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
Vvi5g19 . . . . . . . . Cmo08g01260 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma08g01296 . Car08g01161 . . Cpe17g00082 . . . . . . . . . . . . . . . . . .
Vvi5g20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g01597 . . Cme06g00817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g01537 Chy06g00774 .
Vvi5g21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g01403 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g23 . . . . . . . . . . . Cma14g01573 . Car14g01386 Sed02g1121 . Cpe03g01314 Bhi01g01109 Tan10g1095 Cmetu06g2217 . Hepe05g1358 . Lcy11g1320 . . . . . . . . . . . . . . . . Blo07g00129 Bda11g00490 . . . . Bma06g01454 . . Cmo14g01606 . . . . . . . . . . . . . Cla05g00724 Cam05g0794 Cec05g0799 Cco05g0797 Clacu05g0783 . Cre05g0823 . . . .
Vvi5g24 . . . . . . . . Cmo08g01260 Cmo17g00379 . . . . . . . . . . . . . . Cla06g00405 Cam06g0427 Cec06g0435 Cco06g0434 Clacu06g0413 Cmu06g0413 Cre06g1193 . . Cone7ag0088 Cone4ag0094 . . Chy11g01599 . . . . . . . . . Sed09g0622 . . Cma08g01296 Cma17g00390 Car08g01161 Car17g00360 Cpe12g00341 Cpe17g00082 Bhi12g01966 Tan06g2801 Cmetu11g1241 . . . Lcy12g0887 . . . . . . . . . . Cme11g02103
Vvi5g25 Blo01g00046 . . Bda08g00318 . . . Bma05g01012 . Cmo17g00378 Cma06g01576 . Car06g01339 . Sed02g1123 Cpe08g00140 . Bhi01g01107 Tan10g1093 Cmetu03g1502 Lac11g1008 Hepe05g1360 . Lcy11g1322 Cla06g00406 Cam06g0428 . . Clacu06g0414 Cmu06g0414 Cre06g1194 . Cone15ag0714 Cone7ag0089 . Lsi05g01405 . . Cme06g00815 . . . . Bpe05g00810 . . . . Cmo06g01570 . . Cma17g00389 . Car17g00359 Cpe12g00340 . Bhi12g01965 Tan06g2800 . . . . Lcy12g0886 Cla05g00723 . . . . Cmu05g0745 . . Csa03g01535 Chy06g00772 .
Vvi5g26 Blo01g00045 . . Bda08g00319 . . . Bma05g01011 . Cmo17g00377 . . . . . . . . . . . . . . Cla06g00407 Cam06g0429 Cec06g0436 Cco06g0435 Clacu06g0415 Cmu06g0415 Cre06g1195 . . . . . . Chy11g01596 . . . . . Bpe05g00809 . . . . . . . Cma17g00388 . Car17g00358 Cpe12g00339 . Bhi12g01957 . . . . . Lcy12g0885 . . . . . . . Lsi09g01512 . . Cme11g02101
Vvi5g27 Blo01g00043 . . Bda08g00320 . . . Bma05g01010 . Cmo17g00376 . . . . . . . . . . . . . . Cla06g00408 Cam06g0430 Cec06g0437 Cco06g0436 Clacu06g0416 Cmu06g0416 Cre06g1196 . . . . . Csa06g01841 Chy11g01595 . . . . . Bpe05g00808 . . . Sed09g0619 . . . Cma17g00387 . Car17g00357 Cpe12g00338 . Bhi12g01956 Tan06g2787 Cmetu11g1561 . Hepe03g0028 . Lcy12g0884 . . . . . . . Lsi09g01511 . . Cme11g02100
Vvi5g28 . . . . . Bpe14g01085 . . . . Cma06g01575 Cma14g01575 Car06g01338 Car14g01388 . Cpe08g00141 Cpe03g01316 Bhi01g01104 . . . . . Lcy11g1324 . . . . . . . . . . Cone4ag0095 Lsi05g01407 . . Cme06g00803 Blo02g00466 Blo07g00130 Bda11g00491 Bda13g00228 . Bpe13g00708 Bma02g00940 . . Cmo06g01569 Cmo14g01609 . . . . . . . . . . . . . Cla05g00720 . . . . . . . Csa03g01533 Chy06g00770 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 3290884 3294154 - Bda024756.1 Bda08g00318 318
8 3303179 3310873 - Bda024757.1 Bda08g00319 319
8 3313677 3333093 - Bda024759.1 Bda08g00320 320
11 5171297 5171846 - Bda005226.1 Bda11g00490 490
11 5219203 5220627 + Bda005227.1 Bda11g00491 491
13 2879914 2881221 + Bda001107.1 Bda13g00228 228
1 21214438 21215735 - XM_039046060.1 Bhi01g01104 1104
1 21366816 21370996 + XM_039022085.1 Bhi01g01107 1107
1 21376244 21380205 - XM_039037419.1 Bhi01g01109 1109
12 62171605 62183730 + XM_039018479.1 Bhi12g01956 1956
12 62215943 62228912 + XM_039051183.1 Bhi12g01957 1957
12 62317083 62321392 + XM_039050665.1 Bhi12g01965 1965
12 62325727 62327846 + XM_039050969.1 Bhi12g01966 1966
1 581043 597888 + BLOR00043 Blo01g00043 43
1 603195 609287 + BLOR00045 Blo01g00045 45
1 610816 613721 + BLOR00046 Blo01g00046 46
2 6604981 6606277 + BLOR10196 Blo02g00466 466
7 1748117 1752184 - BLOR18061 Blo07g00129 129
7 1790428 1791857 + BLOR18062 Blo07g00130 130
2 49264752 49266048 - Bma015732.1 Bma02g00940 940
5 48579649 48599261 + Bma022165.1 Bma05g01010 1010
5 48601879 48609582 + Bma022166.1 Bma05g01011 1011
5 48612023 48614971 + Bma022167.1 Bma05g01012 1012
6 51223739 51224629 - Bma024568.1 Bma06g01454 1454
5 21390969 21412211 + Bpe018221.1 Bpe05g00808 808
5 21414712 21423177 + Bpe018222.1 Bpe05g00809 809
5 21424651 21427551 + Bpe018223.1 Bpe05g00810 810
13 13658806 13660233 - Bpe010409.1 Bpe13g00708 708
14 8125160 8126469 + Bpe014459.1 Bpe14g01085 1085
5 6961265 6963285 - CaPI482276_05g007940.1 Cam05g0794 794
6 6390933 6392705 - CaPI482276_06g004270.1 Cam06g0427 427
6 6396909 6401218 - CaPI482276_06g004280.1 Cam06g0428 428
6 6402858 6413354 - CaPI482276_06g004290.1 Cam06g0429 429
6 6419345 6430700 - CaPI482276_06g004300.1 Cam06g0430 430
6 9601606 9602748 - Carg25647-RA Car06g01338 1338
6 9612035 9617697 + Carg25648-RA Car06g01339 1339
8 7783463 7786930 + Carg18903-RA Car08g01161 1161
14 11720238 11723601 + Carg19607-RA Car14g01386 1386
14 11732210 11733174 + Carg19609-RA Car14g01388 1388
17 2273875 2287167 + Carg05564-RA Car17g00357 357
17 2288150 2297793 + Carg05565-RA Car17g00358 358
17 2299171 2303778 + Carg05566-RA Car17g00359 359
17 2306660 2308407 + Carg05567-RA Car17g00360 360
5 6673800 6677666 - CcPI632755_05g007970.1 Cco05g0797 797
6 4763117 4764907 - CcPI632755_06g004340.1 Cco06g0434 434
6 4770042 4786952 - CcPI632755_06g004350.1 Cco06g0435 435
6 4792647 4804311 - CcPI632755_06g004360.1 Cco06g0436 436
5 6698705 6702604 - CePI673135_05g007990.1 Cec05g0799 799
6 4903112 4904837 - CePI673135_06g004350.1 Cec06g0435 435
6 4909081 4925671 - CePI673135_06g004360.1 Cec06g0436 436
6 4932261 4943624 - CePI673135_06g004370.1 Cec06g0437 437
6 5331767 5332908 - Chy6G112980.1 Chy06g00770 770
6 5365874 5369791 + Chy6G113000.1 Chy06g00772 772
6 5375213 5376750 - Chy6G113020.1 Chy06g00774 774
11 22514764 22522234 + Chy11G201750.1 Chy11g01595 1595
11 22528493 22542645 + Chy11G201760.1 Chy11g01596 1596
11 22559104 22560848 + Chy11G201790.1 Chy11g01599 1599
5 6669124 6672948 - ClG42_05g0078300.10 Clacu05g0783 783
6 4928556 4930326 - ClG42_06g0041300.10 Clacu06g0413 413
6 4935298 4938669 - ClG42_06g0041400.10 Clacu06g0414 414
6 4940367 4950805 - ClG42_06g0041500.10 Clacu06g0415 415
6 4956869 4968202 - ClG42_06g0041600.10 Clacu06g0416 416
5 6774419 6775530 - ClCG05G006705.1 Cla05g00720 720
5 6813697 6817978 + ClCG05G006720.1 Cla05g00723 723
5 6822471 6826651 - ClCG05G006740.1 Cla05g00724 724
6 4957797 4960119 - ClCG06G004340.2 Cla06g00405 405
6 4964563 4967908 - ClCG06G004350.1 Cla06g00406 406
6 4969320 4980209 - ClCG06G004360.1 Cla06g00407 407
6 4985504 4998146 - ClCG06G004370.1 Cla06g00408 408
6 9857508 9859264 - CmaCh06G015750.1 Cma06g01575 1575
6 9865219 9869713 + CmaCh06G015760.1 Cma06g01576 1576
8 7863358 7864851 + CmaCh08G012960.1 Cma08g01296 1296
14 11842205 11845344 + CmaCh14G015730.1 Cma14g01573 1573
14 11853396 11854750 + CmaCh14G015750.1 Cma14g01575 1575
17 2167340 2183333 + CmaCh17G003870.1 Cma17g00387 387
17 2184685 2195012 + CmaCh17G003880.1 Cma17g00388 388
17 2196095 2200635 + CmaCh17G003890.1 Cma17g00389 389
17 2203440 2205209 + CmaCh17G003900.1 Cma17g00390 390
6 5359881 5361594 - MELO3C006728.2.1 Cme06g00803 803
6 5519904 5524344 + MELO3C006733.2.1 Cme06g00815 815
6 5527290 5532850 - MELO3C006735.2.1 Cme06g00817 817
11 28635377 28648190 + MELO3C021252.2.1 Cme11g02100 2100
11 28649049 28659985 + MELO3C021251.2.1 Cme11g02101 2101
11 28673868 28676122 + MELO3C021249.2.1 Cme11g02103 2103
3 23063398 23066886 + PI0028141.1 Cmetu03g1502 1502
6 5615989 5618719 - PI0024028.1 Cmetu06g2217 2217
11 3506837 3509277 - PI0023150.1 Cmetu11g1241 1241
11 3549706 3558815 - PI0013818.1 Cmetu11g1561 1561
6 11059146 11060541 - CmoCh06G015690.1 Cmo06g01569 1569
6 11071016 11075457 + CmoCh06G015700.1 Cmo06g01570 1570
8 7940526 7942093 + CmoCh08G012600.1 Cmo08g01260 1260
14 12771084 12774258 + CmoCh14G016060.1 Cmo14g01606 1606
14 12782849 12784062 + CmoCh14G016090.1 Cmo14g01609 1609
17 2314870 2329638 + CmoCh17G003760.1 Cmo17g00376 376
17 2330844 2340546 + CmoCh17G003770.1 Cmo17g00377 377
17 2341369 2345896 + CmoCh17G003780.1 Cmo17g00378 378
17 2349127 2350981 + CmoCh17G003790.1 Cmo17g00379 379
5 6516162 6520234 + CmPI595203_05g007450.1 Cmu05g0745 745
6 4723870 4725640 - CmPI595203_06g004130.1 Cmu06g0413 413
6 4730563 4733934 - CmPI595203_06g004140.1 Cmu06g0414 414
6 4735632 4746074 - CmPI595203_06g004150.1 Cmu06g0415 415
6 4752144 4763483 - CmPI595203_06g004160.1 Cmu06g0416 416
4 451542 453153 - Conep04aG0009600.1 Cone4ag0094 94
4 461075 462329 + Conep04aG0009700.1 Cone4ag0095 95
7 384665 386069 - Conep07aG0008800.1 Cone7ag0088 88
7 387318 389486 - Conep07aG0008900.1 Cone7ag0089 89
15 3963298 3966442 + Conep15aG0072800.1 Cone15ag0714 714
3 10696668 10701389 + Cp4.1LG03g11930.1 Cpe03g01314 1314
3 10708675 10709879 + Cp4.1LG03g11950.1 Cpe03g01316 1316
8 901992 906468 - Cp4.1LG08g05330.1 Cpe08g00140 140
8 915472 916723 + Cp4.1LG08g05380.1 Cpe08g00141 141
12 2251607 2265769 + Cp4.1LG12g03340.1 Cpe12g00338 338
12 2266842 2277240 + Cp4.1LG12g03350.1 Cpe12g00339 339
12 2278701 2284005 + Cp4.1LG12g03330.1 Cpe12g00340 340
12 2286130 2287985 + Cp4.1LG12g03310.1 Cpe12g00341 341
17 472565 473820 + Cp4.1LG17g00140.1 Cpe17g00082 82
5 7323001 7326879 - CrPI670011_05g008230.1 Cre05g0823 823
6 5780366 5782135 - CrPI670011_06g011930.1 Cre06g1193 1193
6 5786322 5790694 - CrPI670011_06g011940.1 Cre06g1194 1194
6 5792410 5802878 - CrPI670011_06g011950.1 Cre06g1195 1195
6 5808828 5820229 - CrPI670011_06g011960.1 Cre06g1196 1196
3 11403153 11405065 - CsaV3_3G015330.1 Csa03g01533 1533
3 11432231 11436875 + CsaV3_3G015350.1 Csa03g01535 1535
3 11439184 11445628 - CsaV3_3G015370.1 Csa03g01537 1537
6 16228642 16256177 - CsaV3_6G026330.1 Csa06g01841 1841
3 309202 327509 - Hsped.03g00280.1 Hepe03g0028 28
5 62130059 62134325 + Hsped.05g13580.1 Hepe05g1358 1358
5 62141251 62147026 - Hsped.05g13600.1 Hepe05g1360 1360
11 11327797 11330785 - Lag0031646.1 Lac11g1008 1008
11 36781972 36786513 + Maker00031747 Lcy11g1320 1320
11 36791924 36797086 - Maker00031736 Lcy11g1322 1322
11 36855724 36857575 + Maker00032065 Lcy11g1324 1324
12 12605898 12619957 + Maker00024985 Lcy12g0884 884
12 12620745 12632700 + Maker00025097 Lcy12g0885 885
12 12693788 12698840 + Maker00025079 Lcy12g0886 886
12 12702299 12703918 + Maker00024738 Lcy12g0887 887
5 21935637 21939996 + Lsi05G014030.1 Lsi05g01403 1403
5 21944978 21949412 - Lsi05G014050.1 Lsi05g01405 1405
5 21990911 21992521 + Lsi05G014070.1 Lsi05g01407 1407
5 23711795 23714625 + Lsi05G015970.1 Lsi05g01597 1597
9 23198554 23223172 + Lsi09G015110.1 Lsi09g01511 1511
9 23223911 23242282 + Lsi09G015120.1 Lsi09g01512 1512
2 48408744 48411052 + Sed0005247.1 Sed02g1121 1121
2 48417058 48422630 - Sed0009218.1 Sed02g1123 1123
9 7698943 7719752 + Sed0005984.1 Sed09g0619 619
9 7775728 7778160 + Sed0012529.1 Sed09g0622 622
6 80081639 80094212 + Tan0010955.1 Tan06g2787 2787
6 80107033 80113975 + Tan0002582.11 Tan06g2800 2800
6 80115458 80116736 + Tan0019489.1 Tan06g2801 2801
10 10408846 10413195 + Tan0019317.1 Tan10g1093 1093
10 10428685 10432603 - Tan0008183.1 Tan10g1095 1095
5 188848 198725 - Vvi5g19 Vvi5g19 19
5 223491 233735 - Vvi5g20 Vvi5g20 20
5 234215 234679 - Vvi5g21 Vvi5g21 21
5 243882 246638 - Vvi5g22 Vvi5g22 22
5 247630 248316 - Vvi5g23 Vvi5g23 23
5 249312 251248 - Vvi5g24 Vvi5g24 24
5 258167 261964 + Vvi5g25 Vvi5g25 25
5 262045 271104 - Vvi5g26 Vvi5g26 26
5 271695 308090 - Vvi5g27 Vvi5g27 27
5 330301 332092 + Vvi5g28 Vvi5g28 28
       

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