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
Vvi2g582 . Blo03g00131 Bda06g01301 Bda08g00614 Bpe05g00542 Bpe07g00204 Bma07g00980 . Cmo06g00856 Cmo16g01141 Cma02g01583 . Car02g01346 . Sed01g4069 Cpe14g00902 Cpe05g00208 Bhi11g00101 Tan01g2125 Cmetu06g1180 Lac11g2359 Hepe06g1729 Mch10g1614 . Cla10g00197 Cam10g0203 Cec10g0208 Cco10g0208 Clacu10g0205 Cmu10g1048 Cre10g0456 Cone8ag0444 Cone12ag0605 Cone6ag0623 . Lsi07g01237 . Chy04g00042 Cme06g02508 Blo03g00823 Blo19g00261 Bda07g00844 . Bpe08g00864 Bpe11g00356 Bma05g00399 Bma12g00679 . Cmo02g01625 . Cma06g00833 Cma16g01091 . Car16g01033 . . . . . . . . . Cla09g01186 Cam09g1250 Cec09g1266 Cco09g1300 . . Cre09g1214 . Csa03g04659 Chy06g02109 Cme04g00054
Vvi2g583 Blo02g01006 Blo03g00130 . Bda08g00615 Bpe05g00541 . . . Cmo06g00857 Cmo16g01140 . . . . Sed07g1316 Cpe14g00901 . Bhi11g00102 Tan01g2126 Cmetu06g1446 . . Mch10g1615 . Cla10g00193 Cam10g0199 Cec10g0205 Cco10g0206 Clacu10g0203 Cmu10g1047 Cre10g0453 Cone8ag0445 Cone12ag0434 . . Lsi07g01236 . . Cme06g02506 . . . . . . Bma05g00398 Bma12g00200 . . . Cma06g00834 Cma16g01090 . Car16g01032 . . . . . . . . . . . . . . . . . Csa03g00210 Chy06g02110 .
Vvi2g584 Blo02g01005 . . . Bpe05g00540 . . . Cmo06g00858 Cmo16g01139 . . . . . Cpe14g00900 . Bhi11g00104 . . . . Mch10g1616 . Cla10g00192 Cam10g0198 Cec10g0204 Cco10g0205 Clacu10g0202 Cmu10g1046 Cre10g0452 . . Cone6ag0622 Cone9ag0625 Lsi07g01235 . . Cme06g02505 . . . . . . Bma05g00397 . . . . Cma06g00835 Cma16g01089 . Car16g01031 . . . . . . . . . . . . . . . . . Csa03g00209 . .
Vvi2g585 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car06g00589 . . . . . . . . . . . . . . . . . . . . .
Vvi2g586 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g587 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g590 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g591 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43697311 43698556 + Bda023155.3 Bda06g01301 1301
7 9888113 9890047 + Bda025981.1 Bda07g00844 844
8 6294583 6295393 - Bda029076.1 Bda08g00614 614
8 6302446 6305638 - Bda029077.1 Bda08g00615 615
11 2427774 2429326 - XM_039047630.1 Bhi11g00101 101
11 2533923 2541253 - XM_039050316.1 Bhi11g00102 102
11 2571245 2581968 + XM_039048801.1 Bhi11g00104 104
2 39035920 39045475 - BLOR10735 Blo02g01005 1005
2 39090128 39091634 + BLOR10736 Blo02g01006 1006
3 3765962 3781045 + BLOR11311 Blo03g00130 130
3 3795118 3807065 + BLOR11312 Blo03g00131 131
3 33753454 33754794 - BLOR12004 Blo03g00823 823
19 15100614 15105931 - BLOR09604 Blo19g00261 261
5 12315759 12328524 - Bma021223.1 Bma05g00397 397
5 12332337 12335691 + Bma021224.1 Bma05g00398 398
5 12342242 12343472 + Bma021225.1 Bma05g00399 399
7 37867461 37868531 + Bma026133.1 Bma07g00980 980
12 2665819 2668967 - Bma007087.2 Bma12g00200 200
12 28321375 28322301 - Bma007868.2 Bma12g00679 679
5 19582642 19591582 - Bpe017957.1 Bpe05g00540 540
5 19595247 19598483 + Bpe017958.1 Bpe05g00541 541
5 19604602 19605819 + Bpe017959.1 Bpe05g00542 542
7 1406375 1407622 - Bpe021014.2 Bpe07g00204 204
8 11015412 11016746 + Bpe022987.1 Bpe08g00864 864
11 2626286 2627575 + Bpe003730.1 Bpe11g00356 356
9 14462791 14464113 + CaPI482276_09g012500.1 Cam09g1250 1250
10 3616593 3627033 - CaPI482276_10g001980.1 Cam10g0198 198
10 3634601 3641483 + CaPI482276_10g001990.1 Cam10g0199 199
10 3708560 3709850 + CaPI482276_10g002030.1 Cam10g0203 203
2 8901172 8902521 - Carg08813-RA Car02g01346 1346
6 3394239 3395837 - Carg23559-RA Car06g00589 589
16 8833579 8843505 - Carg23235-RA Car16g01031 1031
16 8851671 8857800 + Carg23236-RA Car16g01032 1032
16 8875308 8876563 + Carg23237-RA Car16g01033 1033
9 14390648 14391982 + CcPI632755_09g013000.1 Cco09g1300 1300
10 2060307 2070526 - CcPI632755_10g002050.1 Cco10g0205 205
10 2078068 2084994 + CcPI632755_10g002060.1 Cco10g0206 206
10 2147877 2149162 + CcPI632755_10g002080.1 Cco10g0208 208
9 14566522 14567849 + CePI673135_09g012660.1 Cec09g1266 1266
10 2141667 2152391 - CePI673135_10g002040.1 Cec10g0204 204
10 2159981 2166826 + CePI673135_10g002050.1 Cec10g0205 205
10 2228814 2230080 + CePI673135_10g002080.1 Cec10g0208 208
4 463976 465323 - Chy4G067600.1 Chy04g00042 42
6 25262454 25263737 - Chy6G126370.1 Chy06g02109 2109
6 25301353 25307588 - Chy6G126380.1 Chy06g02110 2110
10 2369710 2380156 - ClG42_10g0020200.10 Clacu10g0202 202
10 2387709 2394540 + ClG42_10g0020300.10 Clacu10g0203 203
10 2455667 2456950 + ClG42_10g0020500.10 Clacu10g0205 205
9 14496208 14497922 + ClCG09G012480.1 Cla09g01186 1186
10 2168089 2181815 - ClCG10G001960.2 Cla10g00192 192
10 2188943 2196178 + ClCG10G001970.2 Cla10g00193 193
10 2268968 2270521 + ClCG10G002020.1 Cla10g00197 197
2 8988664 8991219 - CmaCh02G015830.1 Cma02g01583 1583
6 4543687 4545598 - CmaCh06G008330.1 Cma06g00833 833
6 4559473 4565619 - CmaCh06G008340.1 Cma06g00834 834
6 4578203 4591518 + CmaCh06G008350.1 Cma06g00835 835
16 8369222 8382536 - CmaCh16G010890.1 Cma16g01089 1089
16 8388759 8395721 + CmaCh16G010900.1 Cma16g01090 1090
16 8411350 8413142 + CmaCh16G010910.1 Cma16g01091 1091
4 414492 416036 - MELO3C003360.2.1 Cme04g00054 54
6 32026417 32038051 - MELO3C013881.2.1 Cme06g02505 2505
6 32045291 32052092 + MELO3C013882.2.1 Cme06g02506 2506
6 32134855 32137851 + MELO3C013883.2.1 Cme06g02508 2508
6 29272023 29275001 - PI0023117.1 Cmetu06g1180 1180
6 29314183 29321244 - PI0023253.1 Cmetu06g1446 1446
2 9363699 9365695 - CmoCh02G016250.1 Cmo02g01625 1625
6 4807028 4808855 - CmoCh06G008560.1 Cmo06g00856 856
6 4822157 4828807 - CmoCh06G008570.1 Cmo06g00857 857
6 4836106 4849874 + CmoCh06G008580.1 Cmo06g00858 858
16 8105295 8115007 - CmoCh16G011390.1 Cmo16g01139 1139
16 8123364 8130120 + CmoCh16G011400.1 Cmo16g01140 1140
16 8147349 8149098 + CmoCh16G011410.1 Cmo16g01141 1141
10 2520685 2531131 - CmPI595203_10g010460.1 Cmu10g1046 1046
10 2538681 2545509 + CmPI595203_10g010470.1 Cmu10g1047 1047
10 2606614 2607901 + CmPI595203_10g010480.1 Cmu10g1048 1048
6 3091300 3098185 - Conep06aG0064100.1 Cone6ag0622 622
6 3112357 3114148 + Conep06aG0064200.1 Cone6ag0623 623
8 2787220 2789251 - Conep08aG0046100.1 Cone8ag0444 444
8 2822591 2826594 - Conep08aG0046200.1 Cone8ag0445 445
9 2964845 2971300 - Conep09aG0063900.1 Cone9ag0625 625
12 2578826 2582611 - Conep12aG0044900.1 Cone12ag0434 434
12 5368846 5370334 - Conep12aG0062600.1 Cone12ag0605 605
5 1152467 1153812 + Cp4.1LG05g01950.1 Cpe05g00208 208
14 7546584 7556633 - Cp4.1LG14g09060.1 Cpe14g00900 900
14 7567495 7577278 + Cp4.1LG14g09030.1 Cpe14g00901 901
14 7595509 7597336 + Cp4.1LG14g09010.1 Cpe14g00902 902
9 14601580 14602908 + CrPI670011_09g012140.1 Cre09g1214 1214
10 3482425 3492851 - CrPI670011_10g004520.1 Cre10g0452 452
10 3500421 3507294 + CrPI670011_10g004530.1 Cre10g0453 453
10 3570955 3572246 + CrPI670011_10g004560.1 Cre10g0456 456
3 1649875 1661410 - CsaV3_3G002090.1 Csa03g00209 209
3 1666774 1673632 + CsaV3_3G002100.1 Csa03g00210 210
3 40483387 40485320 + CsaV3_3G049650.1 Csa03g04659 4659
6 68354692 68356077 - Hsped.06g17290.1 Hepe06g1729 1729
11 39758567 39759911 - Lag0032997.1 Lac11g2359 2359
7 18012115 18023419 - Lsi07G012350.1 Lsi07g01235 1235
7 18029725 18037248 + Lsi07G012360.1 Lsi07g01236 1236
7 18090927 18092262 + Lsi07G012370.1 Lsi07g01237 1237
10 16221982 16224058 - MC10g1279 Mch10g1614 1614
10 16255568 16262807 - MC10g1280 Mch10g1615 1615
10 16274768 16289703 + MC10g1281 Mch10g1616 1616
1 69619931 69622830 - Sed0015081.3 Sed01g4069 4069
7 10004022 10012645 - Sed0018056.1 Sed07g1316 1316
1 24480034 24482014 - Tan0006044.2 Tan01g2125 2125
1 24546125 24555777 - Tan0006882.1 Tan01g2126 2126
2 6021600 6023561 - Vvi2g582 Vvi2g582 582
2 6039132 6077850 - Vvi2g583 Vvi2g583 583
2 6092735 6112317 + Vvi2g584 Vvi2g584 584
2 6113175 6119879 + Vvi2g585 Vvi2g585 585
2 6121039 6122882 + Vvi2g586 Vvi2g586 586
2 6123709 6126522 - Vvi2g587 Vvi2g587 587
2 6126812 6130313 + Vvi2g588 Vvi2g588 588
2 6130867 6159014 + Vvi2g589 Vvi2g589 589
2 6161354 6173803 + Vvi2g590 Vvi2g590 590
2 6174297 6176424 + Vvi2g591 Vvi2g591 591
       

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