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
Vvi17g66 . . . Bda15g00683 Bpe12g00469 . . . . . Cma10g00039 Cma11g00018 Car10g00031 Car11g00016 Sed12g2534 . Cpe04g01631 Bhi02g00655 Tan09g2405 Cmetu02g0008 . Hepe09g0029 . . Cla06g01762 Cam06g1955 Cec06g2005 Cco06g2010 Clacu06g1913 Cmu06g1853 Cre06g2666 . . Cone13ag0241 . . . . . . . . . . . . Bma08g00268 . Cmo10g00037 Cmo11g00017 . . . . . Cpe18g00921 . . . . . . . . . . . . . . Lsi06g01661 Csa01g00032 Chy02g02683 Cme02g02089
Vvi17g67 . Blo16g00283 Bda06g00716 . . Bpe13g00192 Bma06g00274 . . . Cma10g00041 Cma11g00019 Car10g00032 Car11g00018 Sed08g1505 . Cpe04g01630 Bhi02g00657 Tan09g2404 Cmetu02g1332 . Hepe09g0030 . . Cla06g01761 Cam06g1954 Cec06g2004 Cco06g2009 Clacu06g1912 Cmu06g1852 Cre06g2665 Cone2ag0992 . Cone13ag0240 Cone19ag0225 . . . . . . Bda11g01585 Bda14g01344 Bpe07g00900 Bpe15g00235 Bma03g01234 . . Cmo10g00038 Cmo11g00018 . . . . . Cpe18g00920 . . . . . . . . . . . . . . Lsi06g01659 Csa01g00033 . Cme02g02088
Vvi17g68 . Blo16g00282 . . . Bpe13g00193 Bma06g00273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01586 Bda14g01345 . Bpe15g00234 Bma03g01235 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g69 . . . . . . . . . . . Cma11g00020 . Car11g00019 . . Cpe04g01628 Bhi02g00471 . . . Hepe09g0031 . . Cla06g01760 Cam06g1953 Cec06g2003 Cco06g2008 Clacu06g1911 Cmu06g1851 Cre06g2664 . . Cone13ag0239 . . . . . . . . Bda14g01346 . Bpe15g00232 Bma03g01239 . . . Cmo11g00020 . . . . . . . . . . . . . . . . . . . . Lsi06g01658 Csa01g00034 . Cme02g02086
Vvi17g70 . . Bda06g00718 Bda15g00682 Bpe12g00471 . . Bma12g01088 . . Cma10g00046 Cma11g00021 Car10g00035 Car11g00020 Sed12g2525 . Cpe04g01627 Bhi02g00660 Tan09g2398 Cmetu02g1444 . Hepe09g0033 . . Cla06g01759 Cam06g1951 Cec06g2000 Cco06g2006 Clacu06g1908 Cmu06g1848 Cre06g2662 . . Cone13ag0236 Cone19ag0222 . . . . . Blo15g00199 . . Bpe07g00898 . . Bma08g00267 . Cmo10g00041 Cmo11g00021 . . . . . Cpe18g00919 . . . . . . . . . . . . . . Lsi06g01657 Csa01g00038 Chy02g02681 Cme02g02085
Vvi17g71 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g72 . . . Bda15g00681 Bpe12g00472 . . . . . Cma10g00047 . Car10g00036 . Sed01g2393 . . Bhi02g00661 Tan09g2396 Cmetu07g1239 . . . . Cla06g01758 Cam06g1950 Cec06g1999 Cco06g2005 Clacu06g1907 Cmu06g1847 Cre06g2661 . . . Cone19ag0221 . . . . . . . . . . . Bma08g00266 . Cmo10g00042 . . . . . . Cpe18g00918 . . . . . . . . . . . . . . Lsi06g01656 Csa01g00039 Chy02g02680 Cme02g02083
Vvi17g73 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car18g00111 . . . . . . . . . . . . . . . . . . . .
Vvi17g74 . . Bda06g00720 . . . . Bma12g01086 . . Cma10g00048 . Car10g00037 . Sed03g2779 . . Bhi02g00662 Tan09g2394 Cmetu02g0524 . . . . Cla06g01757 Cam06g1949 Cec06g1998 Cco06g2004 Clacu06g1906 Cmu06g1846 Cre06g2660 . . Cone13ag0234 Cone19ag0220 . . . . . Blo15g00201 . . Bpe07g00896 . . . . Cmo10g00043 . . . . . . . . . . . . . . . . . . . . . . Csa01g00040 Chy02g02679 Cme02g02082
Vvi17g75 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 9874207 9876026 + Bda024017.1 Bda06g00716 716
6 9880448 9885803 - Bda024019.1 Bda06g00718 718
6 9900960 9904541 + Bda024022.1 Bda06g00720 720
11 49176051 49176723 + Bda008458.1 Bda11g01585 1585
11 49179701 49182415 - Bda008459.1 Bda11g01586 1586
14 15516123 15518469 + Bda033244 Bda14g01344 1344
14 15519266 15521722 - Bda011035.2 Bda14g01345 1345
14 15555856 15558712 - Bda011037.2 Bda14g01346 1346
15 10240799 10244187 - Bda012532.1 Bda15g00681 681
15 10246878 10252352 + Bda012533.2 Bda15g00682 682
15 10253171 10257003 + Bda012534.1 Bda15g00683 683
2 9199581 9219525 + XM_039023080.1 Bhi02g00471 471
2 12579934 12587183 - XM_039023326.1 Bhi02g00655 655
2 12587244 12590817 + XM_039023328.1 Bhi02g00657 657
2 12708636 12713691 - XM_039022756.1 Bhi02g00660 660
2 12765669 12768886 + XM_039024687.1 Bhi02g00661 661
2 12769464 12779292 + XM_039023539.1 Bhi02g00662 662
15 2048079 2059355 - BLOR06593 Blo15g00199 199
15 2081169 2084775 + BLOR06595 Blo15g00201 201
16 6747924 6750500 + BLOR07530 Blo16g00282 282
16 6753695 6754321 - BLOR07531 Blo16g00283 283
3 20283296 20285659 + Bma017687.1 Bma03g01234 1234
3 20286451 20288902 - Bma031020 Bma03g01235 1235
3 20377532 20382252 - Bma017691.1 Bma03g01239 1239
6 3772433 3781616 + Bma031277 Bma06g00273 273
6 3789995 3790674 - Bma022908.1 Bma06g00274 274
8 3586015 3589370 - Bma027285.1 Bma08g00266 266
8 3592360 3593751 + Bma027286.1 Bma08g00267 267
8 3655906 3659721 + Bma031431 Bma08g00268 268
12 43161365 43164940 - Bma008432.1 Bma12g01086 1086
12 43171244 43176423 + Bma008433.1 Bma12g01088 1088
7 14996009 14999441 - Bpe021737.1 Bpe07g00896 896
7 15006042 15011167 + Bpe021739.1 Bpe07g00898 898
7 15020873 15022657 - Bpe021741.1 Bpe07g00900 900
12 10450514 10454268 - Bpe005729.1 Bpe12g00469 469
12 10481415 10482848 - Bpe005731.1 Bpe12g00471 471
12 10485787 10489111 + Bpe005732.1 Bpe12g00472 472
13 9879658 9882290 + Bpe006313.2 Bpe13g00192 192
13 9883247 9885881 - Bpe006314.1 Bpe13g00193 193
15 13474516 13479187 + Bpe001167.2 Bpe15g00232 232
15 13510682 13513120 + Bpe001169.1 Bpe15g00234 234
15 13513925 13516208 - Bpe001170.1 Bpe15g00235 235
6 30373438 30377549 - CaPI482276_06g019490.1 Cam06g1949 1949
6 30378551 30381251 - CaPI482276_06g019500.1 Cam06g1950 1950
6 30385433 30390304 + CaPI482276_06g019510.1 Cam06g1951 1951
6 30394940 30412754 + CaPI482276_06g019530.1 Cam06g1953 1953
6 30416037 30419016 - CaPI482276_06g019540.1 Cam06g1954 1954
6 30419610 30425902 + CaPI482276_06g019550.1 Cam06g1955 1955
10 141111 145349 - Carg10263-RA Car10g00031 31
10 145477 148698 + Carg10264-RA Car10g00032 32
10 154296 158970 - Carg10267-RA Car10g00035 35
10 159720 162697 + Carg10268-RA Car10g00036 36
10 163123 167190 + Carg10269-RA Car10g00037 37
11 68708 72560 - Carg24552-RA Car11g00016 16
11 76953 78103 + Carg24550-RA Car11g00018 18
11 80291 95211 - Carg24549-RA Car11g00019 19
11 95864 97350 - Carg24548-RA Car11g00020 20
18 600955 601313 + Carg06676-RA Car18g00111 111
6 30117031 30121070 - CcPI632755_06g020040.1 Cco06g2004 2004
6 30122306 30124982 - CcPI632755_06g020050.1 Cco06g2005 2005
6 30130473 30135324 + CcPI632755_06g020060.1 Cco06g2006 2006
6 30144082 30159371 + CcPI632755_06g020080.1 Cco06g2008 2008
6 30162442 30165813 - CcPI632755_06g020090.1 Cco06g2009 2009
6 30165857 30172216 + CcPI632755_06g020100.1 Cco06g2010 2010
6 33198320 33202125 - CePI673135_06g019980.1 Cec06g1998 1998
6 33203234 33205934 - CePI673135_06g019990.1 Cec06g1999 1999
6 33211750 33216647 + CePI673135_06g020000.1 Cec06g2000 2000
6 33224460 33241365 + CePI673135_06g020030.1 Cec06g2003 2003
6 33242197 33245711 - CePI673135_06g020040.1 Cec06g2004 2004
6 33245771 33252105 + CePI673135_06g020050.1 Cec06g2005 2005
2 29715168 29719004 - Chy2G049460.1 Chy02g02679 2679
2 29719764 29722435 - Chy2G049470.1 Chy02g02680 2680
2 29725669 29732866 + Chy2G049480.1 Chy02g02681 2681
2 29736675 29762573 + Chy2G049500.1 Chy02g02683 2683
6 29424173 29428285 - ClG42_06g0190600.10 Clacu06g1906 1906
6 29429287 29431987 - ClG42_06g0190700.10 Clacu06g1907 1907
6 29436170 29441041 + ClG42_06g0190800.10 Clacu06g1908 1908
6 29448776 29463258 + ClG42_06g0191100.10 Clacu06g1911 1911
6 29466776 29470289 - ClG42_06g0191200.10 Clacu06g1912 1912
6 29470349 29476641 + ClG42_06g0191300.10 Clacu06g1913 1913
6 31081301 31085393 - ClCG06G018070.2 Cla06g01757 1757
6 31086206 31089242 - ClCG06G018080.2 Cla06g01758 1758
6 31093028 31098664 + ClCG06G018090.1 Cla06g01759 1759
6 31102657 31121647 + ClCG06G018100.2 Cla06g01760 1760
6 31124937 31127924 - ClCG06G018120.2 Cla06g01761 1761
6 31128516 31134792 + ClCG06G018130.2 Cla06g01762 1762
10 153513 157756 - CmaCh10G000390.1 Cma10g00039 39
10 158312 160959 + CmaCh10G000410.1 Cma10g00041 41
10 166145 171994 - CmaCh10G000460.1 Cma10g00046 46
10 173020 175994 + CmaCh10G000470.1 Cma10g00047 47
10 176352 180718 + CmaCh10G000480.1 Cma10g00048 48
11 73589 77676 - CmaCh11G000180.1 Cma11g00018 18
11 77960 86348 + CmaCh11G000190.1 Cma11g00019 19
11 85836 100298 - CmaCh11G000200.1 Cma11g00020 20
11 100926 102451 - CmaCh11G000210.1 Cma11g00021 21
2 26709151 26713348 - MELO3C026191.2.1 Cme02g02082 2082
2 26713833 26716787 - MELO3C026190.2.1 Cme02g02083 2083
2 26727907 26729819 + MELO3C026188.2.1 Cme02g02085 2085
2 26730904 26744931 + MELO3C026187.2.1 Cme02g02086 2086
2 26745634 26749970 - MELO3C026186.2.1 Cme02g02088 2088
2 26750253 26755768 + MELO3C026185.2.1 Cme02g02089 2089
2 25073168 25078103 + PI0016888.1 Cmetu02g0008 8
2 25026009 25030645 - PI0017683.1 Cmetu02g0524 524
2 25069571 25072523 - PI0026707.1 Cmetu02g1332 1332
2 25036920 25041790 + PI0007775.1 Cmetu02g1444 1444
7 24631394 24636938 + PI0015936.1 Cmetu07g1239 1239
10 184445 188826 - CmoCh10G000370.1 Cmo10g00037 37
10 189028 194366 + CmoCh10G000380.1 Cmo10g00038 38
10 199251 204135 - CmoCh10G000410.1 Cmo10g00041 41
10 204722 207650 + CmoCh10G000420.1 Cmo10g00042 42
10 208090 212429 + CmoCh10G000430.1 Cmo10g00043 43
11 67832 72027 - CmoCh11G000170.1 Cmo11g00017 17
11 71982 75326 + CmoCh11G000180.1 Cmo11g00018 18
11 80081 94375 - CmoCh11G000200.1 Cmo11g00020 20
11 95780 97331 - CmoCh11G000210.1 Cmo11g00021 21
6 29326989 29331081 - CmPI595203_06g018460.1 Cmu06g1846 1846
6 29332166 29334866 - CmPI595203_06g018470.1 Cmu06g1847 1847
6 29339050 29343924 + CmPI595203_06g018480.1 Cmu06g1848 1848
6 29358165 29375709 + CmPI595203_06g018510.1 Cmu06g1851 1851
6 29376570 29380091 - CmPI595203_06g018520.1 Cmu06g1852 1852
6 29380149 29386419 + CmPI595203_06g018530.1 Cmu06g1853 1853
2 35319606 35319818 + Conep02aG0202600.1 Cone2ag0992 992
13 1532615 1536904 - Conep13aG0024400.1 Cone13ag0234 234
13 1549079 1554369 + Conep13aG0024600.1 Cone13ag0236 236
13 1589170 1603122 + Conep13aG0024900.1 Cone13ag0239 239
13 1605303 1607240 - Conep13aG0025000.1 Cone13ag0240 240
13 1607484 1613353 + Conep13aG0025100.1 Cone13ag0241 241
19 1390564 1394531 - Conep19aG0022600.1 Cone19ag0220 220
19 1395688 1399751 - Conep19aG0022700.1 Cone19ag0221 221
19 1406799 1412111 + Conep19aG0022800.1 Cone19ag0222 222
19 1440153 1441936 - Conep19aG0023100.1 Cone19ag0225 225
4 12601127 12602699 + Cp4.1LG04g16210.1 Cpe04g01627 1627
4 12603291 12617621 + Cp4.1LG04g16260.1 Cpe04g01628 1628
4 12621713 12625416 - Cp4.1LG04g16410.1 Cpe04g01630 1630
4 12625593 12629779 + Cp4.1LG04g16250.1 Cpe04g01631 1631
18 8162127 8169915 - Cp4.1LG18g09190.1 Cpe18g00918 918
18 8170392 8179427 + Cp4.1LG18g09080.1 Cpe18g00919 919
18 8181804 8184244 - Cp4.1LG18g09240.1 Cpe18g00920 920
18 8184293 8188495 + Cp4.1LG18g09100.1 Cpe18g00921 921
6 34158876 34163000 - CrPI670011_06g026600.1 Cre06g2660 2660
6 34164088 34166765 - CrPI670011_06g026610.1 Cre06g2661 2661
6 34170949 34175813 + CrPI670011_06g026620.1 Cre06g2662 2662
6 34182887 34198624 + CrPI670011_06g026640.1 Cre06g2664 2664
6 34201831 34205350 - CrPI670011_06g026650.1 Cre06g2665 2665
6 34205516 34211747 + CrPI670011_06g026660.1 Cre06g2666 2666
1 197789 202641 - CsaV3_1G000320.1 Csa01g00032 32
1 202949 206546 + CsaV3_1G000330.1 Csa01g00033 33
1 208308 223084 - CsaV3_1G000340.1 Csa01g00034 34
1 229341 234264 - CsaV3_1G000380.1 Csa01g00038 38
1 237441 240113 + CsaV3_1G000390.1 Csa01g00039 39
1 240899 244669 + CsaV3_1G000400.1 Csa01g00040 40
9 244188 258031 - Hsped.09g00290.1 Hepe09g0029 29
9 258639 265791 + Hsped.09g00300.1 Hepe09g0030 30
9 266280 277260 - Hsped.09g00310.1 Hepe09g0031 31
9 286423 291343 - Hsped.09g00330.1 Hepe09g0033 33
6 26821244 26829596 - Lsi06G016560.1 Lsi06g01656 1656
6 26833724 26839067 + Lsi06G016570.1 Lsi06g01657 1657
6 26839428 26876535 + Lsi06G016580.1 Lsi06g01658 1658
6 26874488 26880840 - Lsi06G016600.1 Lsi06g01659 1659
6 26881166 26886981 + Lsi06G016610.1 Lsi06g01661 1661
1 17956710 17974519 - Sed0018640.3 Sed01g2393 2393
3 44409569 44415019 + Sed0003726.1 Sed03g2779 2779
8 29604397 29609805 - Sed0024725.1 Sed08g1505 1505
12 34638946 34645617 + Sed0005357.1 Sed12g2525 2525
12 34666160 34674416 + Sed0013194.4 Sed12g2534 2534
9 73581238 73585400 - Tan0009705.2 Tan09g2394 2394
9 73586277 73589227 - Tan0016081.1 Tan09g2396 2396
9 73591344 73597073 + Tan0000380.1 Tan09g2398 2398
9 73698588 73706562 - Tan0008839.1 Tan09g2404 2404
9 73706838 73712048 + Tan0012728.1 Tan09g2405 2405
17 581997 588367 - Vvi17g66 Vvi17g66 66
17 588539 591995 + Vvi17g67 Vvi17g67 67
17 592603 596839 - Vvi17g68 Vvi17g68 68
17 604661 637273 - Vvi17g69 Vvi17g69 69
17 696454 707562 - Vvi17g70 Vvi17g70 70
17 711457 716027 + Vvi17g71 Vvi17g71 71
17 717751 722776 + Vvi17g72 Vvi17g72 72
17 723569 725613 - Vvi17g73 Vvi17g73 73
17 734894 740741 + Vvi17g74 Vvi17g74 74
17 740805 743853 - Vvi17g75 Vvi17g75 75
       

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