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
Vvi16g674 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme09g01533
Vvi16g676 . . . . Bpe03g00111 . . Bma14g02084 . . Cma02g01068 Cma15g01098 Car02g00811 Car15g01009 . Cpe05g00651 . . . . . . . . Cla01g00433 Cam01g0456 Cec01g0445 Cco01g0467 Clacu01g0455 Cmu01g0434 Cre09g2078 . Cone5ag0867 . . Lsi05g01225 . . . . Blo09g00112 . . . . . . . Cmo02g01086 Cmo15g01156 Cma16g00125 . . Car18g01154 Cpe09g00090 Cpe13g00253 Bhi12g00511 . . . Hepe06g0702 . . Cla05g00883 Cam05g0971 Cec05g0975 Cco05g0975 Clacu05g0958 Cmu05g0915 Cre05g0999 Lsi09g00095 Csa03g01712 . .
Vvi16g677 . . Bda05g00075 . Bpe03g00286 . . . . Cmo18g01271 . . . . Sed01g3584 . Cpe14g00107 Bhi01g01319 Tan01g0250 Cmetu06g0041 . Hepe07g0157 Mch10g0153 . . . . . . . . Cone1ag1157 Cone5ag0868 . . Lsi05g01224 . . Cme06g01001 Blo07g00410 . . . . . . . . . . Cma16g00124 Cma18g01248 Car16g00113 Car18g01155 Cpe09g00089 . . . . . . . . . . . . . . . . Csa03g01713 Chy06g00948 .
Vvi16g678 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g679 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g680 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g681 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe13g00050 . . . . . . . . . . . . . . . . . .
Vvi16g682 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g683 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 3709743 3712291 - Bda020665.1 Bda05g00075 75
1 26503837 26510935 + XM_039030384.1 Bhi01g01319 1319
12 16322227 16323790 + XM_039019993.1 Bhi12g00511 511
7 7637735 7641286 + BLOR18342 Blo07g00410 410
9 2265789 2266422 - BLOR21027 Blo09g00112 112
14 44243067 44243725 + Bma012895.1 Bma14g02084 2084
3 1648443 1649112 + Bpe011957.1 Bpe03g00111 111
3 3924281 3929193 + Bpe012138.1 Bpe03g00286 286
1 4866337 4867723 - CaPI482276_01g004560.1 Cam01g0456 456
5 8719734 8722932 - CaPI482276_05g009710.1 Cam05g0971 971
2 5883479 5884491 - Carg08410-RA Car02g00811 811
15 7888705 7889930 + Carg23185-RA Car15g01009 1009
16 678420 682075 + Carg15135-RA Car16g00113 113
18 11355989 11356661 - Carg22102-RA Car18g01154 1154
18 11357416 11360408 - Carg22103-RA Car18g01155 1155
1 4564076 4565567 - CcPI632755_01g004670.1 Cco01g0467 467
5 8494797 8495605 - CcPI632755_05g009750.1 Cco05g0975 975
1 4589465 4590894 - CePI673135_01g004450.1 Cec01g0445 445
5 8473229 8476613 - CePI673135_05g009750.1 Cec05g0975 975
6 6931495 6937403 - Chy6G114760.1 Chy06g00948 948
9 12704642 12705952 - Chy9G167270.1 Chy09g01011 1011
1 4512856 4514281 - ClG42_01g0045500.10 Clacu01g0455 455
5 8430148 8433525 - ClG42_05g0095800.10 Clacu05g0958 958
1 4688960 4690613 - ClCG01G004410.2 Cla01g00433 433
5 8687401 8696936 - ClCG05G008060.2 Cla05g00883 883
2 6363850 6364723 - CmaCh02G010680.1 Cma02g01068 1068
15 6991309 6992403 + CmaCh15G010980.1 Cma15g01098 1098
16 569503 572178 + CmaCh16G001240.1 Cma16g00124 124
16 572213 573452 + CmaCh16G001250.1 Cma16g00125 125
18 9739710 9745355 - CmaCh18G012480.1 Cma18g01248 1248
6 7161971 7172247 - MELO3C006911.2.1 Cme06g01001 1001
9 20427143 20430013 - MELO3C005450.2.1 Cme09g01533 1533
6 7134787 7136258 - PI0013451.1 Cmetu06g0041 41
2 6595091 6596018 - CmoCh02G010860.1 Cmo02g01086 1086
15 8081976 8083466 + CmoCh15G011560.1 Cmo15g01156 1156
18 12357550 12362403 - CmoCh18G012710.1 Cmo18g01271 1271
1 4469665 4471090 - CmPI595203_01g004340.1 Cmu01g0434 434
5 8276985 8280364 - CmPI595203_05g009150.1 Cmu05g0915 915
1 55715755 55719239 - Conep01aG0120600.1 Cone1ag1157 1157
5 3693345 3693951 - Conep05aG0089300.1 Cone5ag0867 867
5 3695064 3696537 - Conep05aG0089400.1 Cone5ag0868 868
5 3972920 3973678 + Cp4.1LG05g06430.1 Cpe05g00651 651
9 523419 525934 + Cp4.1LG09g00860.1 Cpe09g00089 89
9 526874 528271 + Cp4.1LG09g00850.1 Cpe09g00090 90
13 375449 380682 - Cp4.1LG13g00490.1 Cpe13g00050 50
13 1968512 1970202 - Cp4.1LG13g02480.1 Cpe13g00253 253
14 589167 594421 + Cp4.1LG14g06100.1 Cpe14g00107 107
5 9161231 9164615 - CrPI670011_05g009990.1 Cre05g0999 999
9 39846223 39847700 + CrPI670011_09g020780.1 Cre09g2078 2078
3 12823259 12825907 - CsaV3_3G017120.1 Csa03g01712 1712
3 12826760 12830122 - CsaV3_3G017130.1 Csa03g01713 1713
6 51406000 51407272 + Hsped.06g07020.1 Hepe06g0702 702
7 1446658 1447513 + Hsped.07g01570.1 Hepe07g0157 157
5 20140154 20144950 + Lsi05G012240.1 Lsi05g01224 1224
5 20146208 20147191 + Lsi05G012250.1 Lsi05g01225 1225
9 832911 835529 - Lsi09G000950.1 Lsi09g00095 95
10 941772 947759 + MC10g0130 Mch10g0153 153
1 64945278 64945760 + Sed0010259.1 Sed01g3584 3584
1 2154242 2155018 + Tan0000800.1 Tan01g0250 250
16 17025239 17025790 + Vvi16g674 Vvi16g674 674
16 17026798 17029223 + Vvi16g675 Vvi16g675 675
16 17034500 17035794 - Vvi16g676 Vvi16g676 676
16 17036900 17041425 - Vvi16g677 Vvi16g677 677
16 17044211 17047672 + Vvi16g678 Vvi16g678 678
16 17053734 17055618 - Vvi16g679 Vvi16g679 679
16 17084119 17084161 - Vvi16g680 Vvi16g680 680
16 17106360 17111392 - Vvi16g681 Vvi16g681 681
16 17127263 17127530 - Vvi16g682 Vvi16g682 682
16 17139143 17139784 + Vvi16g683 Vvi16g683 683
       

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