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
Vvi19g534 . . . . . . Bma10g00556 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1155 Cone15ag1172 . . . . Blo07g00898 . Bda05g00713 . . Bpe03g00786 . . . . . . . . . Cpe14g00745 . . . . . . . . . . . . . . . . . . .
Vvi19g535 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g536 . . . . Bpe09g00166 . Bma10g00562 Bma13g01068 . . Cma01g01120 Cma09g00960 Car01g00994 Car09g00875 Sed07g2678 Cpe06g00776 Cpe02g00780 Bhi09g01660 Tan01g4573 Cmetu01g1279 . . Mch11g1200 . . . . . . . . . . Cone14ag1156 . Lsi02g01894 Csa07g01104 . . Blo07g00897 Blo10g00841 . Bda12g00921 . Bpe03g00785 . . . Cmo01g01170 Cmo09g00960 . . . . . . . . . . . . . Cla09g01019 Cam09g1075 Cec09g1075 Cco09g1094 . . Cre09g1040 . . . Cme01g01018
Vvi19g537 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1158 Cone15ag1174 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g538 Blo03g00552 . Bda07g00369 . . . . . . . . Cma09g00961 Car01g00993 Car09g00876 Sed04g3225 Cpe06g00777 Cpe02g00781 Bhi09g01662 Tan01g4575 Cmetu01g2068 . . Mch11g1201 . . . . . . . . . . . . Lsi02g01893 Csa07g01105 . . . . . . Bpe11g00554 . . Bma14g00332 . Cmo01g01168 Cmo09g00961 . . . . . . . . . . . . . Cla09g01020 Cam09g1076 Cec09g1076 Cco09g1096 . . Cre09g1042 . . . Cme01g01017
Vvi19g539 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1160 Cone15ag1176 . . . . . . . . . . . . . . . . . . . Cpe14g00744 . . . . . . . . . . . . . . . . . . .
Vvi19g540 . . . . Bpe09g00165 . Bma10g00563 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00896 . Bda05g00712 Bda12g00922 . Bpe03g00784 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g541 . . . . Bpe09g00164 . . Bma13g01069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda12g00923 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g542 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00895 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55382542 55384422 + Bda021850.1 Bda05g00712 712
5 55526826 55534350 - Bda021855.1 Bda05g00713 713
7 4688928 4696737 - Bda025455.1 Bda07g00369 369
12 40304952 40322096 + Bda009466.1 Bda12g00921 921
12 40323364 40327270 - Bda009467.1 Bda12g00922 922
12 40332610 40335799 - Bda009468.2 Bda12g00923 923
9 44760994 44771248 + XM_039041792.1 Bhi09g01660 1660
9 44777648 44798154 - XM_039042013.1 Bhi09g01662 1662
3 21633313 21647395 + BLOR11733 Blo03g00552 552
7 27773838 27776977 + BLOR18827 Blo07g00895 895
7 27777080 27788494 + BLOR18828 Blo07g00896 896
7 27789974 27800438 - BLOR18829 Blo07g00897 897
7 27853954 27866845 - BLOR18830 Blo07g00898 898
10 26845158 26847853 + BLOR02631 Blo10g00841 841
10 6717810 6726209 + Bma004256.1 Bma10g00556 556
10 7039792 7042477 + Bma004267.1 Bma10g00562 562
10 7043915 7045758 - Bma004268.1 Bma10g00563 563
13 43525664 43534167 + Bma010190.1 Bma13g01068 1068
13 43552640 43555921 - Bma010192.2 Bma13g01069 1069
14 4134401 4139842 + Bma010753.1 Bma14g00332 332
3 27807468 27809261 + Bpe012696.1 Bpe03g00784 784
3 27810783 27813396 - Bpe012697.1 Bpe03g00785 785
3 27827283 27834830 - Bpe012698.1 Bpe03g00786 786
9 1097108 1101453 + Bpe023836.1 Bpe09g00164 164
9 1105689 1107712 + Bpe023837.1 Bpe09g00165 165
9 1109101 1118074 - Bpe023838.2 Bpe09g00166 166
11 4250791 4258409 - Bpe003921.1 Bpe11g00554 554
9 11110629 11119297 + CaPI482276_09g010750.1 Cam09g1075 1075
9 11121031 11141916 - CaPI482276_09g010760.1 Cam09g1076 1076
1 9417685 9426634 + Carg22369-RA Car01g00993 993
1 9427448 9434841 - Carg22368-RA Car01g00994 994
9 5352156 5358312 + Carg12829-RA Car09g00875 875
9 5359541 5368307 - Carg12830-RA Car09g00876 876
9 10441906 10450618 + CcPI632755_09g010940.1 Cco09g1094 1094
9 10472057 10474232 - CcPI632755_09g010960.1 Cco09g1096 1096
9 10478245 10485565 + CePI673135_09g010750.1 Cec09g1075 1075
9 10487751 10510654 - CePI673135_09g010760.1 Cec09g1076 1076
9 10710240 10719217 + ClCG09G010920.1 Cla09g01019 1019
9 10720401 10742289 - ClCG09G010930.2 Cla09g01020 1020
1 8231461 8234263 - CmaCh01G011200.1 Cma01g01120 1120
9 4842077 4848315 + CmaCh09G009600.1 Cma09g00960 960
9 4848688 4858205 - CmaCh09G009610.1 Cma09g00961 961
1 12568445 12576714 + MELO3C013152.2.1 Cme01g01017 1017
1 12577561 12586483 - MELO3C013153.2.1 Cme01g01018 1018
1 11013942 11023267 + PI0008183.1 Cmetu01g1279 1279
1 11024085 11032743 - PI0029172.1 Cmetu01g2068 2068
1 9551322 9560579 + CmoCh01G011680.1 Cmo01g01168 1168
1 9562468 9565261 - CmoCh01G011700.1 Cmo01g01170 1170
9 5054802 5057573 + CmoCh09G009600.1 Cmo09g00960 960
9 5058759 5068289 - CmoCh09G009610.1 Cmo09g00961 961
14 9552164 9557455 + Conep14aG0117900.1 Cone14ag1155 1155
14 9560375 9562111 + Conep14aG0118000.1 Cone14ag1156 1156
14 9564756 9566252 + Conep14aG0118200.1 Cone14ag1158 1158
14 9569555 9573194 - Conep14aG0118400.1 Cone14ag1160 1160
15 9462118 9467635 + Conep15aG0120100.1 Cone15ag1172 1172
15 9475035 9476327 + Conep15aG0120300.1 Cone15ag1174 1174
15 9481928 9485616 - Conep15aG0120500.1 Cone15ag1176 1176
2 4964925 4973153 + Cp4.1LG02g00970.1 Cpe02g00780 780
2 4975137 4982891 - Cp4.1LG02g00910.1 Cpe02g00781 781
6 4899725 4905680 + Cp4.1LG06g08770.1 Cpe06g00776 776
6 4906718 4919775 - Cp4.1LG06g08720.1 Cpe06g00777 777
14 5651759 5656520 + Cp4.1LG14g07420.1 Cpe14g00744 744
14 5672982 5678514 - Cp4.1LG14g07440.1 Cpe14g00745 745
9 10650418 10659061 + CrPI670011_09g010400.1 Cre09g1040 1040
9 10680609 10682777 - CrPI670011_09g010420.1 Cre09g1042 1042
7 10670991 10681232 + CsaV3_7G021930.1 Csa07g01104 1104
7 10681538 10691911 - CsaV3_7G021940.1 Csa07g01105 1105
2 24833368 24859625 + Lsi02G018930.1 Lsi02g01893 1893
2 24859953 24867297 - Lsi02G018940.1 Lsi02g01894 1894
11 8440273 8449900 + MC11g0991 Mch11g1200 1200
11 8445424 8459042 - MC11g0992 Mch11g1201 1201
4 42792573 42818421 - Sed0009199.1 Sed04g3225 3225
7 42185966 42192606 - Sed0011428.1 Sed07g2678 2678
1 111568482 111575867 + Tan0010439.1 Tan01g4573 4573
1 111579935 111591996 - Tan0008273.1 Tan01g4575 4575
19 6765148 6778665 + Vvi19g534 Vvi19g534 534
19 6778729 6779511 - Vvi19g535 Vvi19g535 535
19 6806652 6810038 + Vvi19g536 Vvi19g536 536
19 6813687 6814653 + Vvi19g537 Vvi19g537 537
19 6844613 6858752 - Vvi19g538 Vvi19g538 538
19 6870993 6878047 - Vvi19g539 Vvi19g539 539
19 6882418 6884988 - Vvi19g540 Vvi19g540 540
19 6892723 6895966 - Vvi19g541 Vvi19g541 541
19 6895976 6896401 - Vvi19g542 Vvi19g542 542
19 6896417 6898875 - Vvi19g543 Vvi19g543 543
       

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