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
Vvi17g206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g207 . . Bda06g00820 . . . . Bma12g01243 Cmo13g01026 Cmo18g00056 . Cma11g00313 . . . Cpe20g00152 Cpe04g01369 Bhi02g00141 . . . Hepe09g0392 . . Cla06g01420 Cam06g1573 Cec06g1633 Cco06g1625 Clacu06g1535 Cmu06g1489 Cre06g2298 . . . . Lsi02g00233 Csa01g00716 Chy12g01396 Cme12g01830 . Blo15g00059 . Bda14g01083 Bpe07g01047 . . . Sed08g2758 . Cmo11g00318 Cma13g00990 Cma18g00073 . . Cpe09g01113 . Bhi08g01293 Tan05g2192 . . Hepe07g2354 . . Cla04g01045 Cam04g1090 Cec01g1603 Cco01g1651 Clacu04g1116 Cmu04g1099 Cre01g1398 Lsi06g01285 Csa01g00435 Chy02g02310 Cme02g01682
Vvi17g208 . . . . . . . . Cmo13g01027 Cmo18g00055 . Cma11g00312 . Car11g00288 . Cpe20g00151 Cpe04g01370 Bhi02g00139 Tan09g1823 Cmetu02g1004 . Hepe09g0391 . . Cla06g01421 Cam06g1575 Cec06g1635 Cco06g1627 Clacu06g1537 Cmu06g1491 Cre06g2300 Cone2ag0761 Cone16ag0237 . . Lsi02g00232 Csa01g00714 Chy12g01397 Cme12g01831 . . Bda11g01801 . . . . . Sed08g2756 . Cmo11g00317 Cma13g00991 Cma18g00072 Car13g00825 Car18g00063 Cpe09g01114 . Bhi08g01292 Tan05g2193 Cmetu12g0557 Lac10g0289 Hepe07g2355 . . Cla04g01047 Cam04g1091 Cec01g1606 Cco01g1652 Clacu04g1117 Cmu04g1101 Cre01g1400 Lsi06g01286 Csa01g00433 Chy02g02312 Cme02g01684
Vvi17g209 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g210 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g211 . . . . Bpe12g00705 . . . Cmo13g01028 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00231 Csa01g00713 Chy12g01398 Cme12g01832 . . . . . . . . . . . . . . . . . Bhi08g01291 Tan05g2194 Cmetu12g0801 Lac10g0288 . . . Cla04g01048 Cam04g1092 Cec01g1607 Cco01g1653 Clacu04g1118 Cmu04g1102 Cre01g1401 . . . .
Vvi17g212 . . . Bda15g00511 Bpe12g00698 . . . Cmo13g01029 Cmo18g00054 . Cma11g00311 . Car11g00287 Sed12g2115 Cpe20g00149 Cpe04g01371 Bhi02g00135 Tan09g1827 Cmetu02g0991 . Hepe09g0388 . . Cla06g01422 Cam06g1576 Cec06g1636 Cco06g1628 Clacu06g1538 Cmu06g1492 Cre06g2301 Cone2ag0760 . . . Lsi02g00230 Csa01g00712 Chy12g01399 Cme12g01833 Blo13g00175 . . . . . . Bma08g00054 Sed08g2754 . Cmo11g00316 Cma13g00993 Cma18g00071 Car13g00827 Car18g00062 Cpe09g01115 . Bhi08g01290 Tan05g2195 Cmetu12g1142 Lac10g0287 Hepe07g2356 . . Cla04g01050 Cam04g1093 Cec01g1608 Cco01g1654 Clacu04g1119 Cmu04g1103 Cre01g1402 Lsi06g01287 Csa01g00431 Chy02g02313 Cme02g01686
Vvi17g213 Blo04g00849 Blo16g00113 . . . Bpe13g00376 . . Cmo13g01030 Cmo18g00053 . . . . . Cpe20g00148 . . . . . . . . . . . . . . . . . . . Lsi02g00229 Csa01g00710 Chy12g01400 Cme12g01834 . . Bda11g01787 . . . Bma03g00919 . Sed08g1361 . . Cma13g00995 Cma18g00070 Car13g00828 Car18g00061 Cpe09g01116 . Bhi08g01289 Tan05g2196 Cmetu04g1577 Lac10g0286 Hepe07g2357 . . Cla04g01051 Cam04g1094 Cec01g1609 Cco01g1655 Clacu04g1120 Cmu04g1104 Cre01g1403 . . . .
Vvi17g214 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g215 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11432308 11434666 - Bda024151.1 Bda06g00820 820
11 52754900 52755664 + Bda008709.1 Bda11g01787 1787
11 53055218 53059810 + Bda008730.1 Bda11g01801 1801
14 9546459 9549593 - Bda027909.1 Bda14g01083 1083
15 8179700 8181671 + Bda012340.1 Bda15g00511 511
2 2560364 2565179 + XM_039022836.1 Bhi02g00135 135
2 2581887 2590614 - XM_039024642.1 Bhi02g00139 139
2 2685797 2689258 - XM_039022644.1 Bhi02g00141 141
8 39336601 39337828 - XM_039038989.1 Bhi08g01289 1289
8 39357629 39360794 - XM_039037862.1 Bhi08g01290 1290
8 39413042 39415902 + XM_039039249.1 Bhi08g01291 1291
8 39416955 39422761 - XM_039039248.1 Bhi08g01292 1292
8 39449862 39453632 - XM_039040143.1 Bhi08g01293 1293
4 9311617 9312455 + BLOR13761 Blo04g00849 849
13 6520191 6522366 - BLOR05456 Blo13g00175 175
15 471126 473595 + BLOR06453 Blo15g00059 59
16 2656664 2657377 - BLOR07361 Blo16g00113 113
3 9503313 9504026 + Bma017243.1 Bma03g00919 919
8 722377 724417 + Bma027050.1 Bma08g00054 54
12 45445825 45448154 - Bma008608.1 Bma12g01243 1243
7 15966829 15969212 - Bpe021890.1 Bpe07g01047 1047
12 12544701 12546742 - Bpe005958.1 Bpe12g00698 698
12 12617908 12619133 + Bpe005965.1 Bpe12g00705 705
13 11509407 11510138 + Bpe006500.1 Bpe13g00376 376
4 25043275 25046358 + CaPI482276_04g010900.1 Cam04g1090 1090
4 25066644 25075187 + CaPI482276_04g010910.1 Cam04g1091 1091
4 25076487 25079011 - CaPI482276_04g010920.1 Cam04g1092 1092
4 25090649 25093690 + CaPI482276_04g010930.1 Cam04g1093 1093
4 25102477 25103133 + CaPI482276_04g010940.1 Cam04g1094 1094
6 27201963 27204868 + CaPI482276_06g015730.1 Cam06g1573 1573
6 27239582 27243033 + CaPI482276_06g015750.1 Cam06g1575 1575
6 27244752 27248368 - CaPI482276_06g015760.1 Cam06g1576 1576
11 1565333 1568551 + Carg09102-RA Car11g00287 287
11 1570440 1573533 - Carg09101-RA Car11g00288 288
13 8968447 8971946 + Carg04847-RA Car13g00825 825
13 8977287 8980098 + Carg04845-RA Car13g00827 827
13 8984635 8985759 + Carg04844-RA Car13g00828 828
18 309546 310375 - Carg06626-RA Car18g00061 61
18 314462 317022 - Carg06627-RA Car18g00062 62
18 322585 327008 - Carg06628-RA Car18g00063 63
1 29253344 29256418 + CcPI632755_01g016510.1 Cco01g1651 1651
1 29280630 29289817 + CcPI632755_01g016520.1 Cco01g1652 1652
1 29290355 29292950 - CcPI632755_01g016530.1 Cco01g1653 1653
1 29304673 29307718 + CcPI632755_01g016540.1 Cco01g1654 1654
1 29316656 29317517 + CcPI632755_01g016550.1 Cco01g1655 1655
6 26845037 26847974 + CcPI632755_06g016250.1 Cco06g1625 1625
6 26889765 26892885 + CcPI632755_06g016270.1 Cco06g1627 1627
6 26894662 26898596 - CcPI632755_06g016280.1 Cco06g1628 1628
1 30684073 30687148 + CePI673135_01g016030.1 Cec01g1603 1603
1 30719509 30725263 + CePI673135_01g016060.1 Cec01g1606 1606
1 30726583 30729156 - CePI673135_01g016070.1 Cec01g1607 1607
1 30740878 30743825 + CePI673135_01g016080.1 Cec01g1608 1608
1 30752516 30753374 + CePI673135_01g016090.1 Cec01g1609 1609
6 29922992 29925914 + CePI673135_06g016330.1 Cec06g1633 1633
6 29960666 29964111 + CePI673135_06g016350.1 Cec06g1635 1635
6 29965907 29969866 - CePI673135_06g016360.1 Cec06g1636 1636
2 27123174 27125896 + Chy2G045770.1 Chy02g02310 2310
2 27146603 27155580 + Chy2G045790.1 Chy02g02312 2312
2 27156129 27158949 - Chy2G045800.1 Chy02g02313 2313
12 18093154 18104354 + Chy12G219960.1 Chy12g01396 1396
12 18107411 18111817 + Chy12G219970.1 Chy12g01397 1397
12 18112943 18115382 - Chy12G219980.1 Chy12g01398 1398
12 18125161 18126116 + Chy12G219990.1 Chy12g01399 1399
12 18141359 18142822 + Chy12G220000.1 Chy12g01400 1400
4 25414087 25417167 + ClG42_04g0111600.10 Clacu04g1116 1116
4 25438168 25446744 + ClG42_04g0111700.10 Clacu04g1117 1117
4 25448088 25450618 - ClG42_04g0111800.10 Clacu04g1118 1118
4 25462212 25465247 + ClG42_04g0111900.10 Clacu04g1119 1119
4 25474120 25474981 + ClG42_04g0112000.10 Clacu04g1120 1120
6 26257997 26260913 + ClG42_06g0153500.10 Clacu06g1535 1535
6 26295513 26298964 + ClG42_06g0153700.10 Clacu06g1537 1537
6 26300750 26304744 - ClG42_06g0153800.10 Clacu06g1538 1538
4 25632585 25636403 + ClCG04G010630.1 Cla04g01045 1045
4 25661158 25667484 + ClCG04G010640.2 Cla04g01047 1047
4 25669968 25672344 - ClCG04G010650.1 Cla04g01048 1048
4 25683936 25687295 + ClCG04G010670.1 Cla04g01050 1050
4 25696328 25697708 + ClCG04G010680.1 Cla04g01051 1051
6 27749702 27752996 + ClCG06G014330.2 Cla06g01420 1420
6 27780330 27791445 + ClCG06G014340.1 Cla06g01421 1421
6 27792731 27796724 - ClCG06G014350.2 Cla06g01422 1422
11 1543460 1546803 + CmaCh11G003110.1 Cma11g00311 311
11 1548502 1551651 - CmaCh11G003120.1 Cma11g00312 312
11 1558630 1561563 - CmaCh11G003130.1 Cma11g00313 313
13 7667068 7670152 + CmaCh13G009900.1 Cma13g00990 990
13 7674031 7679016 + CmaCh13G009910.1 Cma13g00991 991
13 7684742 7687440 + CmaCh13G009930.1 Cma13g00993 993
13 7691437 7693386 + CmaCh13G009950.1 Cma13g00995 995
18 297974 299152 - CmaCh18G000700.1 Cma18g00070 70
18 303833 306669 - CmaCh18G000710.1 Cma18g00071 71
18 311203 316522 - CmaCh18G000720.1 Cma18g00072 72
18 319769 323723 - CmaCh18G000730.1 Cma18g00073 73
2 23942035 23945327 + MELO3C017357.2.1 Cme02g01682 1682
2 23965259 23968861 + MELO3C017356.2.1 Cme02g01684 1684
2 23977221 23977965 - MELO3C017355.2.1 Cme02g01686 1686
12 24684895 24689034 + MELO3C002132.2.1 Cme12g01830 1830
12 24698071 24703113 + MELO3C002131.2.1 Cme12g01831 1831
12 24703109 24706679 - MELO3C002130.2.1 Cme12g01832 1832
12 24715249 24718109 + MELO3C002129.2.1 Cme12g01833 1833
12 24724103 24725546 + MELO3C002128.2.1 Cme12g01834 1834
2 22394338 22397958 + PI0016399.1 Cmetu02g0991 991
2 22398919 22402573 - PI0007469.1 Cmetu02g1004 1004
4 8936143 8938175 - PI0022787.1 Cmetu04g1577 1577
12 1540094 1545208 - PI0011166.1 Cmetu12g0557 557
12 1536285 1539276 + PI0006563.1 Cmetu12g0801 801
12 1521250 1524077 - PI0027973.1 Cmetu12g1142 1142
11 1528835 1532170 + CmoCh11G003160.1 Cmo11g00316 316
11 1534165 1537423 - CmoCh11G003170.1 Cmo11g00317 317
11 1544782 1547542 - CmoCh11G003180.1 Cmo11g00318 318
13 8657719 8660762 + CmoCh13G010260.1 Cmo13g01026 1026
13 8665145 8670066 + CmoCh13G010270.1 Cmo13g01027 1027
13 8670261 8672338 - CmoCh13G010280.1 Cmo13g01028 1028
13 8676452 8679631 + CmoCh13G010290.1 Cmo13g01029 1029
13 8683639 8685263 + CmoCh13G010300.1 Cmo13g01030 1030
18 341546 342666 - CmoCh18G000530.1 Cmo18g00053 53
18 346478 349433 - CmoCh18G000540.1 Cmo18g00054 54
18 354592 359465 - CmoCh18G000550.1 Cmo18g00055 55
18 363039 366515 - CmoCh18G000560.1 Cmo18g00056 56
4 25594876 25597956 + CmPI595203_04g010990.1 Cmu04g1099 1099
4 25618957 25627561 + CmPI595203_04g011010.1 Cmu04g1101 1101
4 25628904 25631430 - CmPI595203_04g011020.1 Cmu04g1102 1102
4 25643002 25646022 + CmPI595203_04g011030.1 Cmu04g1103 1103
4 25654874 25655735 + CmPI595203_04g011040.1 Cmu04g1104 1104
6 26161360 26164276 + CmPI595203_06g014890.1 Cmu06g1489 1489
6 26198922 26202373 + CmPI595203_06g014910.1 Cmu06g1491 1491
6 26204159 26208152 - CmPI595203_06g014920.1 Cmu06g1492 1492
2 33453510 33455895 + Conep02aG0177700.1 Cone2ag0760 760
2 33462634 33468199 - Conep02aG0177800.1 Cone2ag0761 761
16 1868282 1882520 + Conep16aG0024100.1 Cone16ag0237 237
4 11127430 11130281 + Cp4.1LG04g13660.1 Cpe04g01369 1369
4 11136846 11140096 + Cp4.1LG04g13680.1 Cpe04g01370 1370
4 11141487 11144903 - Cp4.1LG04g13710.1 Cpe04g01371 1371
9 9585119 9589027 + Cp4.1LG09g11110.1 Cpe09g01113 1113
9 9592180 9597480 + Cp4.1LG09g11130.1 Cpe09g01114 1114
9 9602444 9603834 + Cp4.1LG09g11150.1 Cpe09g01115 1115
9 9608565 9610305 + Cp4.1LG09g11090.1 Cpe09g01116 1116
20 838668 840643 - Cp4.1LG20g01490.1 Cpe20g00148 148
20 844047 848044 - Cp4.1LG20g01480.1 Cpe20g00149 149
20 853996 859671 - Cp4.1LG20g01500.1 Cpe20g00151 151
20 863907 867214 - Cp4.1LG20g01520.1 Cpe20g00152 152
1 27245574 27248653 + CrPI670011_01g013980.1 Cre01g1398 1398
1 27270488 27280550 + CrPI670011_01g014000.1 Cre01g1400 1400
1 27281886 27284314 - CrPI670011_01g014010.1 Cre01g1401 1401
1 27295689 27298746 + CrPI670011_01g014020.1 Cre01g1402 1402
1 27307522 27308383 + CrPI670011_01g014030.1 Cre01g1403 1403
6 30925295 30928230 + CrPI670011_06g022980.1 Cre06g2298 2298
6 30963124 30966573 + CrPI670011_06g023000.1 Cre06g2300 2300
6 30968370 30972464 - CrPI670011_06g023010.1 Cre06g2301 2301
1 2700556 2703593 + CsaV3_1G004310.1 Csa01g00431 431
1 2708612 2713565 - CsaV3_1G004330.1 Csa01g00433 433
1 2730713 2734038 - CsaV3_1G004350.1 Csa01g00435 435
1 4504091 4506311 - CsaV3_1G007100.1 Csa01g00710 710
1 4514227 4517339 - CsaV3_1G007120.1 Csa01g00712 712
1 4525912 4529061 + CsaV3_1G007130.1 Csa01g00713 713
1 4529190 4534612 - CsaV3_1G007140.1 Csa01g00714 714
1 4542181 4546111 - CsaV3_1G007160.1 Csa01g00716 716
7 67893777 67897661 + Hsped.07g23540.1 Hepe07g2354 2354
7 67916465 67920663 + Hsped.07g23550.1 Hepe07g2355 2355
7 67936044 67938635 + Hsped.07g23560.1 Hepe07g2356 2356
7 67944777 67947007 + Hsped.07g23570.1 Hepe07g2357 2357
9 3470547 3476525 + Hsped.09g03880.1 Hepe09g0388 388
9 3491854 3497666 - Hsped.09g03910.1 Hepe09g0391 391
9 3521003 3525391 - Hsped.09g03920.1 Hepe09g0392 392
10 2167392 2168253 - Lag0024331.1 Lac10g0286 286
10 2174339 2178007 - Lag0024332.1 Lac10g0287 287
10 2187534 2189774 + Lag0024333.1 Lac10g0288 288
10 2190820 2195741 - Lag0024334.1 Lac10g0289 289
2 1924961 1926486 - Lsi02G002290.1 Lsi02g00229 229
2 1934707 1937954 - Lsi02G002300.1 Lsi02g00230 230
2 1969051 1971445 + Lsi02G002310.1 Lsi02g00231 231
2 1972142 1978002 - Lsi02G002320.1 Lsi02g00232 232
2 1993902 1997759 - Lsi02G002330.1 Lsi02g00233 233
6 23382208 23383577 + Lsi06G012850.1 Lsi06g01285 1285
6 23414624 23425059 + Lsi06G012860.1 Lsi06g01286 1286
6 23429509 23434309 - Lsi06G012870.1 Lsi06g01287 1287
8 28211182 28213438 - Sed0017105.1 Sed08g1361 1361
8 39203507 39206982 - Sed0002793.1 Sed08g2754 2754
8 39218730 39227099 - Sed0012848.1 Sed08g2756 2756
8 39232887 39237280 - Sed0013364.2 Sed08g2758 2758
12 31821764 31826014 + Sed0003514.1 Sed12g2115 2115
5 72861968 72866042 + Tan0001423.2 Tan05g2192 2192
5 72895478 72901838 + Tan0015477.1 Tan05g2193 2193
5 72902797 72905153 - Tan0014260.1 Tan05g2194 2194
5 72919538 72922718 + Tan0001726.1 Tan05g2195 2195
5 72935508 72937758 + Tan0021978.1 Tan05g2196 2196
9 69654251 69658227 + Tan0001141.1 Tan09g1823 1823
9 69661710 69665151 - Tan0005197.1 Tan09g1827 1827
17 2148937 2150067 - Vvi17g206 Vvi17g206 206
17 2150072 2152622 + Vvi17g207 Vvi17g207 207
17 2183405 2193451 + Vvi17g208 Vvi17g208 208
17 2193456 2193654 - Vvi17g209 Vvi17g209 209
17 2193668 2196996 - Vvi17g210 Vvi17g210 210
17 2199754 2201874 - Vvi17g211 Vvi17g211 211
17 2230449 2232935 + Vvi17g212 Vvi17g212 212
17 2254243 2255631 + Vvi17g213 Vvi17g213 213
17 2264174 2265053 + Vvi17g214 Vvi17g214 214
17 2265249 2268301 + Vvi17g215 Vvi17g215 215
       

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