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
Vvi17g616 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g617 Blo04g00786 . . . . . . . Cmo13g01138 . . . Car10g00205 . . . Cpe04g01473 . . . . . . . . . . . . . . . . . . . . . . . . . Bda14g00867 . . Bma03g00844 . . Cmo10g00232 . Cma13g01086 . Car13g00924 . . Cpe18g00772 . . . . . . . . . . . . . . . . . .
Vvi17g618 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme02g01848
Vvi17g619 . . Bda06g00531 . . Bpe13g00303 . Bma12g00975 . . . Cma11g00116 . . . . . . . . . . . . Cla06g01560 Cam06g1724 Cec06g1785 Cco06g1785 Clacu06g1692 Cmu06g1637 Cre06g2448 . Cone16ag0195 . . Lsi02g00100 Csa01g00579 Chy12g01517 Cme12g01963 . Blo15g00328 . . Bpe07g00765 . . . . . Cmo11g00129 . . . . . . Bhi08g01122 . . . Hepe07g2481 . . Cla04g01174 Cam04g1231 Cec01g1742 Cco01g1788 Clacu04g1258 Cmu04g1237 Cre01g1532 Lsi06g01434 Csa01g00271 Chy02g02463 .
Vvi17g620 . . Bda06g00532 . . . . Bma12g00976 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo15g00327 . . Bpe07g00766 . . . . Cmo10g00171 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g621 . . . . . . Bma06g00128 Bma12g00977 . . Cma10g00160 . Car10g00202 . . . . Bhi02g00275 . . . . . . . . . . . . . . . . . . . . . . Blo15g00326 . . Bpe07g00767 . . . . . . . . . . . Cpe18g00774 . . . . . . . . . . . . . . . . Chy02g02461 .
Vvi17g622 . . . . Bpe12g00529 . . . Cmo13g00940 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00101 Csa01g00580 Chy12g01516 Cme12g01962 . . . . . . . . Sed08g2099 . . Cma13g00913 . Car13g00753 . . . Bhi08g01121 Tan05g2402 Cmetu12g1770 . . . . Cla04g01173 Cam04g1230 Cec01g1741 Cco01g1787 Clacu04g1257 Cmu04g1236 Cre01g1531 . . . .
Vvi17g623 . . . Bda15g00616 . . . Bma12g00978 . . . . Car10g00201 . . . . . . . . . . . . . . . . . . . . . . Lsi02g00102 Csa01g00581 Chy12g01515 Cme12g01961 . Blo15g00325 . . Bpe07g00768 . . . . . . . . . . . Cpe18g00775 Bhi08g01118 . . . . . . Cla04g01172 Cam04g1229 Cec01g1740 Cco01g1786 Clacu04g1256 Cmu04g1235 Cre01g1530 . . . .
Vvi17g624 . . . . . . . . . . Cma10g00225 . Car10g00209 Car11g00122 . . Cpe04g01470 Bhi02g00262 Tan09g2060 . . . . . Cla06g01553 Cam06g1716 Cec06g1777 Cco06g1776 Clacu06g1684 Cmu06g1629 Cre06g2440 . . Cone13ag0044 Cone19ag0049 . . . . . . . . . . . . . Cmo10g00236 Cmo11g00201 . . . . . Cpe18g00768 . . . . . . . . . . . . . . Lsi06g01427 Csa01g00277 Chy02g02455 Cme02g01843
Vvi17g625 . . Bda06g00528 . . . . Bma12g00972 . . . . . Car11g00178 . . Cpe04g01469 Bhi02g00257 . . . . . . . . . . . . . . . . . . . . . . Blo15g00330 . . Bpe07g00762 . . . . . Cmo11g00202 . . . . Cpe09g01050 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7533388 7549308 - Bda023784.1 Bda06g00528 528
6 7572207 7575569 - Bda023788.1 Bda06g00531 531
6 7583751 7592149 + Bda023790.1 Bda06g00532 532
14 6682717 6684303 - Bda027642.1 Bda14g00867 867
15 9335231 9337538 - Bda012459.1 Bda15g00616 616
2 4787917 4834240 - XM_039023727.1 Bhi02g00257 257
2 4904620 4915817 + XM_039024273.1 Bhi02g00262 262
2 5208296 5222697 - XM_039024250.1 Bhi02g00275 275
8 35682415 35686682 - XM_039038004.1 Bhi08g01118 1118
8 35690025 35692255 - XM_039038007.1 Bhi08g01121 1121
8 35695624 35701228 + XM_039039341.1 Bhi08g01122 1122
4 7804806 7806205 - BLOR13698 Blo04g00786 786
15 3768687 3770563 - BLOR06719 Blo15g00325 325
15 3808995 3827162 + BLOR06720 Blo15g00326 326
15 3828445 3841969 - BLOR06721 Blo15g00327 327
15 3844887 3848304 + BLOR06722 Blo15g00328 328
15 3864628 3897941 + BLOR06724 Blo15g00330 330
3 8082838 8084349 - Bma017160.1 Bma03g00844 844
6 1722979 1728153 - Bma022746.1 Bma06g00128 128
12 41787310 41803553 - Bma008316.1 Bma12g00972 972
12 41816285 41820269 - Bma008319.1 Bma12g00975 975
12 41822898 41832046 + Bma008320.1 Bma12g00976 976
12 41833035 41841710 - Bma008321.1 Bma12g00977 977
12 41848692 41850485 + Bma008322.1 Bma12g00978 978
7 14135625 14154014 - Bpe021608.1 Bpe07g00762 762
7 14166602 14169932 - Bpe021611.1 Bpe07g00765 765
7 14173631 14181885 + Bpe021612.1 Bpe07g00766 766
7 14182940 14194795 - Bpe026081 Bpe07g00767 767
7 14197517 14199331 + Bpe021613.1 Bpe07g00768 768
12 11202382 11202742 + Bpe005795.1 Bpe12g00529 529
13 10866251 10870486 + Bpe006429.1 Bpe13g00303 303
4 26321232 26324359 - CaPI482276_04g012290.1 Cam04g1229 1229
4 26328828 26330373 - CaPI482276_04g012300.1 Cam04g1230 1230
4 26335129 26338821 + CaPI482276_04g012310.1 Cam04g1231 1231
6 28497650 28509090 - CaPI482276_06g017160.1 Cam06g1716 1716
6 28541287 28548012 - CaPI482276_06g017240.1 Cam06g1724 1724
10 972926 976432 - Carg17942-RA Car10g00201 201
10 977968 991406 + Carg17941-RA Car10g00202 202
10 993235 994305 - Carg17938-RA Car10g00205 205
10 1010085 1015572 - Carg17934-RA Car10g00209 209
11 686196 688241 + Carg18159-RA Car11g00122 122
11 1022365 1034382 + Carg09211-RA Car11g00178 178
13 8537249 8545485 + Carg07703-RA Car13g00753 753
13 9512034 9514540 + Carg04747-RA Car13g00924 924
1 30575812 30578950 - CcPI632755_01g017860.1 Cco01g1786 1786
1 30582632 30584983 - CcPI632755_01g017870.1 Cco01g1787 1787
1 30589609 30593308 + CcPI632755_01g017880.1 Cco01g1788 1788
6 28197803 28204011 - CcPI632755_06g017760.1 Cco06g1776 1776
6 28244719 28247482 - CcPI632755_06g017850.1 Cco06g1785 1785
1 31995054 32001027 - CePI673135_01g017400.1 Cec01g1740 1740
1 32005557 32007102 - CePI673135_01g017410.1 Cec01g1741 1741
1 32011863 32015569 + CePI673135_01g017420.1 Cec01g1742 1742
6 31270232 31276566 - CePI673135_06g017770.1 Cec06g1777 1777
6 31314897 31317709 - CePI673135_06g017850.1 Cec06g1785 1785
2 28163928 28167748 - Chy2G047220.1 Chy02g02455 2455
2 28196898 28197654 - Chy2G047280.1 Chy02g02461 2461
2 28212025 28214720 - Chy2G047300.1 Chy02g02463 2463
12 18950958 18954444 - Chy12G221150.1 Chy12g01515 1515
12 18957634 18958515 - Chy12G221160.1 Chy12g01516 1516
12 18962571 18966198 + Chy12G221170.1 Chy12g01517 1517
4 26676317 26679435 - ClG42_04g0125600.10 Clacu04g1256 1256
4 26683944 26685491 - ClG42_04g0125700.10 Clacu04g1257 1257
4 26690245 26693940 + ClG42_04g0125800.10 Clacu04g1258 1258
6 27553693 27562185 - ClG42_06g0168400.10 Clacu06g1684 1684
6 27600282 27603053 - ClG42_06g0169200.10 Clacu06g1692 1692
4 26916215 26919333 - ClCG04G011970.1 Cla04g01172 1172
4 26923842 26925389 - ClCG04G011980.2 Cla04g01173 1173
4 26928513 26934011 + ClCG04G011990.2 Cla04g01174 1174
6 29108853 29115449 - ClCG06G015770.1 Cla06g01553 1553
6 29153898 29156670 - ClCG06G015850.2 Cla06g01560 1560
10 725322 728051 + CmaCh10G001600.1 Cma10g00160 160
10 1000181 1005534 - CmaCh10G002250.1 Cma10g00225 225
11 621168 625835 - CmaCh11G001160.1 Cma11g00116 116
13 7296812 7304092 + CmaCh13G009130.1 Cma13g00913 913
13 8208255 8209895 + CmaCh13G010860.1 Cma13g01086 1086
2 25121856 25127283 - MELO3C017212.2.1 Cme02g01843 1843
2 25150328 25151050 - MELO3C017207.2.1 Cme02g01848 1848
12 25490076 25494806 - MELO3C002012.2.1 Cme12g01961 1961
12 25497961 25499586 - MELO3C002011.2.1 Cme12g01962 1962
12 25501940 25507056 + MELO3C002010.2.1 Cme12g01963 1963
12 633461 635029 + PI0014863.1 Cmetu12g1770 1770
10 772495 774896 + CmoCh10G001710.1 Cmo10g00171 171
10 1040713 1045946 - CmoCh10G002320.1 Cmo10g00232 232
10 1059254 1064570 - CmoCh10G002360.1 Cmo10g00236 236
11 653243 655951 + CmoCh11G001290.1 Cmo11g00129 129
11 978871 988248 - CmoCh11G002010.1 Cmo11g00201 201
11 988401 1001707 + CmoCh11G002020.1 Cmo11g00202 202
13 8235433 8242191 + CmoCh13G009400.1 Cmo13g00940 940
13 9226740 9228909 + CmoCh13G011380.1 Cmo13g01138 1138
4 26858267 26861384 - CmPI595203_04g012350.1 Cmu04g1235 1235
4 26865894 26867441 - CmPI595203_04g012360.1 Cmu04g1236 1236
4 26872200 26875895 + CmPI595203_04g012370.1 Cmu04g1237 1237
6 27462387 27470828 - CmPI595203_06g016290.1 Cmu06g1629 1629
6 27508913 27511684 - CmPI595203_06g016370.1 Cmu06g1637 1637
13 261096 264521 + Conep13aG0004700.1 Cone13ag0044 44
16 1266180 1270939 + Conep16aG0019900.1 Cone16ag0195 195
19 321581 324779 + Conep19aG0005300.1 Cone19ag0049 49
4 11681094 11693666 - Cp4.1LG04g14780.1 Cpe04g01469 1469
4 11694683 11700170 + Cp4.1LG04g14700.1 Cpe04g01470 1470
4 11710465 11713728 + Cp4.1LG04g14730.1 Cpe04g01473 1473
9 9183071 9188935 + Cp4.1LG09g10520.1 Cpe09g01050 1050
18 7328122 7333813 + Cp4.1LG18g07620.1 Cpe18g00768 768
18 7349112 7351385 + Cp4.1LG18g07630.1 Cpe18g00772 772
18 7351938 7367693 - Cp4.1LG18g07750.1 Cpe18g00774 774
18 7369554 7372778 + Cp4.1LG18g07650.1 Cpe18g00775 775
1 28518421 28524818 - CrPI670011_01g015300.1 Cre01g1530 1530
1 28528937 28530919 - CrPI670011_01g015310.1 Cre01g1531 1531
1 28535646 28539340 + CrPI670011_01g015320.1 Cre01g1532 1532
6 32258587 32266956 - CrPI670011_06g024400.1 Cre06g2440 2440
6 32304148 32306922 - CrPI670011_06g024480.1 Cre06g2448 2448
1 1707643 1712138 + CsaV3_1G002710.1 Csa01g00271 271
1 1744354 1749683 + CsaV3_1G002770.1 Csa01g00277 277
1 3715813 3720928 - CsaV3_1G005790.1 Csa01g00579 579
1 3722835 3724386 + CsaV3_1G005800.1 Csa01g00580 580
1 3727778 3731264 + CsaV3_1G005810.1 Csa01g00581 581
7 69121408 69125838 - Hsped.07g24810.1 Hepe07g2481 2481
2 821665 826936 - Lsi02G001000.1 Lsi02g00100 100
2 829709 831837 + Lsi02G001010.1 Lsi02g00101 101
2 834811 838796 + Lsi02G001020.1 Lsi02g00102 102
6 24820216 24826130 - Lsi06G014270.1 Lsi06g01427 1427
6 24870711 24875046 - Lsi06G014340.1 Lsi06g01434 1434
8 35105646 35107290 - Sed0013431.2 Sed08g2099 2099
5 75245777 75247901 + Tan0011444.4 Tan05g2402 2402
9 71105898 71112056 + Tan0008096.1 Tan09g2060 2060
17 7517363 7520896 + Vvi17g616 Vvi17g616 616
17 7520917 7524572 + Vvi17g617 Vvi17g617 617
17 7527949 7530932 - Vvi17g618 Vvi17g618 618
17 7531885 7537040 - Vvi17g619 Vvi17g619 619
17 7542209 7555873 + Vvi17g620 Vvi17g620 620
17 7556256 7599691 - Vvi17g621 Vvi17g621 621
17 7601651 7602915 + Vvi17g622 Vvi17g622 622
17 7609545 7613137 + Vvi17g623 Vvi17g623 623
17 7615880 7632396 - Vvi17g624 Vvi17g624 624
17 7636531 7658790 + Vvi17g625 Vvi17g625 625
       

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