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
Vvi5g1099 . . . . . Bpe14g01050 . . . . Cma06g01625 . . . Sed02g1052 Cpe08g00102 Cpe03g01265 Bhi01g02618 Tan10g1227 Cmetu07g0599 . Hepe05g1285 . Lcy11g1242 . . . . . . . . . . Cone11ag0636 . . . . . Blo07g00195 . Bda13g00264 . Bpe13g00639 Bma02g00980 . . Cmo06g01621 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1100 . . . . . . . . Cmo08g00877 Cmo17g00554 . . . . . . . . . . . . . . Cla08g00393 Cam08g0814 Cec08g0389 Cco08g0484 Clacu08g0523 . Cre08g0354 . . . Cone11ag0637 . . . . Blo02g00439 Blo07g00107 . Bda13g00263 . Bpe13g00727 Bma02g00979 Bma06g01433 . . . Cma08g00905 Cma17g00570 . Car17g00525 Cpe12g00484 . . . . . . . . . . . . . . . Lsi09g01570 . . Cme11g02164
Vvi5g1101 . . . . . . . . . . . . . . Sed02g1054 . . Bhi01g02616 Tan10g1226 Cmetu01g1559 . Hepe05g1286 . Lcy11g1244 . . . . . . . . . . . . . . Cme07g01844 . . . . . . . . . . . . . . . . . . . . . . . . Cla07g01589 Cam07g1685 Cec07g1782 Cco07g1743 Clacu07g1669 Cmu07g1636 Cre07g2010 . . . .
Vvi5g1102 . . Bda03g00986 . . . . . . . . Cma14g01510 Car06g01380 Car14g01333 . . . Bhi01g02615 . . . . . Lcy11g1245 . . . . . . . . . . . . . . . . Blo07g00109 . . . Bpe13g00726 . Bma06g01434 . . Cmo14g01543 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00160 . . . Bpe13g00681 . Bma06g01484 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1106 . . . . . . . . . . Cma06g01627 Cma14g01502 Car06g01383 . Sed12g0673 Cpe08g00100 Cpe03g01263 Bhi01g02620 Tan10g1229 Cmetu07g0452 . Hepe05g1284 . Lcy11g1240 . . . . . . . . . Cone18ag0866 . . . . Cme07g01848 . Blo07g00156 . . . Bpe13g00725 . Bma06g01435 . Cmo06g01626 Cmo14g01538 . . . . . . . . . . . . . Cla07g01587 Cam07g1683 Cec07g1779 Cco07g1741 Clacu07g1667 Cmu07g1634 Cre07g2008 . . . .
Vvi5g1107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g00262 . . Bma02g00977 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 8923167 8924805 - Bda017000.1 Bda03g00986 986
13 3284271 3284717 + Bda001141.2 Bda13g00262 262
13 3317498 3327918 - Bda001143.1 Bda13g00263 263
13 3329649 3339728 - Bda001144.1 Bda13g00264 264
1 64689252 64691077 - XM_039049850.1 Bhi01g02615 2615
1 64790466 64791054 + XM_039042507.1 Bhi01g02616 2616
1 64794251 64828181 - XM_039048392.1 Bhi01g02618 2618
1 64898646 64900714 + XM_039042373.1 Bhi01g02620 2620
2 5865001 5899437 + BLOR10169 Blo02g00439 439
7 1531859 1541139 + BLOR18039 Blo07g00107 107
7 1546905 1548410 - BLOR18041 Blo07g00109 109
7 2043138 2044297 + BLOR18088 Blo07g00156 156
7 2078173 2088647 - BLOR18092 Blo07g00160 160
7 2422363 2430739 - BLOR18127 Blo07g00195 195
2 50132025 50132450 + Bma015780.1 Bma02g00977 977
2 50172823 50184020 - Bma015782.1 Bma02g00979 979
2 50185494 50210275 - Bma015783.1 Bma02g00980 980
6 51057248 51068052 + Bma024548.1 Bma06g01433 1433
6 51069595 51071091 - Bma024549.1 Bma06g01434 1434
6 51072011 51073535 - Bma024550.1 Bma06g01435 1435
6 51413881 51416518 - Bma024596.1 Bma06g01484 1484
13 13269496 13272478 + Bpe010339.1 Bpe13g00639 639
13 13500644 13503326 + Bpe010382.1 Bpe13g00681 681
13 13818304 13820441 + Bpe010422.1 Bpe13g00725 725
13 13821057 13822559 + Bpe010423.1 Bpe13g00726 726
13 13825440 13834887 - Bpe010424.1 Bpe13g00727 727
14 7839712 7849433 + Bpe014424.2 Bpe14g01050 1050
7 31520291 31530397 - CaPI482276_07g016830.1 Cam07g1683 1683
7 31557770 31558075 - CaPI482276_07g016850.1 Cam07g1685 1685
8 10500811 10530796 - CaPI482276_08g008140.1 Cam08g0814 814
6 9918564 9920051 - Carg15496-RA Car06g01380 1380
6 9938736 9941408 + Carg15493-RA Car06g01383 1383
14 11276085 11278918 + Carg24806-RA Car14g01333 1333
17 4854084 4881476 + Carg22633-RA Car17g00525 525
7 31504286 31514409 - CcPI632755_07g017410.1 Cco07g1741 1741
7 31542947 31543252 - CcPI632755_07g017430.1 Cco07g1743 1743
8 12257461 12285697 - CcPI632755_08g004840.1 Cco08g0484 484
7 33436222 33446409 - CePI673135_07g017790.1 Cec07g1779 1779
7 33472444 33472749 - CePI673135_07g017820.1 Cec07g1782 1782
8 10849415 10850008 - CePI673135_08g003890.1 Cec08g0389 389
7 31370851 31380956 - ClG42_07g0166700.10 Clacu07g1667 1667
7 31408322 31408627 - ClG42_07g0166900.10 Clacu07g1669 1669
8 10273392 10326817 - ClG42_08g0052300.10 Clacu08g0523 523
7 33146175 33157563 - ClCG07G016650.2 Cla07g01587 1587
7 33184408 33184713 - ClCG07G016680.1 Cla07g01589 1589
8 10463058 10501817 - ClCG08G003800.1 Cla08g00393 393
6 10110516 10119827 - CmaCh06G016250.1 Cma06g01625 1625
6 10126633 10129222 + CmaCh06G016270.1 Cma06g01627 1627
8 5613224 5627991 - CmaCh08G009050.1 Cma08g00905 905
14 11385548 11387057 - CmaCh14G015020.1 Cma14g01502 1502
14 11421964 11424587 + CmaCh14G015100.1 Cma14g01510 1510
17 4659953 4688185 + CmaCh17G005700.1 Cma17g00570 570
7 23903070 23903726 + MELO3C017674.2.1 Cme07g01844 1844
7 23929164 23930502 + MELO3C017677.2.1 Cme07g01848 1848
11 29025917 29035476 + MELO3C021207.2.1 Cme11g02164 2164
1 22550286 22551023 - PI0009068.1 Cmetu01g1559 1559
7 2996274 2997778 - PI0025157.1 Cmetu07g0452 452
7 3009154 3020069 + PI0020559.2 Cmetu07g0599 599
6 11321025 11329959 - CmoCh06G016210.1 Cmo06g01621 1621
6 11338205 11342185 + CmoCh06G016260.1 Cmo06g01626 1626
8 5663352 5673604 - CmoCh08G008770.1 Cmo08g00877 877
14 12294869 12305174 - CmoCh14G015380.1 Cmo14g01538 1538
14 12332990 12334477 + CmoCh14G015430.1 Cmo14g01543 1543
17 5643411 5673739 + CmoCh17G005540.1 Cmo17g00554 554
7 31622644 31632746 - CmPI595203_07g016340.1 Cmu07g1634 1634
7 31660141 31660446 - CmPI595203_07g016360.1 Cmu07g1636 1636
11 4171926 4177487 + Conep11aG0065300.1 Cone11ag0636 636
11 4183390 4192076 + Conep11aG0065400.1 Cone11ag0637 637
18 5978717 5981384 + Conep18aG0089200.1 Cone18ag0866 866
3 10246421 10248610 - Cp4.1LG03g12430.1 Cpe03g01263 1263
3 10257315 10271922 + Cp4.1LG03g12520.1 Cpe03g01265 1265
8 634410 637201 - Cp4.1LG08g05710.1 Cpe08g00100 100
8 644776 653466 + Cp4.1LG08g05790.1 Cpe08g00102 102
12 4710903 4738932 + Cp4.1LG12g04850.1 Cpe12g00484 484
7 35627284 35637382 - CrPI670011_07g020080.1 Cre07g2008 2008
7 35663741 35664046 - CrPI670011_07g020100.1 Cre07g2010 2010
8 11420639 11439819 - CrPI670011_08g003540.1 Cre08g0354 354
5 60545688 60556114 - Hsped.05g12840.1 Hepe05g1284 1284
5 60576409 60594619 + Hsped.05g12850.1 Hepe05g1285 1285
5 60595766 60596452 - Hsped.05g12860.1 Hepe05g1286 1286
11 35309802 35312129 - Maker00005250 Lcy11g1240 1240
11 35359848 35362145 + Maker00005206 Lcy11g1242 1242
11 35384115 35384417 - Maker00005297 Lcy11g1244 1244
11 35405121 35406605 + Maker00005274 Lcy11g1245 1245
9 23816173 23830919 + Lsi09G015700.1 Lsi09g01570 1570
2 47864173 47877978 - Sed0006717.1 Sed02g1052 1052
2 47889461 47890175 - Sed0004601.1 Sed02g1054 1054
12 4020038 4023560 - Sed0008422.2 Sed12g0673 673
10 12986570 12987211 + Tan0022276.1 Tan10g1226 1226
10 13097423 13129305 - Tan0001955.1 Tan10g1227 1227
10 13178171 13180587 + Tan0022844.1 Tan10g1229 1229
5 19988254 20024363 + Vvi5g1099 Vvi5g1099 1099
5 20038979 20071503 + Vvi5g1100 Vvi5g1100 1100
5 20086118 20089205 - Vvi5g1101 Vvi5g1101 1101
5 20096187 20097943 - Vvi5g1102 Vvi5g1102 1102
5 20109282 20118389 + Vvi5g1103 Vvi5g1103 1103
5 20139030 20140948 + Vvi5g1104 Vvi5g1104 1104
5 20145286 20148310 - Vvi5g1105 Vvi5g1105 1105
5 20174783 20177177 + Vvi5g1106 Vvi5g1106 1106
5 20191283 20210800 + Vvi5g1107 Vvi5g1107 1107
5 20212998 20214065 + Vvi5g1108 Vvi5g1108 1108
       

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