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
Vvi2g702 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g705 Blo02g00985 . Bda06g01262 Bda08g00638 . . . . Cmo06g00645 Cmo16g01225 . . . . Sed10g1395 Cpe14g00974 . Bhi11g00015 Tan08g0173 Cmetu05g1605 . . Mch10g1679 . Cla10g00139 Cam10g0138 Cec10g0148 Cco10g0148 Clacu10g0142 Cmu10g0989 Cre10g0400 . . . . Lsi07g01178 . . Cme06g02455 . . . . . . Bma05g00705 . . . . Cma06g00639 Cma16g01175 Car06g00570 Car16g01108 . . . . . . . . . . . . . . . . . Csa03g00150 Chy06g02159 .
Vvi2g706 Blo02g00983 . . . . Bpe07g00232 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0482 Cone12ag0477 . . . . . . . . . . . . . Bma12g00234 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g707 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g708 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0480 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g709 Blo02g00982 . Bda06g01261 Bda08g00639 Bpe05g00520 Bpe07g00233 . . Cmo06g00644 Cmo16g01226 . . . . Sed02g0067 Cpe14g00975 . Bhi11g00014 Tan01g2212 Cmetu06g0720 . . Mch10g1680 . Cla10g00138 Cam10g0137 Cec10g0147 Cco10g0147 Clacu10g0141 Cmu10g0988 Cre10g0399 Cone8ag0484 Cone12ag0481 . . Lsi07g01177 . . Cme06g02454 . . . . . . Bma05g00704 Bma12g00235 . . . Cma06g00638 Cma16g01176 Car06g00569 Car16g01109 . . . . . . . . . . . . . . . . . Csa03g00149 Chy06g02160 .
Vvi2g710 . . . . . . . . Cmo06g00642 Cmo16g01227 . . . . . Cpe14g00976 . Bhi11g00013 . . . . . . Cla10g00137 Cam10g0136 Cec10g0146 Cco10g0146 Clacu10g0140 Cmu10g0987 Cre10g0398 . Cone12ag0564 . . Lsi07g01175 . . Cme06g02453 Blo03g00876 . Bda07g00083 Bda09g00754 Bpe08g00810 Bpe11g00320 . . . . . Cma06g00637 Cma16g01177 Car06g00568 Car16g01110 . . . . . . . . . . . . . . . . . Csa03g00147 Chy06g02162 .
Vvi2g711 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43102901 43106337 + Bda023101.1 Bda06g01261 1261
6 43108079 43111683 - Bda023102.1 Bda06g01262 1262
7 1071650 1074768 - Bda025141.1 Bda07g00083 83
8 6570681 6574078 + Bda029100.1 Bda08g00638 638
8 6575545 6579450 - Bda034011 Bda08g00639 639
9 13345566 13348733 + Bda031460.1 Bda09g00754 754
11 208331 210338 - XM_039050430.1 Bhi11g00013 13
11 223022 227982 + XM_039047189.1 Bhi11g00014 14
11 228859 234976 - XM_039047188.1 Bhi11g00015 15
2 37993441 37997352 + BLOR10712 Blo02g00982 982
2 38003864 38005836 - BLOR10713 Blo02g00983 983
2 38010572 38013807 - BLOR10715 Blo02g00985 985
3 34606342 34610057 + BLOR12057 Blo03g00876 876
5 41032743 41037056 + Bma021777.1 Bma05g00704 704
5 41049002 41060546 - Bma021778.1 Bma05g00705 705
12 3039218 3042837 + Bma007124.1 Bma12g00234 234
12 3044573 3048195 - Bma007125.1 Bma12g00235 235
5 19384275 19388543 + Bpe017937.1 Bpe05g00520 520
7 1653079 1656672 + Bpe021043.1 Bpe07g00232 232
7 1658418 1662089 - Bpe021044.1 Bpe07g00233 233
8 10141074 10144049 - Bpe022931.1 Bpe08g00810 810
11 2355334 2358440 - Bpe003694.1 Bpe11g00320 320
10 2982875 2985631 - CaPI482276_10g001360.1 Cam10g0136 136
10 2991112 2995953 + CaPI482276_10g001370.1 Cam10g0137 137
10 2998688 3003116 - CaPI482276_10g001380.1 Cam10g0138 138
6 3248566 3252107 - Carg23395-RA Car06g00568 568
6 3253771 3259020 + Carg23394-RA Car06g00569 569
6 3260122 3263592 - Carg23393-RA Car06g00570 570
16 9533326 9539270 + Carg26208-RA Car16g01108 1108
16 9558909 9563117 - Carg23600-RA Car16g01109 1109
16 9564824 9567522 + Carg23599-RA Car16g01110 1110
10 1400322 1408491 - CcPI632755_10g001460.1 Cco10g0146 146
10 1408786 1413196 + CcPI632755_10g001470.1 Cco10g0147 147
10 1415915 1420338 - CcPI632755_10g001480.1 Cco10g0148 148
10 1414232 1422607 - CePI673135_10g001460.1 Cec10g0146 146
10 1422902 1427292 + CePI673135_10g001470.1 Cec10g0147 147
10 1430056 1434419 - CePI673135_10g001480.1 Cec10g0148 148
6 25885527 25890816 + Chy6G126870.1 Chy06g02159 2159
6 25892952 25897081 - Chy6G126880.1 Chy06g02160 2160
6 25904130 25907685 + Chy6G126900.1 Chy06g02162 2162
10 1704340 1712689 - ClG42_10g0014000.10 Clacu10g0140 140
10 1712984 1717623 + ClG42_10g0014100.10 Clacu10g0141 141
10 1719777 1724541 - ClG42_10g0014200.10 Clacu10g0142 142
10 1447892 1458363 - ClCG10G001390.2 Cla10g00137 137
10 1458241 1463513 + ClCG10G001400.2 Cla10g00138 138
10 1465094 1470423 - ClCG10G001410.1 Cla10g00139 139
6 3125927 3133068 - CmaCh06G006370.1 Cma06g00637 637
6 3134427 3139489 + CmaCh06G006380.1 Cma06g00638 638
6 3140360 3144356 - CmaCh06G006390.1 Cma06g00639 639
16 8997737 9004661 + CmaCh16G011750.1 Cma16g01175 1175
16 9005154 9009976 - CmaCh16G011760.1 Cma16g01176 1176
16 9011699 9014615 + CmaCh16G011770.1 Cma16g01177 1177
6 31564383 31566792 - MELO3C013833.2.1 Cme06g02453 2453
6 31570340 31575247 + MELO3C013834.2.1 Cme06g02454 2454
6 31576186 31582531 - MELO3C013835.2.1 Cme06g02455 2455
5 805392 807585 - PI0001703.1 Cmetu05g1605 1605
6 29836336 29840400 - PI0000212.1 Cmetu06g0720 720
6 3231369 3233829 - CmoCh06G006420.1 Cmo06g00642 642
6 3236126 3241755 + CmoCh06G006440.1 Cmo06g00644 644
6 3242367 3246508 - CmoCh06G006450.1 Cmo06g00645 645
16 8775979 8782264 + CmoCh16G012250.1 Cmo16g01225 1225
16 8783964 8788453 - CmoCh16G012260.1 Cmo16g01226 1226
16 8790149 8792914 + CmoCh16G012270.1 Cmo16g01227 1227
10 1855513 1863820 - CmPI595203_10g009870.1 Cmu10g0987 987
10 1864115 1868749 + CmPI595203_10g009880.1 Cmu10g0988 988
10 1870895 1875659 - CmPI595203_10g009890.1 Cmu10g0989 989
8 3315936 3319087 + Conep08aG0050300.1 Cone8ag0482 482
8 3325737 3328582 - Conep08aG0050500.1 Cone8ag0484 484
12 3100575 3104852 + Conep12aG0049600.1 Cone12ag0477 477
12 3109379 3110699 + Conep12aG0049900.1 Cone12ag0480 480
12 3111080 3114352 - Conep12aG0050000.1 Cone12ag0481 481
12 4132873 4138536 - Conep12aG0058500.1 Cone12ag0564 564
14 8243941 8248632 + Cp4.1LG14g09810.1 Cpe14g00974 974
14 8249458 8254178 - Cp4.1LG14g09830.1 Cpe14g00975 975
14 8255995 8258980 + Cp4.1LG14g09780.1 Cpe14g00976 976
10 2824920 2833372 - CrPI670011_10g003980.1 Cre10g0398 398
10 2833667 2838163 + CrPI670011_10g003990.1 Cre10g0399 399
10 2841037 2845456 - CrPI670011_10g004000.1 Cre10g0400 400
3 1140955 1143227 - CsaV3_3G001470.1 Csa03g00147 147
3 1148834 1152437 + CsaV3_3G001490.1 Csa03g00149 149
3 1154596 1159734 - CsaV3_3G001500.1 Csa03g00150 150
7 17263369 17270547 - Lsi07G011750.1 Lsi07g01175 1175
7 17275748 17281274 + Lsi07G011770.1 Lsi07g01177 1177
7 17282040 17289327 - Lsi07G011780.1 Lsi07g01178 1178
10 16848749 16855062 + MC10g1334 Mch10g1679 1679
10 16855632 16861526 - MC10g1335 Mch10g1680 1680
2 8250840 8254454 - Sed0001604.2 Sed02g0067 67
10 29966654 29968149 - Sed0019165.1 Sed10g1395 1395
1 26239413 26245652 - Tan0011779.1 Tan01g2212 2212
8 1476143 1478156 - Tan0001012.1 Tan08g0173 173
2 8175756 8185460 - Vvi2g702 Vvi2g702 702
2 8203532 8211263 + Vvi2g703 Vvi2g703 703
2 8212541 8220356 - Vvi2g704 Vvi2g704 704
2 8222937 8233818 + Vvi2g705 Vvi2g705 705
2 8233864 8234512 + Vvi2g706 Vvi2g706 706
2 8259202 8260480 - Vvi2g707 Vvi2g707 707
2 8280639 8285351 + Vvi2g708 Vvi2g708 708
2 8287288 8298042 - Vvi2g709 Vvi2g709 709
2 8319466 8330139 + Vvi2g710 Vvi2g710 710
2 8336137 8337118 - Vvi2g711 Vvi2g711 711
       

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