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
Vvi18g1010 . . . . . . . . Cmo05g00273 Cmo12g00392 . . . Car12g00418 . . Cpe07g00396 Bhi04g00207 . . . Hepe10g0607 . . Cla08g01458 Cam08g1944 Cec08g1518 Cco08g1657 Clacu08g1634 . Cre08g1420 . . Cone17ag1365 Cone20ag0116 . . . Cme03g01922 . . . . . . . . . . . Cma12g00441 Cma05g00269 Car05g00223 . Cpe11g00222 . . . . . . . . . . . . . . . Lsi08g01364 Csa02g02088 Chy03g01426 .
Vvi18g1011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1012 Blo01g01579 . Bda01g00513 . . . . Bma01g02342 Cmo05g00275 Cmo12g00391 . . . Car12g00417 . . Cpe07g00395 . . . . . . . Cla08g01457 . . . . . . . Cone7ag1852 . . . . . Cme03g01921 . . . . . . . . Sed01g2548 . . Cma12g00440 Cma05g00270 . . Cpe11g00223 . Bhi09g02137 Tan01g4934 Cmetu04g1048 . . Mch11g0183 . . . . . . . . Lsi08g01363 Csa02g02090 Chy03g01425 .
Vvi18g1013 . . . . . . . . Cmo05g00276 . . . . . . . . Bhi04g00208 . . . . . . . . . . . . . . . . Cone20ag0115 . . . . . . . . . . . . . . . . Cma05g00271 Car05g00224 . Cpe11g00224 . . . . . . . . . . . . . . . . Csa02g02091 . .
Vvi18g1014 . . . . . . . . . . Cma01g01934 Cma09g00131 Car01g01511 . . Cpe06g00090 . . . . . . . . . . . . . . . Cone4ag1940 Cone7ag1853 . . Lsi04g01705 Csa03g04244 Chy04g00471 . . Blo18g00798 . Bda01g01514 Bpe02g01710 . . . . Cmo01g01997 Cmo09g00128 . . . Car09g00117 . Cpe02g00102 . . . . . . . Cla05g01908 . Cec05g2054 . . . . . . . Cme04g00517
Vvi18g1015 . . . . . . . . Cmo05g00277 Cmo12g00390 . . . Car12g00416 . . Cpe07g00394 Bhi04g00209 . . . Hepe10g0604 . . Cla08g01456 Cam08g1941 Cec08g1515 Cco08g1654 Clacu08g1631 . Cre08g1417 . . . . . . Chy04g00470 Cme03g01919 . . . . . . . . . . . Cma12g00439 . Car05g00225 . Cpe11g00225 . . . . . . . . . . . . . . . Lsi08g01362 Csa02g02092 Chy03g01423 Cme04g00516
Vvi18g1016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1017 . . . . . . . . Cmo05g00278 . Cma01g01935 Cma09g00130 Car01g01512 . . Cpe06g00089 . Bhi04g00210 . . . Hepe10g0603 . . Cla08g01455 Cam08g1940 Cec08g1514 Cco08g1653 Clacu08g1630 . Cre08g1416 Cone4ag1941 . . Cone20ag0114 Lsi04g01706 Csa03g04245 . Cme03g01918 . . . Bda01g01515 Bpe02g01711 . Bma01g00744 . . Cmo01g01998 Cmo09g00127 . Cma05g00273 Car05g00226 Car09g00116 Cpe11g00226 Cpe02g00101 . . . . . . . Cla05g01907 Cam05g2044 Cec05g2053 Cco05g2107 Clacu05g2036 Cmu05g1915 Cre05g2037 Lsi08g01361 Csa02g02094 Chy03g01421 .
Vvi18g1018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1019 . . . . . . . . . Cmo12g00389 . . . Car12g00414 Sed05g2303 . Cpe07g00393 Bhi04g00211 Tan02g0772 Cmetu01g1870 . Hepe02g0484 . . Cla08g01454 Cam08g1939 Cec08g1513 Cco08g1652 Clacu08g1629 . Cre08g1415 . . . . . . . Cme03g01917 . Blo18g00796 . . . . . . . . . Cma12g00438 . . . . . . . . . . . . . . . . . . . Lsi08g01359 Csa02g02095 Chy03g01420 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32105898 32107981 + Bda002518.1 Bda01g00513 513
1 50992669 50997573 + Bda003772.1 Bda01g01514 1514
1 50998471 51004816 - Bda003773.1 Bda01g01515 1515
4 5011327 5016855 - XM_039030264.1 Bhi04g00207 207
4 5058130 5064943 - XM_039028974.1 Bhi04g00208 208
4 5067304 5069168 - XM_039030283.1 Bhi04g00209 209
4 5109000 5110228 - XM_039028446.1 Bhi04g00210 210
4 5114522 5118515 - XM_039029670.1 Bhi04g00211 211
9 60470675 60472969 + XM_039042723.1 Bhi09g02137 2137
1 55587913 55596115 - BLOR01579 Blo01g01579 1579
18 23336330 23339053 + BLOR09284 Blo18g00796 796
18 23347692 23352061 - BLOR09286 Blo18g00798 798
1 6845557 6853878 + Bma000959.2 Bma01g00744 744
1 81018885 81020672 - Bma003208.1 Bma01g02342 2342
2 19591409 19596175 + Bpe009542.1 Bpe02g01710 1710
2 19597096 19605053 - Bpe009543.1 Bpe02g01711 1711
5 29119804 29120425 + CaPI482276_05g020440.1 Cam05g2044 2044
8 25317884 25322025 + CaPI482276_08g019390.1 Cam08g1939 1939
8 25328578 25329567 + CaPI482276_08g019400.1 Cam08g1940 1940
8 25333344 25334343 + CaPI482276_08g019410.1 Cam08g1941 1941
8 25358467 25364061 + CaPI482276_08g019440.1 Cam08g1944 1944
1 12794727 12800277 + Carg17166-RA Car01g01511 1511
1 12800636 12801725 - Carg17167-RA Car01g01512 1512
5 1162540 1165762 - Carg11778-RA Car05g00223 223
5 1169839 1176976 - Carg11776-RA Car05g00224 224
5 1177976 1178953 - Carg11775-RA Car05g00225 225
5 1180687 1182264 - Carg11774-RA Car05g00226 226
9 564670 565728 + Carg08700-RA Car09g00116 116
9 566386 568854 - Carg08701-RA Car09g00117 117
12 2643948 2648608 + Carg04022-RA Car12g00414 414
12 2652475 2653928 + Carg04024-RA Car12g00416 416
12 2657909 2660602 + Carg04025-RA Car12g00417 417
12 2668017 2671081 + Carg04026-RA Car12g00418 418
5 30054712 30055333 + CcPI632755_05g021070.1 Cco05g2107 2107
8 27998364 28002518 + CcPI632755_08g016520.1 Cco08g1652 1652
8 28009245 28010235 + CcPI632755_08g016530.1 Cco08g1653 1653
8 28014119 28015077 + CcPI632755_08g016540.1 Cco08g1654 1654
8 28038960 28044414 + CcPI632755_08g016570.1 Cco08g1657 1657
5 32427557 32429039 + CePI673135_05g020530.1 Cec05g2053 2053
5 32429709 32434967 - CePI673135_05g020540.1 Cec05g2054 2054
8 26859127 26863275 + CePI673135_08g015130.1 Cec08g1513 1513
8 26869722 26870856 + CePI673135_08g015140.1 Cec08g1514 1514
8 26874907 26875867 + CePI673135_08g015150.1 Cec08g1515 1515
8 26901967 26907464 + CePI673135_08g015180.1 Cec08g1518 1518
3 16926396 16929663 + Chy3G064000.1 Chy03g01420 1420
3 16932781 16939673 + Chy3G064010.1 Chy03g01421 1421
3 16946761 16947836 + Chy3G064030.1 Chy03g01423 1423
3 16950055 16956385 + Chy3G064050.1 Chy03g01425 1425
3 16966823 16971304 + Chy3G064060.1 Chy03g01426 1426
4 4387568 4388198 + Chy4G071880.1 Chy04g00470 470
4 4388839 4393987 - Chy4G071890.1 Chy04g00471 471
5 29319433 29320054 + ClG42_05g0203600.10 Clacu05g2036 2036
8 26063891 26068026 + ClG42_08g0162900.10 Clacu08g1629 1629
8 26074617 26075606 + ClG42_08g0163000.10 Clacu08g1630 1630
8 26079352 26080328 + ClG42_08g0163100.10 Clacu08g1631 1631
8 26104440 26110017 + ClG42_08g0163400.10 Clacu08g1634 1634
5 30917341 30918612 + ClCG05G018670.2 Cla05g01907 1907
5 30918204 30924526 - ClCG05G018680.2 Cla05g01908 1908
8 27436366 27440766 + ClCG08G014660.2 Cla08g01454 1454
8 27447256 27448706 + ClCG08G014670.2 Cla08g01455 1455
8 27452030 27454353 + ClCG08G014680.1 Cla08g01456 1456
8 27456476 27463411 + ClCG08G014690.2 Cla08g01457 1457
8 27480000 27490928 + ClCG08G014700.2 Cla08g01458 1458
1 12568834 12574799 + CmaCh01G019340.1 Cma01g01934 1934
1 12574707 12575858 - CmaCh01G019350.1 Cma01g01935 1935
5 1139345 1143059 - CmaCh05G002690.1 Cma05g00269 269
5 1147661 1151351 - CmaCh05G002700.1 Cma05g00270 270
5 1151708 1154380 - CmaCh05G002710.1 Cma05g00271 271
5 1157654 1159176 - CmaCh05G002730.1 Cma05g00273 273
9 561624 562596 + CmaCh09G001300.1 Cma09g00130 130
9 563148 568452 - CmaCh09G001310.1 Cma09g00131 131
12 2287015 2291955 + CmaCh12G004380.1 Cma12g00438 438
12 2293396 2296987 + CmaCh12G004390.1 Cma12g00439 439
12 2297184 2303994 + CmaCh12G004400.1 Cma12g00440 440
12 2311487 2314983 + CmaCh12G004410.1 Cma12g00441 441
3 27274447 27278231 + MELO3C010976.2.1 Cme03g01917 1917
3 27281405 27283145 + MELO3C010975.2.1 Cme03g01918 1918
3 27287107 27288136 + MELO3C010974.2.1 Cme03g01919 1919
3 27294107 27297122 + MELO3C010973.2.1 Cme03g01921 1921
3 27307800 27309388 + MELO3C030117.2.1 Cme03g01922 1922
4 4248737 4250256 + MELO3C003791.2.1 Cme04g00516 516
4 4250310 4255941 - MELO3C003792.2.1 Cme04g00517 517
1 5873698 5875629 - PI0017694.1 Cmetu01g1870 1870
4 29011995 29013962 + PI0022528.1 Cmetu04g1048 1048
1 14104998 14110775 + CmoCh01G019970.1 Cmo01g01997 1997
1 14111135 14112186 - CmoCh01G019980.1 Cmo01g01998 1998
5 1177374 1180900 - CmoCh05G002730.1 Cmo05g00273 273
5 1184654 1187396 - CmoCh05G002750.1 Cmo05g00275 275
5 1189306 1191978 - CmoCh05G002760.1 Cmo05g00276 276
5 1193035 1194012 - CmoCh05G002770.1 Cmo05g00277 277
5 1196725 1198308 - CmoCh05G002780.1 Cmo05g00278 278
9 586308 587339 + CmoCh09G001270.1 Cmo09g00127 127
9 587447 592567 - CmoCh09G001280.1 Cmo09g00128 128
12 2409820 2417031 + CmoCh12G003890.1 Cmo12g00389 389
12 2418405 2420239 + CmoCh12G003900.1 Cmo12g00390 390
12 2421232 2426929 + CmoCh12G003910.1 Cmo12g00391 391
12 2433817 2437515 + CmoCh12G003920.1 Cmo12g00392 392
5 29042322 29045827 + CmPI595203_05g019150.1 Cmu05g1915 1915
4 13697503 13702021 + Conep04aG0200200.1 Cone4ag1940 1940
4 13701435 13701963 - Conep04aG0200300.1 Cone4ag1941 1941
7 11990432 11993090 - Conep07aG0190700.1 Cone7ag1852 1852
7 11995199 11999422 + Conep07aG0190800.1 Cone7ag1853 1853
17 9524244 9529026 - Conep17aG0139900.1 Cone17ag1365 1365
20 506043 507500 + Conep20aG0012000.1 Cone20ag0114 114
20 507852 510716 + Conep20aG0012100.1 Cone20ag0115 115
20 515618 519979 + Conep20aG0012200.1 Cone20ag0116 116
2 505349 506763 + Cp4.1LG02g07800.1 Cpe02g00101 101
2 506919 512580 - Cp4.1LG02g07720.1 Cpe02g00102 102
6 438847 439260 + Cp4.1LG06g00820.1 Cpe06g00089 89
6 440406 445419 - Cp4.1LG06g00960.1 Cpe06g00090 90
7 2540050 2545273 + Cp4.1LG07g03960.1 Cpe07g00393 393
7 2546677 2551111 + Cp4.1LG07g03990.1 Cpe07g00394 394
7 2554741 2557902 + Cp4.1LG07g03940.1 Cpe07g00395 395
7 2566260 2570086 + Cp4.1LG07g03980.1 Cpe07g00396 396
11 1193527 1197153 - Cp4.1LG11g02280.1 Cpe11g00222 222
11 1200758 1203376 - Cp4.1LG11g02300.1 Cpe11g00223 223
11 1205351 1208129 - Cp4.1LG11g02370.1 Cpe11g00224 224
11 1208177 1210162 - Cp4.1LG11g02330.1 Cpe11g00225 225
11 1212049 1213619 - Cp4.1LG11g02340.1 Cpe11g00226 226
5 32371911 32372532 + CrPI670011_05g020370.1 Cre05g2037 2037
8 27127932 27132083 + CrPI670011_08g014150.1 Cre08g1415 1415
8 27139120 27140110 + CrPI670011_08g014160.1 Cre08g1416 1416
8 27144030 27144987 + CrPI670011_08g014170.1 Cre08g1417 1417
8 27169248 27174786 + CrPI670011_08g014200.1 Cre08g1420 1420
2 19015092 19020819 - CsaV3_2G029070.1 Csa02g02088 2088
2 19030830 19033307 - CsaV3_2G029090.1 Csa02g02090 2090
2 19034494 19037166 - CsaV3_2G029100.1 Csa02g02091 2091
2 19038403 19039997 - CsaV3_2G029110.1 Csa02g02092 2092
2 19046636 19047998 - CsaV3_2G029130.1 Csa02g02094 2094
2 19052524 19056602 - CsaV3_2G029140.1 Csa02g02095 2095
3 37179050 37186169 + CsaV3_3G045500.1 Csa03g04244 4244
3 37183680 37187725 - CsaV3_3G045510.1 Csa03g04245 4245
2 4735053 4737698 - Hsped.02g04840.1 Hepe02g0484 484
10 7446386 7448392 + Hsped.10g06030.1 Hepe10g0603 603
10 7452956 7455731 + Hsped.10g06040.1 Hepe10g0604 604
10 7502147 7507595 + Hsped.10g06070.1 Hepe10g0607 607
4 24418735 24424512 + Lsi04G017050.1 Lsi04g01705 1705
4 24424625 24425783 - Lsi04G017060.1 Lsi04g01706 1706
8 21908730 21913753 + Lsi08G013590.1 Lsi08g01359 1359
8 21919285 21920853 + Lsi08G013610.1 Lsi08g01361 1361
8 21923162 21924072 + Lsi08G013620.1 Lsi08g01362 1362
8 21925608 21932482 + Lsi08G013630.1 Lsi08g01363 1363
8 21946512 21953448 + Lsi08G013640.1 Lsi08g01364 1364
11 1177428 1180274 - MC11g_new0023 Mch11g0183 183
1 19312693 19314738 - Sed0013345.2 Sed01g2548 2548
5 35538863 35541405 - Sed0019860.1 Sed05g2303 2303
1 115101613 115103231 + Tan0017185.1 Tan01g4934 4934
2 7324703 7327071 - Tan0007194.1 Tan02g0772 772
18 11256599 11261386 - Vvi18g1010 Vvi18g1010 1010
18 11261402 11261579 + Vvi18g1011 Vvi18g1011 1011
18 11268599 11271421 - Vvi18g1012 Vvi18g1012 1012
18 11275705 11277358 - Vvi18g1013 Vvi18g1013 1013
18 11286577 11293205 + Vvi18g1014 Vvi18g1014 1014
18 11293543 11294740 - Vvi18g1015 Vvi18g1015 1015
18 11294803 11296698 + Vvi18g1016 Vvi18g1016 1016
18 11297037 11299865 - Vvi18g1017 Vvi18g1017 1017
18 11307615 11310938 - Vvi18g1018 Vvi18g1018 1018
18 11311312 11316066 - Vvi18g1019 Vvi18g1019 1019
       

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