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
Vvi4g1212 . . Bda04g00345 . . . Bma09g00240 . . . Cma03g01070 Cma07g00779 Car03g00964 Car07g00767 Sed14g0207 Cpe19g00546 Cpe10g00356 Bhi03g01399 Tan03g1346 Cmetu04g0645 . Hepe04g1136 . . Cla01g01539 Cam01g1610 Cec04g1256 Cco04g1328 Clacu01g1636 Cmu01g1523 Cre04g1201 . . . . Lsi01g01123 . . . . . . . . Bpe06g00282 . . . Cmo03g01065 Cmo07g00803 . . . . . . . . . . . . . . . . . . . . . Csa06g02814 Chy02g01021 .
Vvi4g1213 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1214 . Blo16g00517 . . . Bpe13g00010 . . . Cmo20g01089 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01353 . . . . Bma06g00530 . . . . Cma20g01079 . . . Cpe16g00066 Bhi10g02348 . . . . . . Cla02g00078 Cam02g0081 Cec02g0083 Cco02g0075 Clacu02g0079 Cmu02g0077 Cre02g0417 Lsi10g00700 . . .
Vvi4g1215 . . Bda04g00343 Bda10g00347 . . . Bma15g00824 Cmo02g00591 Cmo20g01088 Cma03g01072 Cma07g00780 Car03g00965 Car07g00768 . . . Bhi03g01397 . . . Hepe04g1135 . . Cla01g01537 Cam01g1607 Cec04g1254 Cco04g1326 Clacu01g1634 Cmu01g1521 Cre04g1199 . . . . Lsi01g01125 . . Cme08g01047 . . . . . Bpe06g00281 . . . Cmo03g01066 Cmo07g00804 . Cma20g01077 . . . . Bhi10g02345 Tan07g0901 . . . . . Cla02g00077 Cam02g0079 Cec02g0082 Cco02g0073 Clacu02g0077 Cmu02g0076 Cre02g0416 Lsi10g00702 Csa06g02812 Chy02g01022 Cme11g00081
Vvi4g1216 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1217 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1218 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1219 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1220 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1221 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 48658751 48660737 - Bda019249.1 Bda04g00343 343
4 48760103 48764019 - Bda019252.1 Bda04g00345 345
10 34097858 34101354 + Bda007146.1 Bda10g00347 347
11 15418332 15422752 - Bda007885.1 Bda11g01353 1353
3 29209625 29214719 - XM_039025355.1 Bhi03g01397 1397
3 29265443 29268594 - XM_039026962.1 Bhi03g01399 1399
10 61216471 61225918 - XM_039044998.1 Bhi10g02345 2345
10 61497650 61508219 + XM_039045828.1 Bhi10g02348 2348
16 21049055 21053543 - BLOR07765 Blo16g00517 517
6 27251741 27256141 + Bma023410.1 Bma06g00530 530
9 10331882 10339006 - Bma029020.1 Bma09g00240 240
15 20240482 20243339 + Bma013946.1 Bma15g00824 824
6 13755274 13757104 - Bpe019776.1 Bpe06g00281 281
6 13788321 13790547 - Bpe025930 Bpe06g00282 282
13 259717 264113 - Bpe006091.1 Bpe13g00010 10
1 29637568 29641322 - CaPI482276_01g016070.1 Cam01g1607 1607
1 29682249 29684336 - CaPI482276_01g016100.1 Cam01g1610 1610
2 1893873 1901624 - CaPI482276_02g000790.1 Cam02g0079 79
2 1931988 1936242 + CaPI482276_02g000810.1 Cam02g0081 81
3 7474437 7476916 + Carg10557-RA Car03g00964 964
3 7481299 7483675 + Carg10556-RA Car03g00965 965
7 3998196 4000142 + Carg05289-RA Car07g00767 767
7 4005272 4013841 + Carg05290-RA Car07g00768 768
2 770456 778239 - CcPI632755_02g000730.1 Cco02g0073 73
2 807968 812220 + CcPI632755_02g000750.1 Cco02g0075 75
4 28581671 28585359 - CcPI632755_04g013260.1 Cco04g1326 1326
4 28628561 28630644 - CcPI632755_04g013280.1 Cco04g1328 1328
2 764182 772049 - CePI673135_02g000820.1 Cec02g0082 82
2 813305 817560 + CePI673135_02g000830.1 Cec02g0083 83
4 32128548 32132313 - CePI673135_04g012540.1 Cec04g1254 1254
4 32172101 32174182 - CePI673135_04g012560.1 Cec04g1256 1256
2 6898409 6900498 + Chy2G032880.1 Chy02g01021 1021
2 6920765 6923225 + Chy2G032890.1 Chy02g01022 1022
1 28434093 28437791 - ClG42_01g0163400.10 Clacu01g1634 1634
1 28481783 28483870 - ClG42_01g0163600.10 Clacu01g1636 1636
2 779069 786756 - ClG42_02g0007700.10 Clacu02g0077 77
2 814638 818887 + ClG42_02g0007900.10 Clacu02g0079 79
1 29966743 29984292 - ClCG01G015700.1 Cla01g01537 1537
1 30034526 30037744 - ClCG01G015720.1 Cla01g01539 1539
2 769400 787908 - ClCG02G000730.1 Cla02g00077 77
2 819383 824096 + ClCG02G000740.1 Cla02g00078 78
3 7369633 7371704 + CmaCh03G010700.1 Cma03g01070 1070
3 7376133 7378102 + CmaCh03G010720.1 Cma03g01072 1072
7 3520989 3524751 + CmaCh07G007790.1 Cma07g00779 779
7 3528513 3531145 + CmaCh07G007800.1 Cma07g00780 780
20 8164616 8172190 - CmaCh20G010770.1 Cma20g01077 1077
20 8289789 8294875 + CmaCh20G010790.1 Cma20g01079 1079
8 6815908 6821191 + MELO3C008025.2.1 Cme08g01047 1047
11 651255 654868 - MELO3C023269.2.1 Cme11g00081 81
4 7305086 7308596 + PI0022770.1 Cmetu04g0645 645
2 3540127 3542339 - CmoCh02G005910.1 Cmo02g00591 591
3 7936736 7939997 + CmoCh03G010650.1 Cmo03g01065 1065
3 7944503 7946483 + CmoCh03G010660.1 Cmo03g01066 1066
7 3696220 3698608 + CmoCh07G008030.1 Cmo07g00803 803
7 3703448 3705932 + CmoCh07G008040.1 Cmo07g00804 804
20 10336094 10345605 - CmoCh20G010880.1 Cmo20g01088 1088
20 10375329 10380313 + CmoCh20G010890.1 Cmo20g01089 1089
1 28782420 28786080 - CmPI595203_01g015210.1 Cmu01g1521 1521
1 28831215 28833301 - CmPI595203_01g015230.1 Cmu01g1523 1523
2 778278 785968 - CmPI595203_02g000760.1 Cmu02g0076 76
2 813920 818170 + CmPI595203_02g000770.1 Cmu02g0077 77
10 2095567 2098744 - Cp4.1LG10g03250.1 Cpe10g00356 356
16 1293251 1298411 - Cp4.1LG16g00680.1 Cpe16g00066 66
19 4627206 4631318 - Cp4.1LG19g11990.1 Cpe19g00546 546
2 1321769 1329424 - CrPI670011_02g004160.1 Cre02g0416 416
2 1357459 1361717 + CrPI670011_02g004170.1 Cre02g0417 417
4 30646996 30650735 - CrPI670011_04g011990.1 Cre04g1199 1199
4 30691261 30693341 - CrPI670011_04g012010.1 Cre04g1201 1201
6 24539677 24542137 - CsaV3_6G041980.1 Csa06g02812 2812
6 24560912 24564864 - CsaV3_6G042000.1 Csa06g02814 2814
4 66430436 66441343 - Hsped.04g11350.1 Hepe04g1135 1135
4 66472052 66475385 - Hsped.04g11360.1 Hepe04g1136 1136
1 9306083 9308660 + Lsi01G011230.1 Lsi01g01123 1123
1 9353369 9357587 + Lsi01G011250.1 Lsi01g01125 1125
10 9783469 9790336 - Lsi10G007000.1 Lsi10g00700 700
10 9835323 9844407 + Lsi10G007020.1 Lsi10g00702 702
14 2325340 2329971 - Sed0022459.1 Sed14g0207 207
3 70031209 70034502 - Tan0007470.3 Tan03g1346 1346
7 16952750 16980087 + Tan0008538.2 Tan07g0901 901
4 20975647 20978345 + Vvi4g1212 Vvi4g1212 1212
4 20985265 20986429 + Vvi4g1213 Vvi4g1213 1213
4 20988398 20996526 - Vvi4g1214 Vvi4g1214 1214
4 21012615 21016482 + Vvi4g1215 Vvi4g1215 1215
4 21017334 21020793 - Vvi4g1216 Vvi4g1216 1216
4 21026430 21027195 + Vvi4g1217 Vvi4g1217 1217
4 21074079 21075193 + Vvi4g1218 Vvi4g1218 1218
4 21075194 21076353 + Vvi4g1219 Vvi4g1219 1219
4 21086939 21093820 + Vvi4g1220 Vvi4g1220 1220
4 21096320 21098453 + Vvi4g1221 Vvi4g1221 1221
       

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