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
Vvi18g1300 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1302 . . . . . . . . . . . Cma09g01168 . . . Cpe06g00920 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00784 . Sed10g1782 . Cmo09g01168 . . . Car09g01044 . . Bhi09g01618 Tan01g2956 Cmetu01g2252 . . Mch11g1579 . Cla09g00995 Cam09g1053 Cec09g1054 Cco09g1069 . . Cre09g1017 . . . .
Vvi18g1303 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1304 Blo01g01752 . . Bda03g00414 Bpe02g00190 Bpe04g00380 Bma04g00391 Bma01g02535 . . . Cma09g01172 . . . Cpe06g00918 . . . . . . . . . . . . . . . . . . Cone20ag0680 . . . . . . Bda11g00850 . . . . . . . Cmo09g01170 . . . Car09g01046 . . Bhi09g01620 . . . . . . Cla09g00997 Cam09g1055 Cec09g1057 Cco09g1071 . . Cre09g1019 . . . .
Vvi18g1305 . . . . . . . . . Cmo15g00558 . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0681 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1306 . . . . . . . . . . . Cma09g01283 . . . . . . . . . . . . Cla08g00264 Cam08g0704 . Cco08g0349 Clacu08g0411 . Cre08g0236 . . . . . . . . . . . Bda13g01432 . . . . . . Cmo09g01240 . . . Car09g01096 . . . . . . . . . . . . . . . . . . . .
Vvi18g1307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1308 Blo01g01751 . . . Bpe02g00191 . . Bma01g02533 . . Cma01g00931 Cma09g01282 Car01g00826 . . . . . . . . . . . . . . . . . . . . . Cone20ag0682 . . . . . . Bda11g00851 . . . . . . Cmo01g00954 Cmo09g01238 . . . Car09g01095 . Cpe02g00940 . . . . . . . . . . . . . . . . . .
Vvi18g1309 Blo01g01750 Blo12g00768 . Bda03g00412 Bpe02g00192 Bpe04g00378 Bma04g00389 Bma01g02532 . . . . Car01g00848 . . Cpe06g00956 . . . . . . . . Cla08g00312 Cam08g0750 Cec08g0303 . Clacu08g0461 . . . . . Cone20ag0683 . . . . . . Bda11g00852 . . . . . . . Cmo09g01216 . . . Car09g01087 . . . . . . . . . . . . . . . . Lsi08g00258 . Chy03g00282 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3559843 3562548 - Bda016377.1 Bda03g00412 412
3 3605484 3612561 + Bda016379.1 Bda03g00414 414
11 8361776 8368048 - Bda005600.1 Bda11g00850 850
11 8388898 8389635 + Bda005602.1 Bda11g00851 851
11 8390767 8393743 + Bda005603.1 Bda11g00852 852
13 37028995 37033134 - Bda000261.2 Bda13g01432 1432
9 43605036 43608984 + XM_039044274.1 Bhi09g01618 1618
9 43657252 43670029 - XM_039043696.1 Bhi09g01620 1620
1 57289251 57289678 - BLOR01750 Blo01g01750 1750
1 57290931 57291668 - BLOR01751 Blo01g01751 1751
1 57296293 57302825 + BLOR01752 Blo01g01752 1752
12 26031879 26036429 + BLOR04787 Blo12g00768 768
1 7184803 7186764 - Bma001006.1 Bma01g00784 784
1 83020611 83023485 - Bma003414.1 Bma01g02532 2532
1 83024581 83025318 - Bma003415.1 Bma01g02533 2533
1 83052772 83059757 + Bma003416.6 Bma01g02535 2535
4 3190077 3192718 - Bma018851.1 Bma04g00389 389
4 3202551 3209195 + Bma018853.1 Bma04g00391 391
2 1316194 1323292 - Bpe008040.1 Bpe02g00190 190
2 1327412 1328149 + Bpe008041.1 Bpe02g00191 191
2 1329313 1332283 + Bpe008042.1 Bpe02g00192 192
4 2383606 2386285 - Bpe025616 Bpe04g00378 378
4 2393596 2400002 + Bpe015068.1 Bpe04g00380 380
8 5726501 5750789 + CaPI482276_08g007040.1 Cam08g0704 704
8 7412959 7417320 - CaPI482276_08g007500.1 Cam08g0750 750
9 10889612 10893015 + CaPI482276_09g010530.1 Cam09g1053 1053
9 10900045 10911843 - CaPI482276_09g010550.1 Cam09g1055 1055
1 6278106 6278828 - Carg27789-RA Car01g00826 826
1 6956660 6960988 - Carg26570-RA Car01g00848 848
9 7801203 7806722 - Carg28002-RA Car09g01044 1044
9 7810570 7817730 - Carg28000-RA Car09g01046 1046
9 10176064 10177891 + Carg28172-RA Car09g01087 1087
9 11115955 11116677 - Carg24104-RA Car09g01095 1095
9 11143651 11147359 + Carg24105-RA Car09g01096 1096
8 6908565 6923669 + CcPI632755_08g003490.1 Cco08g0349 349
9 10212505 10215925 + CcPI632755_09g010690.1 Cco09g1069 1069
9 10223044 10234798 - CcPI632755_09g010710.1 Cco09g1071 1071
8 6633490 6637840 + CePI673135_08g003030.1 Cec08g0303 303
9 10250003 10253440 + CePI673135_09g010540.1 Cec09g1054 1054
9 10260450 10272243 - CePI673135_09g010570.1 Cec09g1057 1057
3 3009198 3013587 + Chy3G052620.1 Chy03g00282 282
8 5552038 5576317 + ClG42_08g0041100.10 Clacu08g0411 411
8 7239997 7244349 - ClG42_08g0046100.10 Clacu08g0461 461
8 5522766 5543779 + ClCG08G002560.1 Cla08g00264 264
8 7350055 7355140 - ClCG08G003020.1 Cla08g00312 312
9 10461982 10479343 + ClCG09G010650.2 Cla09g00995 995
9 10485940 10499301 - ClCG09G010680.2 Cla09g00997 997
1 5787559 5788281 + CmaCh01G009310.1 Cma01g00931 931
9 6948960 6953018 - CmaCh09G011680.1 Cma09g01168 1168
9 6967695 6975402 - CmaCh09G011720.1 Cma09g01172 1172
9 8822951 8823673 - CmaCh09G012820.1 Cma09g01282 1282
9 8826279 8828560 + CmaCh09G012830.1 Cma09g01283 1283
1 9516067 9519871 - PI0003737.1 Cmetu01g2252 2252
1 5912764 5913486 - CmoCh01G009540.1 Cmo01g00954 954
9 7633404 7639310 - CmoCh09G011680.1 Cmo09g01168 1168
9 7642155 7649242 - CmoCh09G011700.1 Cmo09g01170 1170
9 9403453 9408992 + CmoCh09G012160.1 Cmo09g01216 1216
9 10615482 10616204 - CmoCh09G012380.1 Cmo09g01238 1238
9 10655142 10663420 + CmoCh09G012400.1 Cmo09g01240 1240
15 2665527 2669676 + CmoCh15G005580.1 Cmo15g00558 558
20 4192664 4201348 - Conep20aG0070100.1 Cone20ag0680 680
20 4202925 4203744 + Conep20aG0070200.1 Cone20ag0681 681
20 4212310 4213086 - Conep20aG0070300.1 Cone20ag0682 682
20 4214125 4224656 + Conep20aG0070400.1 Cone20ag0683 683
2 7719502 7720224 + Cp4.1LG02g09350.1 Cpe02g00940 940
6 6554358 6561841 + Cp4.1LG06g09270.1 Cpe06g00918 918
6 6584069 6588761 + Cp4.1LG06g09250.1 Cpe06g00920 920
6 8185049 8190744 + Cp4.1LG06g09620.1 Cpe06g00956 956
8 6074609 6099286 + CrPI670011_08g002360.1 Cre08g0236 236
9 10421573 10425069 + CrPI670011_09g010170.1 Cre09g1017 1017
9 10432024 10443811 - CrPI670011_09g010190.1 Cre09g1019 1019
8 5903906 5908965 + Lsi08G002580.1 Lsi08g00258 258
11 13761557 13765089 - MC11g1259 Mch11g1579 1579
10 34898039 34901550 + Sed0020468.1 Sed10g1782 1782
1 68218213 68222157 + Tan0001342.1 Tan01g2956 2956
18 17868091 17887668 + Vvi18g1300 Vvi18g1300 1300
18 18007180 18008566 - Vvi18g1301 Vvi18g1301 1301
18 18019983 18028031 + Vvi18g1302 Vvi18g1302 1302
18 18028101 18028743 - Vvi18g1303 Vvi18g1303 1303
18 18029531 18043172 - Vvi18g1304 Vvi18g1304 1304
18 18120983 18122034 - Vvi18g1305 Vvi18g1305 1305
18 18136887 18146114 - Vvi18g1306 Vvi18g1306 1306
18 18146214 18146944 - Vvi18g1307 Vvi18g1307 1307
18 18213106 18223429 - Vvi18g1308 Vvi18g1308 1308
18 18227133 18232345 + Vvi18g1309 Vvi18g1309 1309
       

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