733 6140382 + XM_039023873.1 Bhi02g00330 330
2 6146238 6152210 + XM_039023053.1 Bhi02g00331 331
4 7327486 7328505 - BLOR13680 Blo04g00768 768
4 7382206 7383330 - BLOR13681 Blo04g00769 769
13 158292 161741 + BLOR05293 Blo13g00012 12
13 195089 196246 + BLOR05294 Blo13g00013 13
15 3443093 3444241 - BLOR06701 Blo15g00307 307
16 4236827 4239502 + BLOR07435 Blo16g00187 187
16 4242243 4252571 + BLOR07436 Blo16g00188 188
6 2220914 2223589 + Bma022791.1 Bma06g00176 176
8 2682222 2683386 - Bma027226.1 Bma08g00216 216
8 2697955 2700640 - Bma027228.1 Bma08g00217 217
12 42072358 42073224 + Bma008345.1 Bma12g00998 998
12 42079259 42081773 + Bma008346.1 Bma12g00999 999
7 14287029 14288171 + Bpe021630.1 Bpe07g00785 785
7 14291607 14294175 + Bpe021631.1 Bpe07g00786 786
12 11337583 11341096 + Bpe005814.1 Bpe12g00550 550
12 11348752 11349915 + Bpe005815.1 Bpe12g00551 551
13 10741108 10742106 - Bpe006411.1 Bpe13g00286 286
13 10748746 10751335 - Bpe006412.1 Bpe13g00287 287
13 10753563 10756507 - Bpe006413.1 Bpe13g00288 288
13 10758179 10760566 - Bpe006414.1 Bpe13g00289 289
15 16956020 16957153 + Bpe001537.1 Bpe15g00603 603
15 16963063 16964082 + Bpe001539.1 Bpe15g00605 605
4 26608002 26609297 + CaPI482276_04g012710.1 Cam04g1271 1271
4 26613264 26617939 + CaPI482276_04g012720.1 Cam04g1272 1272
4 26628138 26629943 + CaPI482276_04g012750.1 Cam04g1275 1275
6 28886272 28887450 + CaPI482276_06g017700.1 Cam06g1770 1770
10 839601 840770 - Carg10408-RA Car10g00176 176
11 825970 829528 - Carg18183-RA Car11g00146 146
11 831723 832850 - Carg18184-RA Car11g00147 147
13 9659431 9661136 - Carg04714-RA Car13g00957 957
13 9663924 9667598 - Carg04712-RA Car13g00959 959
13 9671101 9672330 - Carg04711-RA Car13g00960 960
13 9673317 9676516 - Carg04710-RA Car13g00961 961
13 9680954 9683632 - Carg04709-RA Car13g00963 963
1 30871870 30873165 + CcPI632755_01g018260.1 Cco01g1826 1826
1 30877139 30881829 + CcPI632755_01g018270.1 Cco01g1827 1827
1 30897842 30899657 + CcPI632755_01g018300.1 Cco01g1830 1830
6 28593417 28594613 + CcPI632755_06g018290.1 Cco06g1829 1829
1 32290692 32291987 + CePI673135_01g017790.1 Cec01g1779 1779
1 32295945 32300734 + CePI673135_01g017800.1 Cec01g1780 1780
1 32310893 32312717 + CePI673135_01g017830.1 Cec01g1783 1783
6 31656827 31658023 + CePI673135_06g018220.1 Cec06g1822 1822
2 28485684 28486931 + Chy2G047710.1 Chy02g02504 2504
2 28491058 28495706 + Chy2G047720.1 Chy02g02505 2505
12 19144764 19149865 + Chy12G221490.1 Chy12g01549 1549
12 19150916 19152208 + Chy12G221500.1 Chy12g01550 1550
12 19155926 19159882 + Chy12G221510.1 Chy12g01551 1551
12 19166908 19168784 + Chy12G221540.1 Chy12g01554 1554
4 26964135 26965430 + ClG42_04g0129900.10 Clacu04g1299 1299
4 26970815 26975639 + ClG42_04g0130000.10 Clacu04g1300 1300
4 26984901 26986727 + ClG42_04g0130300.10 Clacu04g1303 1303
6 27941806 27943002 + ClG42_06g0173300.10 Clacu06g1733 1733
4 27210773 27217249 + ClCG04G012330.2 Cla04g01204 1204
4 27218753 27220048 + ClCG04G012340.1 Cla04g01205 1205
4 27225234 27230617 + ClCG04G012350.1 Cla04g01206 1206
4 27239889 27241715 + ClCG04G012380.1 Cla04g01209 1209
6 29505943 29507139 + ClCG06G016250.1 Cla06g01596 1596
10 850757 851956 - CmaCh10G001860.1 Cma10g00186 186
11 789672 793637 + CmaCh11G001490.1 Cma11g00149 149
13 8356359 8357660 - CmaCh13G011220.1 Cma13g01122 1122
13 8360594 8364128 - CmaCh13G011240.1 Cma13g01124 1124
13 8369626 8372942 - CmaCh13G011260.1 Cma13g01126 1126
13 8377279 8379957 - CmaCh13G011280.1 Cma13g01128 1128
2 25419111 25420541 + MELO3C017168.2.1 Cme02g01890 1890
2 25425086 25430491 + MELO3C017167.2.1 Cme02g01891 1891
12 25691756 25696414 + MELO3C001974.2.1 Cme12g02004 2004
12 25700195 25704686 + MELO3C001973.2.1 Cme12g02005 2005
12 25710988 25713753 + MELO3C001972.2.1 Cme12g02008 2008
2 23758133 23763536 + PI0013627.1 Cmetu02g0840 840
2 23752579 23754358 + PI0002693.1 Cmetu02g1507 1507
10 910288 911457 - CmoCh10G002030.1 Cmo10g00203 203
11 793613 797511 - CmoCh11G001580.1 Cmo11g00158 158
11 799344 800471 - CmoCh11G001590.1 Cmo11g00159 159
13 9377630 9378806 - CmoCh13G011760.1 Cmo13g01176 1176
13 9381846 9385308 - CmoCh13G011780.1 Cmo13g01178 1178
13 9388562 9389791 - CmoCh13G011790.1 Cmo13g01179 1179
13 9390594 9393911 - CmoCh13G011800.1 Cmo13g01180 1180
13 9398355 9401033 - CmoCh13G011820.1 Cmo13g01182 1182
4 27145806 27147101 + CmPI595203_04g012750.1 Cmu04g1275 1275
4 27152486 27157299 + CmPI595203_04g012760.1 Cmu04g1276 1276
4 27166591 27168436 + CmPI595203_04g012790.1 Cmu04g1279 1279
6 27850054 27851250 + CmPI595203_06g016770.1 Cmu06g1677 1677
13 443087 444792 - Conep13aG0007700.1 Cone13ag0073 73
13 448516 451257 + Conep13aG0007900.1 Cone13ag0075 75
13 468140 470762 + Conep13aG0008000.1 Cone13ag0076 76
16 993259 998520 - Conep16aG0016500.1 Cone16ag0161 161
16 999615 1002280 - Conep16aG0016600.1 Cone16ag0162 162
19 448472 452624 + Conep19aG0007900.1 Cone19ag0074 74
19 459768 461381 + Conep19aG0008000.1 Cone19ag0075 75
18 7484052 7484771 + Cp4.1LG18g07860.1 Cpe18g00799 799
20 123242 126262 + Cp4.1LG20g00240.1 Cpe20g00022 22
20 126810 133239 + Cp4.1LG20g00210.1 Cpe20g00023 23
20 134287 135516 + Cp4.1LG20g00110.1 Cpe20g00025 25
20 138885 142847 + Cp4.1LG20g00140.1 Cpe20g00027 27
20 145294 150254 + Cp4.1LG20g00130.1 Cpe20g00029 29
1 28812144 28813439 + CrPI670011_01g015650.1 Cre01g1565 1565
1 28817388 28822125 + CrPI670011_01g015670.1 Cre01g1567 1567
1 28832522 28834326 + CrPI670011_01g015700.1 Cre01g1570 1570
6 32663957 32665153 + CrPI670011_06g024930.1 Cre06g2493 2493
1 1453474 1458268 - CsaV3_1G002270.1 Csa01g00227 227
1 1459334 1463148 - CsaV3_1G002280.1 Csa01g00228 228
1 3515792 3517790 - CsaV3_1G005330.1 Csa01g00533 533
1 3523892 3528780 - CsaV3_1G005360.1 Csa01g00536 536
1 3532296 3533588 - CsaV3_1G005380.1 Csa01g00538 538
1 3534654 3539494 - CsaV3_1G005390.1 Csa01g00539 539
9 998999 1000255 + Hsped.09g01250.1 Hepe09g0125 125
9 1007322 1012316 + Hsped.09g01260.1 Hepe09g0126 126
2 554602 557155 - Lsi02G000610.1 Lsi02g00060 60
2 569738 572347 - Lsi02G000640.1 Lsi02g00064 64
2 575934 577229 - Lsi02G000660.1 Lsi02g00066 66
2 578395 584396 - Lsi02G000670.1 Lsi02g00067 67
6 25231360 25232562 + Lsi06G014720.1 Lsi06g01472 1472
8 1179320 1184776 - Sed0010411.1 Sed08g0208 208
8 1194138 1195904 - Sed0023822.1 Sed08g0209 209
9 71602131 71604119 + Tan0007642.1 Tan09g2130 2130
9 71610339 71616237 + Tan0013757.3 Tan09g2132 2132
17 6571629 6582153 - Vvi17g536 Vvi17g536 536
17 6588504 6590555 - Vvi17g537 Vvi17g537 537
17 6601152 6607419 - Vvi17g538 Vvi17g538 538
17 6613319 6614938 - Vvi17g539 Vvi17g539 539
17 6616973 6623015 - Vvi17g540 Vvi17g540 540
17 6634543 6638502 - Vvi17g541 Vvi17g541 541
17 6639929 6640340 - Vvi17g542 Vvi17g542 542
17 6658309 6659280 - Vvi17g543 Vvi17g543 543
17 6661140 6663435 + Vvi17g544 Vvi17g544 544
17 6668794 6671476 - Vvi17g545 Vvi17g545 545
       

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