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
Vvi4g162 Blo01g01446 . . . . Bpe02g00508 . Bma01g02194 . . . Cma05g00414 . . . . . . . . . . . . . . . . . . . . . Cone17ag0945 Cone20ag0288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g163 . . . . Bpe02g01560 . . . . . . . Car09g00314 . . . . . . . . . . . Cla05g01627 Cam05g1736 Cec05g1744 Cco05g1801 Clacu05g1727 Cmu05g1612 Cre05g1740 . . . . Lsi04g01386 . . . . . Bda01g01347 . . . . . Sed05g1795 . Cmo09g00363 Cma09g00364 . . . . . Bhi09g03082 Tan01g3472 Cmetu07g0807 . . Mch11g0452 . . . . . . . . . . . .
Vvi4g164 Blo01g01444 . . . . Bpe02g00509 . . Cmo05g00425 . . Cma05g00413 . . Sed08g1804 . . Bhi04g01517 Tan02g1581 Cmetu03g0930 . Hepe08g1436 . Lcy13g2222 . . . . . . . . . Cone17ag0947 Cone20ag0290 . . . . . . . . . . . . . . . . . . Car05g00348 Cpe11g00353 . . . . . . . . Cla08g00985 Cam08g1434 Cec08g1012 Cco08g1135 Clacu08g1139 . Cre08g0923 Lsi08g00831 . Chy03g00655 .
Vvi4g165 Blo01g01443 . Bda01g00641 . . Bpe02g00510 . . . . . . Car09g00315 . . . Cpe06g00260 . . . . . . . Cla05g01629 Cam05g1738 Cec05g1746 Cco05g1803 Clacu05g1729 Cmu05g1614 Cre05g1742 . . Cone17ag0948 . Lsi04g01385 . . . . . . . . . . . . . Cmo09g00365 Cma09g00366 . . Car05g00660 . . Bhi09g03080 . . . . . . . . . . . . . . . . Cme07g00175
Vvi4g166 Blo01g01442 . . . . . . . . . Cma01g01701 . . . . . Cpe06g00261 . . . . . . . . . . . . . . Cone4ag1700 Cone7ag1617 . . Lsi04g01384 . . . . . . . . . . . . . . . . Car01g01317 . . Cpe02g00292 . . . . . . . . . . . . . . . . . .
Vvi4g167 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g168 . . . . Bpe02g01561 . . . Cmo05g00424 . . Cma05g00412 . . . . . Bhi04g01519 . . . Hepe08g1437 . Lcy13g2225 . . . . . . . . . Cone17ag0949 Cone20ag0292 . . . . Blo17g00272 Blo18g00260 Bda01g01348 Bda13g01585 Bpe14g00281 . Bma01g00910 Bma02g00549 . . . . . . Car05g00347 Cpe11g00352 . . . . . . . . Cla08g00984 Cam08g1433 Cec08g1011 Cco08g1134 Clacu08g1138 . Cre08g0922 Lsi08g00830 Csa02g02331 Chy03g00654 .
Vvi4g169 Blo01g01441 . . . . Bpe02g00513 . Bma01g02191 . . . . . . Sed08g1807 . . Bhi04g01521 Tan02g1576 Cmetu03g0836 . Hepe08g1439 . Lcy13g2227 . . . . . . . Cone4ag1702 Cone7ag1618 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla08g00982 Cam08g1431 Cec08g1009 Cco08g1132 Clacu08g1136 . Cre08g0920 Lsi08g00828 . Chy03g00652 .
Vvi4g170 . . . Bda03g00122 Bpe02g01563 . Bma04g00110 . . . Cma01g01699 . . . . . . . . . . . . . Cla05g01633 Cam05g1742 Cec05g1751 Cco05g1808 Clacu05g1734 Cmu05g1618 Cre05g1746 . . . . . . . . . Blo18g00259 Bda01g01350 . . Bpe04g00107 Bma01g00908 . Sed13g1913 . . . . Car01g01314 . . Cpe02g00294 Bhi09g03075 Tan01g3482 . . Hepe01g1921 . . . . . . . . . . . . Cme07g00171
Vvi4g171 Blo01g01439 Blo12g01033 Bda01g00643 Bda03g00121 . Bpe02g00514 . Bma01g02190 . . . . Car09g00318 . . . Cpe06g00263 . . . . . . . Cla05g01634 Cam05g1743 Cec05g1752 Cco05g1809 Clacu05g1735 Cmu05g1619 Cre05g1747 Cone4ag1703 Cone7ag1619 . . Lsi04g01381 . . . . . . . . Bpe04g00106 . . . . Cmo09g00370 Cma09g00371 . Car01g01312 . . Cpe02g00295 Bhi09g03073 Tan01g3487 . . Hepe01g1922 . . . . . . . . . . . . Cme07g00170
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33430464 33449310 + Bda002667.1 Bda01g00641 641
1 33464245 33467857 - Bda002669.1 Bda01g00643 643
1 49177330 49177920 + Bda003584.1 Bda01g01347 1347
1 49198409 49205246 + Bda003585.1 Bda01g01348 1348
1 49209441 49212045 - Bda003587.1 Bda01g01350 1350
3 1068728 1072052 + Bda016060.2 Bda03g00121 121
3 1074624 1077516 + Bda016061.1 Bda03g00122 122
13 39355497 39386929 - Bda000453.2 Bda13g01585 1585
4 37718517 37721005 - XM_039028338.1 Bhi04g01517 1517
4 37868124 37928869 + XM_039028482.1 Bhi04g01519 1519
4 38036408 38039739 - XM_039030367.1 Bhi04g01521 1521
9 79456328 79460944 + XM_039044114.1 Bhi09g03073 3073
9 79461785 79466821 + XM_039043958.1 Bhi09g03075 3075
9 79517007 79532226 - XM_039041630.1 Bhi09g03080 3080
9 79574420 79576182 - XM_039043691.1 Bhi09g03082 3082
1 53256025 53259622 + BLOR01439 Blo01g01439 1439
1 53300448 53304694 + BLOR01441 Blo01g01441 1441
1 53307194 53311465 - BLOR01442 Blo01g01442 1442
1 53333028 53346668 - BLOR01443 Blo01g01443 1443
1 53347869 53350374 + BLOR01444 Blo01g01444 1444
1 53374390 53377788 + BLOR01446 Blo01g01446 1446
12 28207603 28217186 - BLOR05052 Blo12g01033 1033
17 2832739 2851902 - BLOR16093 Blo17g00272 272
18 2740871 2746635 + BLOR08747 Blo18g00259 259
18 2747475 2764890 - BLOR08748 Blo18g00260 260
1 8800459 8805484 + Bma001137.1 Bma01g00908 908
1 8809128 8829806 - Bma001139.1 Bma01g00910 910
1 78793558 78797154 + Bma003037.1 Bma01g02190 2190
1 78798872 78801059 + Bma003038.1 Bma01g02191 2191
1 78830665 78838643 + Bma030285 Bma01g02194 2194
2 11098431 11111832 + Bma015065.2 Bma02g00549 549
4 874450 877377 + Bma018556.1 Bma04g00110 110
2 3326678 3328545 - Bpe008348.1 Bpe02g00508 508
2 3330482 3331801 - Bpe008349.1 Bpe02g00509 509
2 3332753 3348190 + Bpe008350.1 Bpe02g00510 510
2 3359602 3361774 - Bpe008353.1 Bpe02g00513 513
2 3363431 3367011 - Bpe008354.1 Bpe02g00514 514
2 18599991 18600602 + Bpe009412.1 Bpe02g01560 1560
2 18601887 18622987 + Bpe009413.1 Bpe02g01561 1561
2 18628409 18630985 - Bpe009415.1 Bpe02g01563 1563
4 741475 744817 + Bpe014827.1 Bpe04g00106 106
4 747244 750167 + Bpe014828.1 Bpe04g00107 107
14 2809984 2829412 + Bpe006934.1 Bpe14g00281 281
5 25954050 25963203 + CaPI482276_05g017360.1 Cam05g1736 1736
5 25982904 25991739 + CaPI482276_05g017380.1 Cam05g1738 1738
5 26040119 26044597 - CaPI482276_05g017420.1 Cam05g1742 1742
5 26046952 26051493 - CaPI482276_05g017430.1 Cam05g1743 1743
8 20602103 20604847 + CaPI482276_08g014310.1 Cam08g1431 1431
8 20616224 20658816 - CaPI482276_08g014330.1 Cam08g1433 1433
8 20661428 20663338 + CaPI482276_08g014340.1 Cam08g1434 1434
1 11765437 11771732 + Carg10725-RA Car01g01312 1312
1 11773500 11775181 + Carg10723-RA Car01g01314 1314
1 11782459 11791893 - Carg10720-RA Car01g01317 1317
5 1988431 2012186 - Carg09312-RA Car05g00347 347
5 2013370 2015323 + Carg09311-RA Car05g00348 348
5 4109701 4113957 - Carg23929-RA Car05g00660 660
9 1735393 1736906 + Carg02793-RA Car09g00314 314
9 1740732 1750364 + Carg02794-RA Car09g00315 315
9 1761810 1772691 - Carg02797-RA Car09g00318 318
5 26745347 26754450 + CcPI632755_05g018010.1 Cco05g1801 1801
5 26773332 26782155 + CcPI632755_05g018030.1 Cco05g1803 1803
5 26828933 26833389 - CcPI632755_05g018080.1 Cco05g1808 1808
5 26835772 26840345 - CcPI632755_05g018090.1 Cco05g1809 1809
8 23126094 23128882 + CcPI632755_08g011320.1 Cco08g1132 1132
8 23140374 23179521 - CcPI632755_08g011340.1 Cco08g1134 1134
8 23182275 23184087 + CcPI632755_08g011350.1 Cco08g1135 1135
5 29025624 29034739 + CePI673135_05g017440.1 Cec05g1744 1744
5 29055431 29064382 + CePI673135_05g017460.1 Cec05g1746 1746
5 29113218 29118587 - CePI673135_05g017510.1 Cec05g1751 1751
5 29119986 29124632 - CePI673135_05g017520.1 Cec05g1752 1752
8 21982100 21984913 + CePI673135_08g010090.1 Cec08g1009 1009
8 21996296 22038629 - CePI673135_08g010110.1 Cec08g1011 1011
8 22041388 22043166 + CePI673135_08g010120.1 Cec08g1012 1012
3 9073528 9075886 + Chy3G056320.1 Chy03g00652 652
3 9086185 9114469 - Chy3G056340.1 Chy03g00654 654
3 9125918 9126539 + Chy3G056350.1 Chy03g00655 655
5 26166559 26167730 + ClG42_05g0172700.10 Clacu05g1727 1727
5 26193557 26202520 + ClG42_05g0172900.10 Clacu05g1729 1729
5 26250958 26255385 - ClG42_05g0173400.10 Clacu05g1734 1734
5 26255456 26262238 - ClG42_05g0173500.10 Clacu05g1735 1735
8 21375317 21378026 + ClG42_08g0113600.10 Clacu08g1136 1136
8 21389391 21429984 - ClG42_08g0113800.10 Clacu08g1138 1138
8 21434711 21436491 + ClG42_08g0113900.10 Clacu08g1139 1139
5 27638470 27639936 + ClCG05G015750.1 Cla05g01627 1627
5 27669456 27678814 + ClCG05G015770.2 Cla05g01629 1629
5 27727395 27732798 - ClCG05G015810.2 Cla05g01633 1633
5 27733881 27739386 - ClCG05G015820.1 Cla05g01634 1634
8 22506428 22509143 + ClCG08G009770.2 Cla08g00982 982
8 22519933 22573580 - ClCG08G009790.2 Cla08g00984 984
8 22576010 22578103 + ClCG08G009800.1 Cla08g00985 985
1 11561030 11575003 + CmaCh01G016990.1 Cma01g01699 1699
1 11576522 11589958 - CmaCh01G017010.1 Cma01g01701 1701
5 1811143 1836052 - CmaCh05G004120.1 Cma05g00412 412
5 1837351 1839228 + CmaCh05G004130.1 Cma05g00413 413
5 1850006 1856847 + CmaCh05G004140.1 Cma05g00414 414
9 1502454 1512899 + CmaCh09G003640.1 Cma09g00364 364
9 1514178 1523998 + CmaCh09G003660.1 Cma09g00366 366
9 1539595 1543947 - CmaCh09G003710.1 Cma09g00371 371
7 1125967 1131459 + MELO3C016919.2.1 Cme07g00170 170
7 1132380 1137223 + MELO3C016918.2.1 Cme07g00171 171
7 1156688 1166811 - MELO3C016915.2.1 Cme07g00175 175
3 6088555 6091722 - PI0027356.1 Cmetu03g0836 836
3 6045873 6048435 - PI0022153.1 Cmetu03g0930 930
7 23582806 23584525 + PI0023198.2 Cmetu07g0807 807
5 1949703 1975994 - CmoCh05G004240.1 Cmo05g00424 424
5 1977162 1979083 + CmoCh05G004250.1 Cmo05g00425 425
9 1573464 1584230 + CmoCh09G003630.1 Cmo09g00363 363
9 1585811 1595548 + CmoCh09G003650.1 Cmo09g00365 365
9 1621851 1626402 - CmoCh09G003700.1 Cmo09g00370 370
5 25877952 25887028 + CmPI595203_05g016120.1 Cmu05g1612 1612
5 25912741 25921705 + CmPI595203_05g016140.1 Cmu05g1614 1614
5 25970134 25974556 - CmPI595203_05g016180.1 Cmu05g1618 1618
5 25974627 25981412 - CmPI595203_05g016190.1 Cmu05g1619 1619
4 12643837 12649687 + Conep04aG0175400.1 Cone4ag1700 1700
4 12655851 12659187 - Conep04aG0175600.1 Cone4ag1702 1702
4 12659874 12663307 - Conep04aG0175700.1 Cone4ag1703 1703
7 10987657 10993813 + Conep07aG0166600.1 Cone7ag1617 1617
7 10996293 11000617 - Conep07aG0166700.1 Cone7ag1618 1618
7 11001039 11004972 - Conep07aG0166800.1 Cone7ag1619 1619
17 7399327 7400674 - Conep17aG0097200.1 Cone17ag0945 945
17 7401655 7403694 - Conep17aG0097400.1 Cone17ag0947 947
17 7408103 7414128 + Conep17aG0097500.1 Cone17ag0948 948
17 7414370 7432396 + Conep17aG0097600.1 Cone17ag0949 949
20 1294910 1296447 - Conep20aG0030100.1 Cone20ag0288 288
20 1297310 1299463 - Conep20aG0030300.1 Cone20ag0290 290
20 1301520 1313442 + Conep20aG0030500.1 Cone20ag0292 292
2 1515662 1527468 + Cp4.1LG02g05930.1 Cpe02g00292 292
2 1531594 1536425 - Cp4.1LG02g05810.1 Cpe02g00294 294
2 1537135 1543773 - Cp4.1LG02g05680.1 Cpe02g00295 295
6 1392701 1402986 + Cp4.1LG06g02620.1 Cpe06g00260 260
6 1405488 1413091 + Cp4.1LG06g02650.1 Cpe06g00261 261
6 1419342 1424600 - Cp4.1LG06g02690.1 Cpe06g00263 263
11 1901097 1926414 - Cp4.1LG11g03590.1 Cpe11g00352 352
11 1926931 1928962 + Cp4.1LG11g03480.1 Cpe11g00353 353
5 29116096 29117260 + CrPI670011_05g017400.1 Cre05g1740 1740
5 29135965 29144906 + CrPI670011_05g017420.1 Cre05g1742 1742
5 29192328 29196771 - CrPI670011_05g017460.1 Cre05g1746 1746
5 29199104 29203737 - CrPI670011_05g017470.1 Cre05g1747 1747
8 22356558 22359317 + CrPI670011_08g009200.1 Cre08g0920 920
8 22370890 22416632 - CrPI670011_08g009220.1 Cre08g0922 922
8 22419407 22421177 + CrPI670011_08g009230.1 Cre08g0923 923
2 20731294 20735980 + CsaV3_2G031500.1 Csa02g02331 2331
1 84034459 84039549 - Hsped.01g19210.1 Hepe01g1921 1921
1 84040819 84046490 - Hsped.01g19220.1 Hepe01g1922 1922
8 17221631 17223607 - Hsped.08g14360.1 Hepe08g1436 1436
8 17233581 17277033 + Hsped.08g14370.1 Hepe08g1437 1437
8 17289900 17294016 - Hsped.08g14390.1 Hepe08g1439 1439
13 41099808 41101704 - Maker00025136 Lcy13g2222 2222
13 41134946 41144254 + Maker00025152 Lcy13g2225 2225
13 41151804 41156815 - Maker00025407 Lcy13g2227 2227
4 21614125 21625658 + Lsi04G013810.1 Lsi04g01381 1381
4 21632518 21641808 - Lsi04G013840.1 Lsi04g01384 1384
4 21656444 21664316 - Lsi04G013850.1 Lsi04g01385 1385
4 21671928 21674084 - Lsi04G013870.1 Lsi04g01386 1386
8 16682974 16695543 + Lsi08G008280.1 Lsi08g00828 828
8 16705509 16745098 - Lsi08G008300.1 Lsi08g00830 830
8 16748003 16750301 + Lsi08G008310.1 Lsi08g00831 831
11 2835310 2836962 + MC11g0364 Mch11g0452 452
5 31550591 31552457 + Sed0017046.1 Sed05g1795 1795
8 32754440 32756934 - Sed0001574.1 Sed08g1804 1804
8 32808698 32814069 + Sed0000254.1 Sed08g1807 1807
13 24098268 24105968 - Sed0020055.2 Sed13g1913 1913
1 100008259 100009421 + Tan0020388.1 Tan01g3472 3472
1 100057257 100063425 - Tan0009081.4 Tan01g3482 3482
1 100064462 100069992 - Tan0022401.1 Tan01g3487 3487
2 72854448 72857509 + Tan0001376.1 Tan02g1576 1576
2 73112035 73113902 + Tan0000597.1 Tan02g1581 1581
4 1524968 1528585 - Vvi4g162 Vvi4g162 162
4 1529077 1552457 + Vvi4g163 Vvi4g163 163
4 1554758 1557419 - Vvi4g164 Vvi4g164 164
4 1557586 1570570 + Vvi4g165 Vvi4g165 165
4 1578700 1586803 + Vvi4g166 Vvi4g166 166
4 1588077 1591208 - Vvi4g167 Vvi4g167 167
4 1596630 1632504 + Vvi4g168 Vvi4g168 168
4 1639515 1646409 - Vvi4g169 Vvi4g169 169
4 1648095 1654700 - Vvi4g170 Vvi4g170 170
4 1658854 1667251 - Vvi4g171 Vvi4g171 171
       

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