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
Vvi17g26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g27 . Blo16g00290 . . . Bpe13g00184 Bma06g00284 . . . Cma10g00017 . Car10g00012 . . . . Bhi02g00618 . . . Hepe09g0011 . . . . . . . . . . . Cone13ag0257 Cone19ag0242 . . . . . . Bda11g01574 . . . . . . Cmo10g00015 . . . . . . Cpe18g00939 . . . . . . . . . . . . . . Lsi06g01682 Csa01g00009 Chy02g02705 Cme02g02113
Vvi17g28 . Blo16g00289 . . . . Bma06g00283 . . Cmo18g00238 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00527 Csa01g00990 Chy12g01144 Cme12g01562 . . Bda11g01575 . . . . . Sed08g2407 . . . Cma18g00292 Car13g00673 Car18g00249 Cpe09g00942 . Bhi08g01538 Tan05g3011 Cmetu06g0036 Lac10g0613 Hepe07g2082 . . . . . . . . . . . . .
Vvi17g29 . . Bda06g00709 Bda15g00698 . . . . . . Cma10g00018 Cma11g00007 Car10g00013 Car11g00006 . . . . . . . . . . Cla06g01783 Cam06g1977 Cec06g2027 Cco06g2035 Clacu06g1934 Cmu06g1875 Cre06g2687 . . Cone13ag0256 Cone19ag0241 . . . . . Blo15g00190 . . Bpe07g00907 . . . . Cmo10g00016 Cmo11g00006 . . . . . Cpe18g00938 . . . . . . . . . . . . . . Lsi06g01681 Csa01g00010 Chy02g02703 Cme02g02111
Vvi17g30 . . . . Bpe12g00459 . . . . . . . . . Sed01g1068 . Cpe04g01638 Bhi02g00620 Tan09g2434 Cmetu06g1260 . Hepe09g0012 . . . . . . . . . . . . . . . . . . . . . . . . Bma08g00280 . . . . . . . . . . . . . . . . . . . . . . . . . Chy02g02702 .
Vvi17g31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g32 . . . Bda15g00697 Bpe12g00460 . . . . . Cma10g00021 . Car10g00014 . Sed12g2546 . . Bhi02g00621 Tan09g2433 Cmetu02g0933 . Hepe09g0013 . . Cla06g01782 Cam06g1976 Cec06g2025 Cco06g2033 Clacu06g1933 Cmu06g1874 Cre06g2686 . . Cone13ag0255 . . . . . . . . . . . . Bma08g00279 . Cmo10g00018 . . . . . . Cpe18g00937 . . . . . . . . . . . . . . Lsi06g01680 Csa01g00011 Chy02g02701 .
Vvi17g33 . . . . . . . . . . Cma10g00024 . Car10g00016 . . . . Bhi02g00627 . . . . . . Cla06g01779 Cam06g1972 Cec06g2023 Cco06g2030 Clacu06g1930 Cmu06g1870 Cre06g2683 . . Cone13ag0254 . . . . . . . . . . . . . . Cmo10g00021 . . . . . . Cpe18g00936 . . . . . . . . . . . . . . Lsi06g01676 Csa01g00015 Chy02g02698 Cme02g02105
Vvi17g34 . Blo16g00288 . . . Bpe13g00185 Bma06g00282 . Cmo13g00860 . . . . . . Cpe20g00289 . . . . . . . . . . . . . . . . . Cone13ag0253 Cone19ag0238 Lsi02g00526 Csa01g00989 Chy12g01145 Cme12g01564 . . . . . Bpe15g00237 Bma03g01224 . Sed08g2408 . . Cma13g00829 Cma18g00295 Car13g00672 Car18g00248 Cpe09g00943 . Bhi08g01536 Tan05g3009 Cmetu12g2124 . Hepe07g2083 . . Cla03g00378 Cam03g0398 Cec03g0384 Cco03g0399 Clacu03g0397 Cmu03g1002 Cre03g0694 . . . .
Vvi17g35 . . . . . Bpe13g00186 Bma06g00281 . . . Cma10g00026 Cma11g00008 Car10g00018 Car11g00008 . . . Bhi02g00524 . . . . . . Cla06g01777 Cam06g1970 Cec06g2021 Cco06g2028 Clacu06g1928 Cmu06g1868 Cre06g2681 . . . Cone19ag0236 . . . . . . Bda11g01581 . . . . . . Cmo10g00024 Cmo11g00007 . . . . . Cpe18g00933 . . . . . . . . . . . . . . Lsi06g01674 Csa01g00018 Chy02g02696 Cme02g02103
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 9764268 9769375 + Bda024008.2 Bda06g00709 709
11 48941667 48946081 + Bda008444.1 Bda11g01574 1574
11 48947578 48965307 - Bda008445.1 Bda11g01575 1575
11 49077833 49080646 + Bda008452.1 Bda11g01581 1581
15 10391036 10396925 + Bda012551.1 Bda15g00697 697
15 10397329 10402285 - Bda012552.1 Bda15g00698 698
2 10028076 10034884 - XM_039023065.1 Bhi02g00524 524
2 12034365 12039950 + XM_039022744.1 Bhi02g00618 618
2 12088102 12098531 + XM_039023681.1 Bhi02g00620 620
2 12099412 12120592 - XM_039023169.1 Bhi02g00621 621
2 12177976 12186519 - XM_039024780.1 Bhi02g00627 627
8 44148137 44162600 + XM_039038608.1 Bhi08g01536 1536
8 44167390 44170595 + XM_039038768.1 Bhi08g01538 1538
15 1971275 1972428 + BLOR06584 Blo15g00190 190
16 6917296 6930165 + BLOR07536 Blo16g00288 288
16 6960858 6963006 + BLOR07537 Blo16g00289 289
16 6964416 6972953 - BLOR07538 Blo16g00290 290
3 19262576 19277856 - Bma017662.2 Bma03g01224 1224
6 3948710 3951514 - Bma022916.1 Bma06g00281 281
6 3988725 3997142 + Bma022917.1 Bma06g00282 282
6 4002723 4004973 + Bma022918.1 Bma06g00283 283
6 4006564 4008203 - Bma022919.1 Bma06g00284 284
8 3786914 3788905 + Bma027300.1 Bma08g00279 279
8 3794538 3799504 - Bma027301.1 Bma08g00280 280
7 15050510 15055641 - Bpe021748.1 Bpe07g00907 907
12 10338239 10343189 + Bpe005719.1 Bpe12g00459 459
12 10343710 10354371 - Bpe005720.1 Bpe12g00460 460
13 9759644 9763254 + Bpe006304.1 Bpe13g00184 184
13 9764489 9784353 - Bpe006305.1 Bpe13g00185 185
13 9797064 9799661 + Bpe006306.1 Bpe13g00186 186
15 13634644 13647217 + Bpe001173.1 Bpe15g00237 237
3 5118781 5122218 + CaPI482276_03g003980.1 Cam03g0398 398
6 30508909 30510349 - CaPI482276_06g019700.1 Cam06g1970 1970
6 30518888 30521213 + CaPI482276_06g019720.1 Cam06g1972 1972
6 30532536 30542229 + CaPI482276_06g019760.1 Cam06g1976 1976
6 30542653 30559727 - CaPI482276_06g019770.1 Cam06g1977 1977
10 62700 68176 + Carg10244-RA Car10g00012 12
10 69082 73704 + Carg10245-RA Car10g00013 13
10 76162 84787 - Carg10246-RA Car10g00014 14
10 89680 91992 - Carg10248-RA Car10g00016 16
10 95616 97319 + Carg10250-RA Car10g00018 18
11 33028 37570 + Carg24562-RA Car11g00006 6
11 42978 43897 + Carg24560-RA Car11g00008 8
13 8178509 8185550 + Carg07622-RA Car13g00672 672
13 8187877 8190878 + Carg07623-RA Car13g00673 673
18 1444088 1451183 + Carg06815-RA Car18g00248 248
18 1454043 1459137 + Carg06816-RA Car18g00249 249
3 4345649 4349120 + CcPI632755_03g003990.1 Cco03g0399 399
6 30258230 30259671 - CcPI632755_06g020280.1 Cco06g2028 2028
6 30268320 30270564 + CcPI632755_06g020300.1 Cco06g2030 2030
6 30286592 30302256 + CcPI632755_06g020330.1 Cco06g2033 2033
6 30315379 30320344 - CcPI632755_06g020350.1 Cco06g2035 2035
3 4303182 4305986 + CePI673135_03g003840.1 Cec03g0384 384
6 33336302 33337744 - CePI673135_06g020210.1 Cec06g2021 2021
6 33348979 33351304 + CePI673135_06g020230.1 Cec06g2023 2023
6 33358833 33372341 + CePI673135_06g020250.1 Cec06g2025 2025
6 33396158 33403274 - CePI673135_06g020270.1 Cec06g2027 2027
2 29827149 29828662 - Chy2G049630.1 Chy02g02696 2696
2 29833216 29835376 + Chy2G049650.1 Chy02g02698 2698
2 29847718 29867938 + Chy2G049680.1 Chy02g02701 2701
2 29868369 29876415 - Chy2G049690.1 Chy02g02702 2702
2 29876509 29877835 - Chy2G049700.1 Chy02g02703 2703
2 29881835 29885948 - Chy2G049720.1 Chy02g02705 2705
12 16365054 16367882 - Chy12G217440.1 Chy12g01144 1144
12 16372083 16379817 - Chy12G217450.1 Chy12g01145 1145
3 4434537 4437342 + ClG42_03g0039700.10 Clacu03g0397 397
6 29550412 29551854 - ClG42_06g0192800.10 Clacu06g1928 1928
6 29560464 29562790 + ClG42_06g0193000.10 Clacu06g1930 1930
6 29570014 29583586 + ClG42_06g0193300.10 Clacu06g1933 1933
6 29584176 29601120 - ClG42_06g0193400.10 Clacu06g1934 1934
3 4383133 4399514 + ClCG03G004000.2 Cla03g00378 378
6 31212131 31214488 - ClCG06G018270.2 Cla06g01777 1777
6 31222788 31225114 + ClCG06G018290.2 Cla06g01779 1779
6 31232675 31246516 + ClCG06G018320.1 Cla06g01782 1782
6 31246818 31267080 - ClCG06G018330.2 Cla06g01783 1783
10 64046 69908 + CmaCh10G000170.1 Cma10g00017 17
10 70380 79701 + CmaCh10G000180.1 Cma10g00018 18
10 84430 86938 - CmaCh10G000210.1 Cma10g00021 21
10 92799 95307 - CmaCh10G000240.1 Cma10g00024 24
10 98679 100854 + CmaCh10G000260.1 Cma10g00026 26
11 37132 44896 + CmaCh11G000070.1 Cma11g00007 7
11 45311 48475 + CmaCh11G000080.1 Cma11g00008 8
13 6934779 6954838 + CmaCh13G008290.1 Cma13g00829 829
18 1555718 1562158 - CmaCh18G002920.1 Cma18g00292 292
18 1562799 1570390 - CmaCh18G002950.1 Cma18g00295 295
2 26819506 26821142 - MELO3C026171.2.1 Cme02g02103 2103
2 26825327 26827493 + MELO3C026169.2.1 Cme02g02105 2105
2 26869675 26879844 - MELO3C026162.2.1 Cme02g02111 2111
2 26881616 26887678 - MELO3C026161.2.1 Cme02g02113 2113
12 23013361 23016702 - MELO3C002385.2.1 Cme12g01562 1562
12 23019739 23027774 - MELO3C002384.2.1 Cme12g01564 1564
2 25164846 25181036 + PI0001500.13 Cmetu02g0933 933
6 19142470 19145925 - PI0010581.1 Cmetu06g0036 36
6 6505800 6509994 + PI0024234.1 Cmetu06g1260 1260
12 3365491 3373610 + PI0025474.1 Cmetu12g2124 2124
10 102271 107657 + CmoCh10G000150.1 Cmo10g00015 15
10 109443 117408 + CmoCh10G000160.1 Cmo10g00016 16
10 123701 126198 - CmoCh10G000180.1 Cmo10g00018 18
10 131458 133999 - CmoCh10G000210.1 Cmo10g00021 21
10 137127 139267 + CmoCh10G000240.1 Cmo10g00024 24
11 29958 38222 + CmoCh11G000060.1 Cmo11g00006 6
11 39304 41957 + CmoCh11G000070.1 Cmo11g00007 7
13 7869398 7888872 + CmoCh13G008600.1 Cmo13g00860 860
18 1579409 1583411 + CmoCh18G002380.1 Cmo18g00238 238
3 4648530 4652616 + CmPI595203_03g010020.1 Cmu03g1002 1002
6 29460902 29462344 - CmPI595203_06g018680.1 Cmu06g1868 1868
6 29470979 29473223 + CmPI595203_06g018700.1 Cmu06g1870 1870
6 29484575 29494092 + CmPI595203_06g018740.1 Cmu06g1874 1874
6 29494682 29511660 - CmPI595203_06g018750.1 Cmu06g1875 1875
13 1732053 1738388 + Conep13aG0026400.1 Cone13ag0253 253
13 1742222 1744448 + Conep13aG0026500.1 Cone13ag0254 254
13 1750123 1756837 + Conep13aG0026600.1 Cone13ag0255 255
13 1763700 1768006 - Conep13aG0026700.1 Cone13ag0256 256
13 1771296 1776877 - Conep13aG0026800.1 Cone13ag0257 257
19 1548657 1550672 - Conep19aG0024300.1 Cone19ag0236 236
19 1556753 1562505 + Conep19aG0024500.1 Cone19ag0238 238
19 1579727 1585753 - Conep19aG0024800.1 Cone19ag0241 241
19 1587389 1593183 - Conep19aG0024900.1 Cone19ag0242 242
4 12655195 12665950 - Cp4.1LG04g16400.1 Cpe04g01638 1638
9 8431363 8436729 - Cp4.1LG09g09410.1 Cpe09g00942 942
9 8437321 8446251 - Cp4.1LG09g09380.1 Cpe09g00943 943
18 8237124 8238820 - Cp4.1LG18g09460.1 Cpe18g00933 933
18 8242424 8245735 + Cp4.1LG18g09350.1 Cpe18g00936 936
18 8248876 8259980 + Cp4.1LG18g09330.1 Cpe18g00937 937
18 8256920 8267625 - Cp4.1LG18g09410.1 Cpe18g00938 938
18 8268551 8280118 - Cp4.1LG18g09430.1 Cpe18g00939 939
20 1601514 1614106 - Cp4.1LG20g03000.1 Cpe20g00289 289
3 5862860 5865755 + CrPI670011_03g006940.1 Cre03g0694 694
6 34293797 34295243 - CrPI670011_06g026810.1 Cre06g2681 2681
6 34303360 34305685 + CrPI670011_06g026830.1 Cre06g2683 2683
6 34316502 34326526 + CrPI670011_06g026860.1 Cre06g2686 2686
6 34327108 34344287 - CrPI670011_06g026870.1 Cre06g2687 2687
1 68012 78346 + CsaV3_1G000090.1 Csa01g00009 9
1 80792 90944 + CsaV3_1G000100.1 Csa01g00010 10
1 91324 107838 - CsaV3_1G000110.1 Csa01g00011 11
1 117971 120451 - CsaV3_1G000150.1 Csa01g00015 15
1 124097 126120 + CsaV3_1G000180.1 Csa01g00018 18
1 6163231 6171588 + CsaV3_1G009890.1 Csa01g00989 989
1 6174783 6178372 + CsaV3_1G009900.1 Csa01g00990 990
7 65083710 65087691 - Hsped.07g20820.1 Hepe07g2082 2082
7 65091573 65099637 - Hsped.07g20830.1 Hepe07g2083 2083
9 120331 125154 + Hsped.09g00110.1 Hepe09g0011 11
9 128978 136374 + Hsped.09g00120.1 Hepe09g0012 12
9 136595 143406 - Hsped.09g00130.1 Hepe09g0013 13
10 4711912 4714912 + Lag0024658.1 Lac10g0613 613
2 4569255 4578408 + Lsi02G005260.1 Lsi02g00526 526
2 4582571 4585923 + Lsi02G005270.1 Lsi02g00527 527
6 26967425 26969552 - Lsi06G016740.1 Lsi06g01674 1674
6 26974186 26976630 + Lsi06G016760.1 Lsi06g01676 1676
6 26986337 26995553 + Lsi06G016800.1 Lsi06g01680 1680
6 26995479 27004279 - Lsi06G016810.1 Lsi06g01681 1681
6 27009010 27026500 - Lsi06G016820.1 Lsi06g01682 1682
1 7991481 7998150 - Sed0011803.1 Sed01g1068 1068
8 37177970 37181537 - Sed0018212.1 Sed08g2407 2407
8 37186935 37195063 - Sed0027714.1 Sed08g2408 2408
12 34726490 34732594 + Sed0025035.1 Sed12g2546 2546
5 82014573 82022849 + Tan0014699.1 Tan05g3009 3009
5 82028499 82032064 + Tan0000973.1 Tan05g3011 3011
9 73870037 73892229 + Tan0002040.1 Tan09g2433 2433
9 73892477 73900513 - Tan0017749.1 Tan09g2434 2434
17 201291 212911 + Vvi17g26 Vvi17g26 26
17 224845 230250 + Vvi17g27 Vvi17g27 27
17 232690 236378 - Vvi17g28 Vvi17g28 28
17 236873 248571 + Vvi17g29 Vvi17g29 29
17 248578 249243 + Vvi17g30 Vvi17g30 30
17 249496 249796 - Vvi17g31 Vvi17g31 31
17 249999 257710 - Vvi17g32 Vvi17g32 32
17 260725 263753 - Vvi17g33 Vvi17g33 33
17 266766 275866 - Vvi17g34 Vvi17g34 34
17 286803 292529 + Vvi17g35 Vvi17g35 35
       

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