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
Vvi17g346 . . Bda06g00485 . . . . Bma12g00932 . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0272 . . . . . . . . . . Bpe07g00725 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g347 . Blo16g00141 . . . Bpe13g00341 Bma06g00002 . . Cmo18g00031 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00169 Csa01g00653 Chy12g01448 Cme12g01888 . . . Bda14g00913 . Bpe15g00544 Bma03g00889 . . . . . Cma18g00036 . Car18g00030 Cpe09g01144 . Bhi08g01217 Tan05g2282 . Lac10g0222 . . . Cla04g01104 Cam04g1157 Cec01g1667 Cco01g1713 Clacu04g1184 Cmu04g1164 Cre01g1462 . . . .
Vvi17g348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g349 . . . . . . . Bma12g00933 . . Cma10g00243 . Car10g00229 . . . . . . . . . . . Cla06g01479 Cam06g1633 Cec06g1696 Cco06g1690 Clacu06g1599 Cmu06g1548 Cre06g2360 . . . . . . . . . Blo15g00369 . . . . . . . . . . . . . . Cpe18g00750 . . . . . . . . . . . . . . Lsi06g01342 . Chy02g02375 Cme02g01757
Vvi17g350 . . Bda06g00486 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0697 . . . . . . . . . . . Bpe07g00726 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00370 . .
Vvi17g351 . Blo16g00142 . . . Bpe13g00340 Bma06g00003 . Cmo13g01076 Cmo18g00030 . . . . . Cpe20g00110 . . . . . . . . . . . . . . . . . . . Lsi02g00167 Csa01g00651 Chy12g01450 Cme12g01890 . . . . . . . . Sed08g2168 . . Cma13g01036 Cma18g00034 Car13g00868 Car18g00028 . . Bhi08g01214 Tan05g2286 Cmetu12g1594 Lac10g0220 . . . Cla04g01106 Cam04g1159 Cec01g1669 Cco01g1715 Clacu04g1186 Cmu04g1166 Cre01g1464 . . . .
Vvi17g352 . . . Bda15g00522 Bpe12g00687 . . . . . Cma10g00244 . Car10g00230 . . . . . . . . . . . Cla06g01480 Cam06g1635 Cec06g1697 Cco06g1692 Clacu06g1601 Cmu06g1550 Cre06g2362 . . . . . . . . . . . . . . . Bma08g00068 . Cmo10g00261 . . . . . . Cpe18g00749 . . . . . . . . . . . . . . Lsi06g01343 Csa01g00369 Chy02g02376 Cme02g01758
Vvi17g353 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g354 . Blo16g00143 . . . Bpe13g00339 Bma06g00028 . Cmo13g01077 . . . . . . Cpe20g00109 . . . . . . . . . . . . . . . . . . Cone19ag0269 Lsi02g00166 Csa01g00650 Chy12g01451 Cme12g01891 . . . . . . . . Sed08g2167 . . Cma13g01037 . Car13g00869 . . . Bhi08g01212 Tan05g2288 Cmetu12g1525 Lac10g0219 . . . Cla04g01107 Cam04g1160 Cec01g1670 Cco01g1716 Clacu04g1187 Cmu04g1167 Cre01g1465 . . . .
Vvi17g355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6869361 6878224 + Bda023730.1 Bda06g00485 485
6 6880846 6888208 + Bda023731.1 Bda06g00486 486
14 7129662 7132320 - Bda027693.1 Bda14g00913 913
15 8283080 8292287 + Bda012352.2 Bda15g00522 522
8 37682397 37688053 - XM_039038429.1 Bhi08g01212 1212
8 37768424 37772783 + XM_039038119.1 Bhi08g01214 1214
8 37785793 37790098 - XM_039037939.1 Bhi08g01217 1217
15 5036949 5062803 - BLOR06763 Blo15g00369 369
16 3162143 3179487 + BLOR07389 Blo16g00141 141
16 3200376 3202445 - BLOR07390 Blo16g00142 142
16 3205607 3208392 + BLOR07391 Blo16g00143 143
3 8697284 8699841 - Bma017209.1 Bma03g00889 889
6 175225 177401 + Bma031262 Bma06g00002 2
6 178713 179804 - Bma022603.1 Bma06g00003 3
6 581196 588766 - Bma022635.1 Bma06g00028 28
8 856491 867638 + Bma027067.3 Bma08g00068 68
12 40998918 41008488 + Bma008271.1 Bma12g00932 932
12 41011392 41092439 + Bma030518 Bma12g00933 933
7 13794636 13803590 + Bpe021569.1 Bpe07g00725 725
7 13806662 13814051 + Bpe021570.1 Bpe07g00726 726
12 12450217 12461175 - Bpe005946.1 Bpe12g00687 687
13 11239017 11242519 - Bpe006466.1 Bpe13g00339 339
13 11244628 11246493 + Bpe006467.1 Bpe13g00340 340
13 11248632 11250934 - Bpe006468.1 Bpe13g00341 341
15 16541010 16543684 + Bpe001479.1 Bpe15g00544 544
4 25624373 25631123 + CaPI482276_04g011570.1 Cam04g1157 1157
4 25641576 25645892 - CaPI482276_04g011590.1 Cam04g1159 1159
4 25650433 25654984 + CaPI482276_04g011600.1 Cam04g1160 1160
6 27771807 27781459 + CaPI482276_06g016330.1 Cam06g1633 1633
6 27792395 27800933 + CaPI482276_06g016350.1 Cam06g1635 1635
10 1086705 1094211 + Carg17914-RA Car10g00229 229
10 1094784 1099623 + Carg17913-RA Car10g00230 230
13 9203126 9207367 - Carg04804-RA Car13g00868 868
13 9209563 9214980 + Carg04803-RA Car13g00869 869
18 123966 125777 + Carg22758-RA Car18g00028 28
18 129574 133179 - Carg22756-RA Car18g00030 30
1 29872111 29878855 + CcPI632755_01g017130.1 Cco01g1713 1713
1 29897618 29901876 - CcPI632755_01g017150.1 Cco01g1715 1715
1 29906444 29911258 + CcPI632755_01g017160.1 Cco01g1716 1716
6 27452068 27470015 + CcPI632755_06g016900.1 Cco06g1690 1690
6 27481069 27486287 + CcPI632755_06g016920.1 Cco06g1692 1692
1 31305920 31312668 + CePI673135_01g016670.1 Cec01g1667 1667
1 31323373 31327310 - CePI673135_01g016690.1 Cec01g1669 1669
1 31331893 31336727 + CePI673135_01g016700.1 Cec01g1670 1670
6 30522860 30532696 + CePI673135_06g016960.1 Cec06g1696 1696
6 30535564 30551252 + CePI673135_06g016970.1 Cec06g1697 1697
2 27575528 27583275 + Chy2G046420.1 Chy02g02375 2375
2 27584562 27590552 + Chy2G046430.1 Chy02g02376 2376
12 18461481 18466744 + Chy12G220480.1 Chy12g01448 1448
12 18479892 18482077 - Chy12G220500.1 Chy12g01450 1450
12 18486558 18491319 + Chy12G220510.1 Chy12g01451 1451
4 26013568 26020236 + ClG42_04g0118400.10 Clacu04g1184 1184
4 26030651 26034267 - ClG42_04g0118600.10 Clacu04g1186 1186
4 26038767 26043598 + ClG42_04g0118700.10 Clacu04g1187 1187
6 26825772 26835595 + ClG42_06g0159900.10 Clacu06g1599 1599
6 26837521 26853573 + ClG42_06g0160100.10 Clacu06g1601 1601
4 26234073 26240991 + ClCG04G011220.2 Cla04g01104 1104
4 26251267 26255644 - ClCG04G011240.2 Cla04g01106 1106
4 26259383 26264214 + ClCG04G011250.2 Cla04g01107 1107
6 28340784 28351304 + ClCG06G014940.1 Cla06g01479 1479
6 28354118 28369547 + ClCG06G014950.2 Cla06g01480 1480
10 1077552 1085064 + CmaCh10G002430.1 Cma10g00243 243
10 1085603 1093271 + CmaCh10G002440.1 Cma10g00244 244
13 7909794 7914512 - CmaCh13G010360.1 Cma13g01036 1036
13 7916211 7921332 + CmaCh13G010370.1 Cma13g01037 1037
18 133053 134936 + CmaCh18G000340.1 Cma18g00034 34
18 138340 143242 - CmaCh18G000360.1 Cma18g00036 36
2 24499946 24508159 + MELO3C017295.2.1 Cme02g01757 1757
2 24511215 24519964 + MELO3C017294.2.1 Cme02g01758 1758
12 25037356 25041031 + MELO3C002080.2.1 Cme12g01888 1888
12 25050101 25053009 - MELO3C002078.2.1 Cme12g01890 1890
12 25056801 25062123 + MELO3C002077.2.1 Cme12g01891 1891
12 1147035 1152750 - PI0004687.1 Cmetu12g1525 1525
12 1155808 1158901 + PI0013405.3 Cmetu12g1594 1594
10 1165774 1167276 + CmoCh10G002610.1 Cmo10g00261 261
13 8915049 8919542 - CmoCh13G010760.1 Cmo13g01076 1076
13 8921631 8926739 + CmoCh13G010770.1 Cmo13g01077 1077
18 128803 130461 + CmoCh18G000300.1 Cmo18g00030 30
18 133609 138416 - CmoCh18G000310.1 Cmo18g00031 31
4 26195281 26201947 + CmPI595203_04g011640.1 Cmu04g1164 1164
4 26212360 26215976 - CmPI595203_04g011660.1 Cmu04g1166 1166
4 26220515 26225346 + CmPI595203_04g011670.1 Cmu04g1167 1167
6 26728523 26738328 + CmPI595203_06g015480.1 Cmu06g1548 1548
6 26747558 26756298 + CmPI595203_06g015500.1 Cmu06g1550 1550
2 32472495 32494288 + Conep02aG0171000.1 Cone2ag0697 697
16 3050248 3085503 - Conep16aG0262100.1 Cone16ag0272 272
19 1854712 1860018 - Conep19aG0027900.1 Cone19ag0269 269
9 9769724 9772854 + Cp4.1LG09g11530.1 Cpe09g01144 1144
18 7241662 7246564 - Cp4.1LG18g07530.1 Cpe18g00749 749
18 7247328 7255517 - Cp4.1LG18g07560.1 Cpe18g00750 750
20 602439 608237 - Cp4.1LG20g01170.1 Cpe20g00109 109
20 609973 614294 + Cp4.1LG20g01120.1 Cpe20g00110 110
1 27841043 27847689 + CrPI670011_01g014620.1 Cre01g1462 1462
1 27858535 27867312 - CrPI670011_01g014640.1 Cre01g1464 1464
1 27867591 27872437 + CrPI670011_01g014650.1 Cre01g1465 1465
6 31528909 31538774 + CrPI670011_06g023600.1 Cre06g2360 2360
6 31549652 31550134 + CrPI670011_06g023620.1 Cre06g2362 2362
1 2302142 2306176 - CsaV3_1G003690.1 Csa01g00369 369
1 2306890 2315293 - CsaV3_1G003700.1 Csa01g00370 370
1 4164529 4169255 - CsaV3_1G006500.1 Csa01g00650 650
1 4173436 4176355 + CsaV3_1G006510.1 Csa01g00651 651
1 4188353 4192903 - CsaV3_1G006530.1 Csa01g00653 653
10 1721094 1725908 - Lag0024264.1 Lac10g0219 219
10 1730341 1732937 + Lag0024265.1 Lac10g0220 220
10 1740597 1745043 - Lag0024267.1 Lac10g0222 222
2 1407139 1412886 - Lsi02G001660.1 Lsi02g00166 166
2 1419119 1422999 + Lsi02G001670.1 Lsi02g00167 167
2 1432246 1435318 - Lsi02G001690.1 Lsi02g00169 169
6 24001247 24012779 + Lsi06G013420.1 Lsi06g01342 1342
6 24013808 24019162 + Lsi06G013430.1 Lsi06g01343 1343
8 35599107 35603429 - Sed0001727.1 Sed08g2167 2167
8 35607368 35611801 + Sed0022338.1 Sed08g2168 2168
5 74167582 74173307 + Tan0004279.2 Tan05g2282 2282
5 74181899 74185781 - Tan0020970.1 Tan05g2286 2286
5 74195309 74201614 + Tan0010164.1 Tan05g2288 2288
17 3969398 3996695 + Vvi17g346 Vvi17g346 346
17 3997332 4001446 + Vvi17g347 Vvi17g347 347
17 4009898 4011992 + Vvi17g348 Vvi17g348 348
17 4013613 4030933 + Vvi17g349 Vvi17g349 349
17 4031361 4061477 + Vvi17g350 Vvi17g350 350
17 4062833 4068708 - Vvi17g351 Vvi17g351 351
17 4069033 4078199 + Vvi17g352 Vvi17g352 352
17 4079991 4081808 - Vvi17g353 Vvi17g353 353
17 4126785 4142234 + Vvi17g354 Vvi17g354 354
17 4143097 4144453 - Vvi17g355 Vvi17g355 355
       

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