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
Vvi5g1149 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01934 . . . . . . Bma02g00992 . . . . . . . . . . . . . . . . . Cla07g01567 Cam07g1667 Cec07g1761 Cco07g1724 Clacu07g1651 Cmu07g1617 Cre07g1991 . . . .
Vvi5g1150 . Blo12g00253 Bda03g00983 . Bpe04g00912 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1151 . . . . . Bpe14g00997 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone11ag0622 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1152 . . . . . . . . . . Cma06g01637 . Car06g01392 . Sed12g0651 Cpe08g00091 . Bhi01g02650 Tan10g1252 Cmetu07g1677 . Hepe05g1258 . Lcy11g1201 . . . . . . . . . . . . . . Cme07g01869 . . . . . . . Bma06g01425 . Cmo06g01636 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1153 . . . . . Bpe14g01045 . . . . Cma06g01639 Cma14g01486 Car06g01394 Car14g01322 Sed12g0649 Cpe08g00089 Cpe03g01250 Bhi01g02654 Tan10g1257 Cmetu07g1360 . Hepe05g1254 . Lcy11g1198 . . . . . . . . Cone15ag0594 . . . . . Cme07g01871 . . . . . . . . . Cmo06g01638 Cmo14g01521 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1154 Blo01g00234 . . Bda08g00117 . . . . Cmo08g00084 Cmo17g00573 . . . . . . . . . . . . . . Cla08g00447 Cam08g0877 Cec08g0458 Cco08g0579 Clacu08g0595 . Cre08g0417 . . . . . . . . . . . . Bpe05g01020 . . . . . . . Cma17g00591 Car08g00068 Car17g00546 Cpe12g00503 Cpe17g00993 . . . . . . . . . . . . . . . . . .
Vvi5g1155 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1156 . . . . . Bpe14g01044 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 8891832 8896500 + Bda016996.3 Bda03g00983 983
8 995207 998400 + Bda024521.1 Bda08g00117 117
1 65935052 65937281 + XM_039025808.1 Bhi01g02650 2650
1 65946487 65969072 + XM_039029258.1 Bhi01g02654 2654
1 2906738 2910073 - BLOR00234 Blo01g00234 234
12 15651303 15655758 - BLOR04272 Blo12g00253 253
2 50439777 50442528 - Bma030918 Bma02g00992 992
6 50985243 50987792 - Bma024539.1 Bma06g01425 1425
4 6091166 6095830 + Bpe015576.1 Bpe04g00912 912
5 22838103 22841300 - Bpe018431.1 Bpe05g01020 1020
14 7361437 7365307 + Bpe014370.1 Bpe14g00997 997
14 7802410 7804305 + Bpe014418.1 Bpe14g01044 1044
14 7805410 7816367 - Bpe014419.3 Bpe14g01045 1045
7 31242236 31244989 - CaPI482276_07g016670.1 Cam07g1667 1667
8 12876044 12886585 - CaPI482276_08g008770.1 Cam08g0877 877
6 10004376 10006946 + Carg15484-RA Car06g01392 1392
6 10014334 10015730 + Carg15482-RA Car06g01394 1394
8 393761 404755 + Carg04910-RA Car08g00068 68
14 11193327 11198647 - Carg22433-RA Car14g01322 1322
17 5083038 5095171 - Carg22612-RA Car17g00546 546
7 31237759 31240520 - CcPI632755_07g017240.1 Cco07g1724 1724
8 14923053 14934644 - CcPI632755_08g005790.1 Cco08g0579 579
7 33150342 33153087 - CePI673135_07g017610.1 Cec07g1761 1761
8 13364800 13375924 - CePI673135_08g004580.1 Cec08g0458 458
7 31095904 31098655 - ClG42_07g0165100.10 Clacu07g1651 1651
8 13107146 13117723 - ClG42_08g0059500.10 Clacu08g0595 595
7 32862358 32865501 - ClCG07G016430.1 Cla07g01567 1567
8 13588241 13599708 - ClCG08G004290.1 Cla08g00447 447
6 10191393 10194423 + CmaCh06G016370.1 Cma06g01637 1637
6 10199389 10202546 + CmaCh06G016390.1 Cma06g01639 1639
14 11280955 11287078 - CmaCh14G014860.1 Cma14g01486 1486
17 4886141 4899294 - CmaCh17G005910.1 Cma17g00591 591
7 24099461 24102727 + MELO3C017697.2.1 Cme07g01869 1869
7 24108216 24115130 + MELO3C017699.2.1 Cme07g01871 1871
7 24541628 24548278 - MELO3C017758.2.1 Cme07g01934 1934
7 2800743 2805831 - PI0002446.1 Cmetu07g1360 1360
7 2812251 2814814 - PI0003772.1 Cmetu07g1677 1677
6 11405229 11408372 + CmoCh06G016360.1 Cmo06g01636 1636
6 11413574 11417992 + CmoCh06G016380.1 Cmo06g01638 1638
8 430438 439573 + CmoCh08G000840.1 Cmo08g00084 84
14 12187832 12193552 - CmoCh14G015210.1 Cmo14g01521 1521
17 5880772 5893332 - CmoCh17G005730.1 Cmo17g00573 573
7 31347803 31350554 - CmPI595203_07g016170.1 Cmu07g1617 1617
11 3900805 3904367 - Conep11aG0063800.1 Cone11ag0622 622
15 3025405 3028219 - Conep15aG0060500.1 Cone15ag0592 592
15 3048205 3051678 + Conep15aG0060700.1 Cone15ag0594 594
3 10139238 10145133 - Cp4.1LG03g12530.1 Cpe03g01250 1250
8 556360 564862 - Cp4.1LG08g05870.1 Cpe08g00089 89
8 569474 573004 - Cp4.1LG08g05900.1 Cpe08g00091 91
12 4925056 4937800 - Cp4.1LG12g05130.1 Cpe12g00503 503
17 7530245 7540746 + Cp4.1LG17g09950.1 Cpe17g00993 993
7 35357545 35360301 - CrPI670011_07g019910.1 Cre07g1991 1991
8 14005439 14016747 - CrPI670011_08g004170.1 Cre08g0417 417
5 59720813 59732255 - Hsped.05g12540.1 Hepe05g1254 1254
5 59762075 59764358 - Hsped.05g12580.1 Hepe05g1258 1258
11 34435677 34439690 - Maker00005240 Lcy11g1198 1198
11 34454514 34459116 - Maker00005213 Lcy11g1201 1201
12 3871358 3878393 - Sed0004128.1 Sed12g0649 649
12 3886801 3889391 - Sed0019898.1 Sed12g0651 651
10 14124778 14127259 + Tan0007153.1 Tan10g1252 1252
10 14137056 14146030 + Tan0004930.2 Tan10g1257 1257
5 21098679 21109331 + Vvi5g1149 Vvi5g1149 1149
5 21109914 21114224 + Vvi5g1150 Vvi5g1150 1150
5 21119195 21124358 - Vvi5g1151 Vvi5g1151 1151
5 21125136 21127612 + Vvi5g1152 Vvi5g1152 1152
5 21129968 21137218 - Vvi5g1153 Vvi5g1153 1153
5 21138853 21161143 - Vvi5g1154 Vvi5g1154 1154
5 21181513 21182849 + Vvi5g1155 Vvi5g1155 1155
5 21182890 21183569 + Vvi5g1156 Vvi5g1156 1156
5 21184285 21193888 + Vvi5g1157 Vvi5g1157 1157
5 21209342 21210050 - Vvi5g1158 Vvi5g1158 1158
       

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