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
Vvi1g771 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g772 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo06g00863 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g773 . . . . . Bpe10g00824 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g774 . . . . . . . . Cmo04g01664 . . . . . . . Cpe01g01408 Bhi07g01713 . . Lac13g0232 Hepe10g1668 . . . . . . . . . . . . . Lsi04g00516 Csa05g02363 Chy10g00930 Cme10g00496 . . Bda07g01567 . . . . . . . . Cma04g01591 . Car04g01637 . . . . . . . . . . . . . . . . . . . . .
Vvi1g775 . . . . . . . . . . . . . . . . Cpe01g01410 Bhi07g01712 . . Lac13g0234 . . . . . . . . . . . . . . . . Chy10g00931 . . . . . . . . . . . . Cma04g01593 . Car04g01639 . . . . . . . . . . . . . . . . . . . . .
Vvi1g776 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0643 Cone12ag0628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g778 . . . Bda11g01252 Bpe13g01448 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g779 . Blo16g01148 Bda01g02234 . . . . Bma15g00199 Cmo04g01665 . . . . . . . . Bhi07g01711 . . . Hepe10g1669 . . Cla05g02516 Cam05g2700 Cec05g2734 Cco05g2768 Clacu05g2703 Cmu05g2557 Cre05g2672 Cone13ag1015 Cone19ag1009 Cone8ag0642 Cone12ag0627 Lsi04g00515 Csa05g02366 . Cme10g00495 . . Bda07g01568 . . . Bma01g00063 Bma06g00632 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g780 . . . . . . . . Cmo04g01667 . . . . . . . Cpe01g01411 Bhi07g01710 . . Lac13g0235 . . . Cla05g02515 . . . . . . . Cone19ag1007 . . Lsi04g00513 Csa05g02368 Chy10g00932 Cme10g00493 . . Bda07g01567 . Bpe11g01735 . . . . . . Cma04g01594 . Car04g01640 . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 58166437 58168382 - Bda004579.1 Bda01g02234 2234
7 29099221 29100474 - Bda028430.1 Bda07g01567 1567
7 29111521 29113776 - Bda028431.1 Bda07g01568 1568
11 13116211 13118811 - Bda007767.1 Bda11g01252 1252
7 47395671 47397212 - XM_039035608.1 Bhi07g01710 1710
7 47402535 47405822 - XM_039037002.1 Bhi07g01711 1711
7 47447308 47449343 + XM_039035375.1 Bhi07g01712 1712
7 47449373 47450406 - XM_039035376.1 Bhi07g01713 1713
6 31895231 31898253 - BLOR17446 Blo06g00863 863
16 40010602 40013059 + BLOR21935 Blo16g01148 1148
1 642030 644652 - Bma000230.1 Bma01g00063 63
6 33527117 33531242 - Bma023578.1 Bma06g00632 632
15 2027740 2040778 - Bma013181.1 Bma15g00199 199
10 14264358 14268197 + Bpe003128.3 Bpe10g00824 824
11 13720878 13721848 - Bpe005051.1 Bpe11g01735 1735
13 19745385 19746357 - Bpe011112.1 Bpe13g01448 1448
5 34393106 34395959 + CaPI482276_05g027000.1 Cam05g2700 2700
4 9436416 9437432 - Carg01763-RA Car04g01637 1637
4 9446143 9447961 + Carg01761-RA Car04g01639 1639
4 9447852 9449370 - Carg01760-RA Car04g01640 1640
5 35521311 35524964 + CcPI632755_05g027680.1 Cco05g2768 2768
5 37842827 37846415 + CePI673135_05g027340.1 Cec05g2734 2734
10 14929061 14938216 - Chy10G181240.1 Chy10g00930 930
10 14947609 14949387 + Chy10G181250.1 Chy10g00931 931
10 14949841 14950537 - Chy10G181260.1 Chy10g00932 932
5 34600131 34602968 + ClG42_05g0270300.10 Clacu05g2703 2703
5 36506572 36507745 + ClCG05G025040.2 Cla05g02515 2515
5 36524494 36528007 + ClCG05G025060.1 Cla05g02516 2516
4 8046324 8047350 - CmaCh04G015910.1 Cma04g01591 1591
4 8055764 8059064 + CmaCh04G015930.1 Cma04g01593 1593
4 8058180 8058860 - CmaCh04G015940.1 Cma04g01594 1594
10 3171568 3173144 + MELO3C012025.2.1 Cme10g00493 493
10 3184437 3187893 + MELO3C012023.2.1 Cme10g00495 495
10 3192216 3194003 + MELO3C012022.2.1 Cme10g00496 496
4 8463855 8464890 - CmoCh04G016640.1 Cmo04g01664 1664
4 8468889 8471314 - CmoCh04G016650.1 Cmo04g01665 1665
4 8475585 8476664 - CmoCh04G016670.1 Cmo04g01667 1667
5 34338005 34340841 + CmPI595203_05g025570.1 Cmu05g2557 2557
8 6340215 6343205 - Conep08aG0066300.1 Cone8ag0642 642
8 6364683 6369863 + Conep08aG0066400.1 Cone8ag0643 643
12 5632982 5636078 - Conep12aG0065000.1 Cone12ag0627 627
12 5646784 5651271 + Conep12aG0065100.1 Cone12ag0628 628
13 8489773 8493027 + Conep13aG0104600.1 Cone13ag1015 1015
19 7526001 7527035 + Conep19aG0103900.1 Cone19ag1007 1007
19 7532746 7535602 + Conep19aG0104100.1 Cone19ag1009 1009
1 8463165 8465625 - Cp4.1LG01g13020.1 Cpe01g01408 1408
1 8473939 8477180 + Cp4.1LG01g13040.1 Cpe01g01410 1410
1 8475663 8481227 - Cp4.1LG01g12980.1 Cpe01g01411 1411
5 37693389 37697010 + CrPI670011_05g026720.1 Cre05g2672 2672
5 25911596 25914963 - CsaV3_5G031830.1 Csa05g02363 2363
5 25920091 25922586 - CsaV3_5G031850.1 Csa05g02366 2366
5 25933543 25934758 - CsaV3_5G031870.1 Csa05g02368 2368
10 53371135 53372172 - Hsped.10g16680.1 Hepe10g1668 1668
10 53378694 53381562 - Hsped.10g16690.1 Hepe10g1669 1669
13 1651196 1652271 - Lag0040028.1 Lac13g0232 232
13 1670351 1672221 + Lag0040030.1 Lac13g0234 234
13 1672599 1673273 - Lag0040031.1 Lac13g0235 235
4 4766256 4767575 + Lsi04G005130.1 Lsi04g00513 513
4 4784510 4788810 + Lsi04G005150.1 Lsi04g00515 515
4 4793788 4795258 + Lsi04G005160.1 Lsi04g00516 516
1 9395439 9397294 + Vvi1g771 Vvi1g771 771
1 9410541 9423702 - Vvi1g772 Vvi1g772 772
1 9424058 9437701 + Vvi1g773 Vvi1g773 773
1 9449743 9452855 + Vvi1g774 Vvi1g774 774
1 9454039 9455898 - Vvi1g775 Vvi1g775 775
1 9457363 9477097 - Vvi1g776 Vvi1g776 776
1 9477542 9478317 - Vvi1g777 Vvi1g777 777
1 9478447 9494585 - Vvi1g778 Vvi1g778 778
1 9503469 9506746 + Vvi1g779 Vvi1g779 779
1 9510815 9518104 + Vvi1g780 Vvi1g780 780
       

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