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
Vvi1g1131 . Blo16g01185 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1115 Cone19ag1101 . . Lsi04g00647 . . Cme10g00627 . . . . . . . Bma06g00583 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1132 . . . . . . . . Cmo04g01907 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1133 Blo01g00375 Blo16g01186 Bda01g02195 . Bpe13g00517 . . Bma15g00248 . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag1103 Cone8ag0719 . . . . . Blo06g00818 . . . . . Bma01g00027 Bma06g00582 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1134 Blo01g00374 . Bda01g02194 . Bpe13g00518 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0720 . . . . . . . . . . . Bma01g00026 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1135 . . . . . Bpe10g00775 . Bma15g00247 Cmo04g01908 . . . . . Sed01g2093 . Cpe01g01594 Bhi07g01862 Tan04g0103 Cmetu10g0385 Lac13g0093 Hepe10g1549 . . Cla05g02631 Cam05g2824 Cec05g2859 Cco05g2892 Clacu05g2827 Cmu05g2675 Cre05g2792 Cone13ag1119 Cone19ag1104 . . Lsi04g00648 . . Cme10g00628 . . . . . . . . . . . Cma04g01810 . Car04g01823 . . . . . . . . . . . . . . . . . . . . .
Vvi1g1136 . . Bda01g02193 . Bpe13g00519 . Bma14g01878 Bma15g00246 . Cmo18g00710 . Cma18g00723 . Car18g00669 Sed06g1724 Cpe09g00566 Cpe01g01595 Bhi07g01864 Tan04g0101 Cmetu10g0075 . Hepe10g0079 . . . . . . . . . Cone13ag1120 Cone19ag1105 Cone8ag0721 . Lsi04g00650 . . Cme10g00629 Blo06g00819 . . . . . Bma01g00025 . . . . Cma04g01812 . Car04g01824 . . . . . . . . . . . . . . . . . . . . .
Vvi1g1137 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1138 Blo01g00373 . Bda01g02192 . Bpe13g00520 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0722 . . . . . . . . . . . Bma01g00024 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1140 . . . . . Bpe10g00776 . Bma15g00245 Cmo04g01909 Cmo18g00709 . Cma18g00721 . Car18g00668 Sed01g2092 Cpe09g00567 Cpe01g01597 Bhi07g01866 Tan04g0099 Cmetu10g1838 Lac13g0091 Hepe10g1545 . . Cla05g02632 Cam05g2826 Cec05g2862 Cco05g2894 Clacu05g2830 Cmu05g2677 Cre05g2794 . Cone19ag1106 . . Lsi04g00651 . . Cme10g00631 Blo06g00820 . . . . . . . . . . Cma04g01813 . Car04g01825 . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57865841 57866773 + Bda032996 Bda01g02192 2192
1 57867763 57869587 - Bda004533.2 Bda01g02193 2193
1 57870679 57877660 + Bda004534.1 Bda01g02194 2194
1 57878800 57881842 + Bda004535.1 Bda01g02195 2195
7 50621282 50625281 + XM_039036823.1 Bhi07g01862 1862
7 50628655 50632354 + XM_039036146.1 Bhi07g01864 1864
7 50633913 50635957 - XM_039036976.1 Bhi07g01866 1866
1 4329163 4330101 + BLOR00373 Blo01g00373 373
1 4334099 4340890 + BLOR00374 Blo01g00374 374
1 4342274 4346116 + BLOR00375 Blo01g00375 375
6 31433843 31436457 - BLOR17401 Blo06g00818 818
6 31450686 31460551 + BLOR17402 Blo06g00819 819
6 31461421 31463562 - BLOR17403 Blo06g00820 820
16 40385869 40387170 + BLOR21972 Blo16g01185 1185
16 40407577 40411242 - BLOR21973 Blo16g01186 1186
1 367802 368812 + Bma000195.1 Bma01g00024 24
1 369691 371516 - Bma000196.1 Bma01g00025 25
1 382189 382765 + Bma000197.1 Bma01g00026 26
1 386212 389231 + Bma030162 Bma01g00027 27
6 31176507 31179882 + Bma023506.1 Bma06g00582 582
6 31181381 31182681 + Bma023507.1 Bma06g00583 583
14 40230481 40231681 + Bma012662.2 Bma14g01878 1878
15 2467908 2469454 + Bma013231.1 Bma15g00245 245
15 2471069 2475145 - Bma013232.1 Bma15g00246 246
15 2476785 2480320 - Bma030771 Bma15g00247 247
15 2483549 2485020 + Bma013233.1 Bma15g00248 248
10 13944083 13947630 + Bpe024713 Bpe10g00775 775
10 13953573 13955032 - Bpe003082.1 Bpe10g00776 776
13 12498140 12501250 - Bpe010223.1 Bpe13g00517 517
13 12502735 12509664 - Bpe010224.1 Bpe13g00518 518
13 12511021 12512588 + Bpe010225.1 Bpe13g00519 519
13 12513529 12514539 - Bpe010226.1 Bpe13g00520 520
5 35309922 35312444 + CaPI482276_05g028240.1 Cam05g2824 2824
5 35314132 35316318 - CaPI482276_05g028260.1 Cam05g2826 2826
4 10564450 10568514 + Carg14282-RA Car04g01823 1823
4 10569747 10571896 + Carg14281-RA Car04g01824 1824
4 10572584 10574848 - Carg14280-RA Car04g01825 1825
18 7898337 7901267 + Carg21251-RA Car18g00668 668
18 7902803 7905220 - Carg21252-RA Car18g00669 669
5 36472875 36475397 + CcPI632755_05g028920.1 Cco05g2892 2892
5 36477095 36479259 - CcPI632755_05g028940.1 Cco05g2894 2894
5 38784482 38787004 + CePI673135_05g028590.1 Cec05g2859 2859
5 38789334 38790890 - CePI673135_05g028620.1 Cec05g2862 2862
5 35533592 35536114 + ClG42_05g0282700.10 Clacu05g2827 2827
5 35538457 35541841 - ClG42_05g0283000.10 Clacu05g2830 2830
5 37502251 37512361 + ClCG05G026250.2 Cla05g02631 2631
5 37513342 37515680 - ClCG05G026270.1 Cla05g02632 2632
4 9123219 9127406 + CmaCh04G018100.1 Cma04g01810 1810
4 9128645 9131544 + CmaCh04G018120.1 Cma04g01812 1812
4 9131708 9133857 - CmaCh04G018130.1 Cma04g01813 1813
18 6536358 6538941 + CmaCh18G007210.1 Cma18g00721 721
18 6540510 6543140 - CmaCh18G007230.1 Cma18g00723 723
10 3994880 3996615 + MELO3C011899.2.1 Cme10g00627 627
10 3998074 4001807 + MELO3C011898.2.1 Cme10g00628 628
10 4004398 4006800 + MELO3C011897.2.1 Cme10g00629 629
10 4009274 4011100 - MELO3C011895.2.1 Cme10g00631 631
10 17931129 17934233 - PI0024365.1 Cmetu10g0075 75
10 17935922 17939934 - PI0009002.1 Cmetu10g0385 385
10 17928962 17929147 + PI0025999.1 Cmetu10g1838 1838
4 9722486 9723967 + CmoCh04G019070.1 Cmo04g01907 1907
4 9725158 9733836 + CmoCh04G019080.1 Cmo04g01908 1908
4 9733878 9735642 - CmoCh04G019090.1 Cmo04g01909 1909
18 8927614 8931648 + CmoCh18G007090.1 Cmo18g00709 709
18 8932623 8935851 - CmoCh18G007100.1 Cmo18g00710 710
5 35271976 35274498 + CmPI595203_05g026750.1 Cmu05g2675 2675
5 35276839 35280228 - CmPI595203_05g026770.1 Cmu05g2677 2677
8 7250529 7254812 - Conep08aG0074200.1 Cone8ag0719 719
8 7255450 7264308 - Conep08aG0074300.1 Cone8ag0720 720
8 7269235 7272663 + Conep08aG0074400.1 Cone8ag0721 721
8 7273751 7275888 - Conep08aG0074500.1 Cone8ag0722 722
8 7286476 7291685 + Conep08aG0074700.1 Cone8ag0724 724
13 8937144 8938928 + Conep13aG0114700.1 Cone13ag1115 1115
13 8948814 8952564 + Conep13aG0115100.1 Cone13ag1119 1119
13 8955048 8958263 + Conep13aG0115200.1 Cone13ag1120 1120
19 7967049 7968368 + Conep19aG0113500.1 Cone19ag1101 1101
19 7973234 7975933 - Conep19aG0113700.1 Cone19ag1103 1103
19 7976280 7979750 + Conep19aG0113800.1 Cone19ag1104 1104
19 7979938 7982235 + Conep19aG0113900.1 Cone19ag1105 1105
19 7983508 7985420 - Conep19aG0114000.1 Cone19ag1106 1106
1 9736879 9740962 + Cp4.1LG01g15830.1 Cpe01g01594 1594
1 9742253 9744408 + Cp4.1LG01g15860.1 Cpe01g01595 1595
1 9748111 9748665 - Cp4.1LG01g16100.1 Cpe01g01597 1597
9 3913525 3916056 + Cp4.1LG09g06130.1 Cpe09g00566 566
9 3917309 3920349 - Cp4.1LG09g06090.1 Cpe09g00567 567
5 38635799 38638322 + CrPI670011_05g027920.1 Cre05g2792 2792
5 38640037 38644084 - CrPI670011_05g027940.1 Cre05g2794 2794
10 767872 770019 + Hsped.10g00790.1 Hepe10g0079 79
10 52220338 52222258 + Hsped.10g15450.1 Hepe10g1545 1545
10 52231333 52234213 - Hsped.10g15490.1 Hepe10g1549 1549
13 653203 659589 + Lag0039887.1 Lac13g0091 91
13 666735 671866 - Lag0039889.1 Lac13g0093 93
4 5925866 5937452 + Lsi04G006470.1 Lsi04g00647 647
4 5939481 5943128 + Lsi04G006480.1 Lsi04g00648 648
4 5946555 5949320 + Lsi04G006500.1 Lsi04g00650 650
4 5950735 5953609 - Lsi04G006510.1 Lsi04g00651 651
1 15634446 15636989 + Sed0021695.6 Sed01g2092 2092
1 15637309 15641034 - Sed0005823.1 Sed01g2093 2093
6 41925827 41929269 + Sed0005139.1 Sed06g1724 1724
4 704105 706820 + Tan0010803.1 Tan04g0099 99
4 708781 711783 - Tan0017847.2 Tan04g0101 101
4 713964 718186 - Tan0005833.1 Tan04g0103 103
1 19335592 19336894 - Vvi1g1131 Vvi1g1131 1131
1 19370000 19372078 + Vvi1g1132 Vvi1g1132 1132
1 19401812 19415232 - Vvi1g1133 Vvi1g1133 1133
1 19418611 19452763 - Vvi1g1134 Vvi1g1134 1134
1 19466226 19475589 + Vvi1g1135 Vvi1g1135 1135
1 19480170 19484452 + Vvi1g1136 Vvi1g1136 1136
1 19486354 19493500 + Vvi1g1137 Vvi1g1137 1137
1 19493535 19497183 - Vvi1g1138 Vvi1g1138 1138
1 19500061 19509471 + Vvi1g1139 Vvi1g1139 1139
1 19509483 19511756 - Vvi1g1140 Vvi1g1140 1140
       

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