Hierarchical alignments with the P. vulgaris genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Fabaceae genomes. We used P. vulgaris as a reference, and by comparing homologous gene locus maps and Ks values between P. vulgaris and other Fabaceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created two hierarchical lists of homologous genes using P. vulgaris as a reference.
  The relevant gene ids can be obtained from the Fabaceae blast and match under the Tools module. This link is Fabaceae blast and match.
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Select Download Tree Pvu Acco Accr Adu Aed Aev Ahy_1 Ahy_2 Aip Alju Amo_1 Amo_2 Apr Arst Bach Bisa Bva Car Cca Dere Dod Enph Glsi Gma_1 Gma_2 Gso_1 Gso_2 Lal_1 Lal_2 Lal_3 Lan_1 Lan_2 Lan_3 Lapu Lasa Lele_1 Lele_2 Lele_3 Lele_4 Lja Mal Mepo Mesa Mibi Mtr Phac Phco Prci Psa Pste Pumo Rops Seca Spst Ssu Sto Tpr Trre Tsu Vian Vifa Vimu Viun Vivi Vra
Pvu1g0061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco2g00069 . . . . . . Spst8g02022 . . . . . . . . . . .
Pvu1g0062 . . . Aed11g0040 . . . . . . Amo06g0857 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Vra6g2030
Pvu1g0063 . . . . . . . . . . Amo06g0856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco2g00071 . . . . . . Spst8g02020 . . . . . . . . . . Vra6g2031
Pvu1g0064 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco2g00072 . . . . . . . . . . . . . . . . . .
Pvu1g0065 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco2g00073 . . . . . . . . . . . . . . . . . Vra6g2032
Pvu1g0066 . . . . Aev07g0680 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa6g00283 . . . . . . Mepo4g01881 Mesa1g00044 . Mtr1g0717 . . . Psa6g0065 . . . . Spst8g02327 . . . Trre1g00070 . . . . . Vivi3g00619 .
Pvu1g0067 . . . . . . . . . . . Apr9g0633 . . . . . . . . . . Gma17g02464 . . Gso17g2188 . . . . . . . Lasa6g00282 . . . . . . . Mesa1g00045 . Mtr1g0716 Phac1g00061 Phco2g00075 . Psa6g0066 . . . . . . . . . . . . . . . Vra6g2033
Pvu1g0068 . . Adu06g01281 . . . Ahy6g1280 . . . . . . . . . Car04g03589 Cca05g00366 . . . . . Gma14g02134 Gso14g1849 . . . . . . . Lapu8g01021 . . . . . Lja5g3324 Mal1g6070 . . . . Phac1g00062 . . Psa6g0067 . . Rops9g02608 . Spst8g02016 . . Tpr1g3877 . Tsu01g00196 . . . Viun8g00105 Vivi4g05916 Vra6g2034
Pvu1g0069 Acco05g2972 Accr3g00084 . Aed11g0050 Aev07g0686 Ahy16g0059 . Aip06g00050 . . Amo06g0869 Apr9g0632 Arst6g01689 Bach3g02411 Bisa05g0617 Bva10g00919 . Cca05g00365 Dere05g2801 . Enph7g1478 Glsi10g0133 Gma17g02463 . . Gso17g2187 Lal8g0535 . Lal10g0884 Lan10g0520 . . . Lasa5g04527 Lele25g0070 Lele26g0083 Lele27g2018 Lele28g0081 . Mal1g6069 . . . . . Phco2g00076 Prci2g0106 Psa6g0068 Pste8g01395 Pumo9g00067 Rops9g02610 Seca8g04036 . Ssu5g0063 Sto5g0136 . . . . . . Viun8g00106 Vivi4g05914 .
Pvu1g0070 . . Adu06g01280 Aed11g0051 . Ahy16g0060 Ahy6g1279 Aip06g00051 . . Amo06g0870 . Arst6g01687 . . . . Cca05g00364 . . . . . . . . Lal8g0536 . . Lan10g0521 . . Lapu8g01020 . . . . . Lja5g3323 Mal1g6068 . . . . . Phco2g00077 . . . Pumo9g00068 Rops9g02611 Seca4g00420 Spst8g02015 . . . . . . . . Viun8g00107 Vivi3g00594 .
   
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Select Species Gene Chromosome Start End Strand
Pvu Pvu1g0061 Chr1 497748 498484 +
Phco Phco2g00069 Chr2 668316 668858 +
Spst Spst8g02022 Chr8 27790423 27790947 -
Pvu Pvu1g0062 Chr1 502277 508483 +
Aed Aed11g0040 Chr11 271132 276166 -
Amo Amo06g0857 Chr06 11821685 11827244 -
Vra Vra6g2030 Chr6 36889576 36895052 +
Pvu Pvu1g0063 Chr1 510755 518820 -
Amo Amo06g0856 Chr06 11815591 11821440 +
Phco Phco2g00071 Chr2 680640 689496 -
Spst Spst8g02020 Chr8 27768099 27777210 +
Vra Vra6g2031 Chr6 36896642 36904592 -
Pvu Pvu1g0064 Chr1 522216 523489 +
Phco Phco2g00072 Chr2 692447 693725 +
Pvu Pvu1g0065 Chr1 526509 527693 +
Phco Phco2g00073 Chr2 695913 697086 +
Vra Vra6g2032 Chr6 36911369 36912413 +
Pvu Pvu1g0066 Chr1 533059 533969 +
Aev Aev07g0680 Chr07 4320048 4320649 -
Lasa Lasa6g00283 Chr6 8535213 8535870 -
Mepo Mepo4g01881 Chr4 24100679 24101717 -
Mesa Mesa1g00044 Chr1 614587 615698 +
Mtr Mtr1g0717 Chr1 8108718 8110226 -
Psa Psa6g0065 Chr6 1903304 1905080 +
Spst Spst8g02327 Chr8 34300106 34300669 -
Trre Trre1g00070 Chr1 516403 517876 +
Vivi Vivi3g00619 Chr3 10263165 10263933 -
Pvu Pvu1g0067 Chr1 536352 536885 +
Apr Apr9g0633 Chr9 10234137 10235051 -
Gma Gma17g02464 Chr17 42665190 42666361 -
Gso Gso17g2188 Chr17 41577554 41578559 -
Lasa Lasa6g00282 Chr6 8516277 8516809 -
Mesa Mesa1g00045 Chr1 622178 623040 +
Mtr Mtr1g0716 Chr1 8101646 8102785 -
Phac Phac1g00061 Chr1 458773 465953 +
Phco Phco2g00075 Chr2 701962 702486 +
Psa Psa6g0066 Chr6 1932488 1933101 +
Vra Vra6g2033 Chr6 36919149 36920099 +
Pvu Pvu1g0068 Chr1 540402 540934 +
Adu Adu06g01281 Chr06 17434751 17435806 -
Ahy Ahy6g1280 Chr6 19323297 19324129 -
Car Car04g03589 Chr04 65095975 65096963 -
Cca Cca05g00366 Chr05 8042799 8044369 -
Gma Gma14g02134 Chr14 52503715 52504830 -
Gso Gso14g1849 Chr14 50925055 50926100 -
Lapu Lapu8g01021 Chr8 28314477 28316021 -
Lja Lja5g3324 Chr5 64401553 64403024 -
Mal Mal1g6070 Chr1 139126503 139128860 -
Phac Phac1g00062 Chr1 468153 469309 -
Psa Psa6g0067 Chr6 1936671 1937024 +
Rops Rops9g02608 Chr9 48877618 48878560 +
Spst Spst8g02016 Chr8 27721651 27722163 -
Tpr Tpr1g3877 Chr1 42883917 42885791 -
Tsu Tsu01g00196 Chr01 1528600 1529847 +
Viun Viun8g00105 Chr8 615948 617338 +
Vivi Vivi4g05916 Chr4 196096881 196097907 -
Vra Vra6g2034 Chr6 36922821 36923667 -
Pvu Pvu1g0069 Chr1 543644 544185 +
Acco Acco05g2972 Chr05 44365379 44365805 -
Accr Accr3g00084 Chr3 1061315 1061753 +
Aed Aed11g0050 Chr11 341656 342416 +
Aev Aev07g0686 Chr07 4373203 4373791 +
Ahy Ahy16g0059 Chr16 543377 544413 +
Aip Aip06g00050 Chr06 474873 476240 +
Amo Amo06g0869 Chr06 11933093 11934047 +
Apr Apr9g0632 Chr9 10226683 10227276 +
Arst Arst6g01689 Chr6 17468070 17468877 -
Bach Bach3g02411 Chr3 30406715 30407252 -
Bisa Bisa05g0617 Chr05 10176787 10177308 +
Bva Bva10g00919 Chr10 6933130 6933866 -
Cca Cca05g00365 Chr05 8005320 8006194 +
Dere Dere05g2801 Chr05 38676180 38676693 -
Enph Enph7g1478 Chr7 19979374 19980402 -
Glsi Glsi10g0133 Chr10 987899 988392 +
Gma Gma17g02463 Chr17 42654858 42655929 +
Gso Gso17g2187 Chr17 41567263 41568334 +
Lal Lal8g0535 Chr8 3658666 3660256 +
Lal Lal10g0884 Chr10 16345088 16346455 -
Lan Lan10g0520 Chr10 4160259 4161698 +
Lasa Lasa5g04527 Chr5 670277322 670277840 -
Lele Lele25g0070 Chr25 420969 421372 +
Lele Lele26g0083 Chr26 453682 454087 +
Lele Lele27g2018 Chr27 24299606 24300011 -
Lele Lele28g0081 Chr28 454038 454449 +
Mal Mal1g6069 Chr1 139104292 139107380 -
Phco Phco2g00076 Chr2 708736 709209 +
Prci Prci2g0106 Chr2 857174 857837 +
Psa Psa6g0068 Chr6 1954698 1956148 +
Pste Pste8g01395 Chr8 7571931 7573089 -
Pumo Pumo9g00067 Chr9 1040924 1041840 +
Rops Rops9g02610 Chr9 48897634 48898214 +
Seca Seca8g04036 Chr8 115833868 115835601 -
Ssu Ssu5g0063 Chr5 1193183 1193939 -
Sto Sto5g0136 Chr5 796217 796714 +
Viun Viun8g00106 Chr8 615989 617336 +
Vivi Vivi4g05914 Chr4 196078327 196079149 -
Pvu Pvu1g0070 Chr1 546205 547249 -
Adu Adu06g01280 Chr06 17420670 17421004 -
Aed Aed11g0051 Chr11 345247 346115 -
Ahy Ahy16g0060 Chr16 547843 548923 +
Ahy Ahy6g1279 Chr6 19317979 19318644 -
Aip Aip06g00051 Chr06 480325 481252 +
Amo Amo06g0870 Chr06 11938672 11939266 +
Arst Arst6g01687 Chr6 17453880 17454365 -
Cca Cca05g00364 Chr05 7986841 7987644 +
Lal Lal8g0536 Chr8 3663123 3664070 +
Lan Lan10g0521 Chr10 4165754 4166448 +
Lapu Lapu8g01020 Chr8 28308832 28309718 +
Lja Lja5g3323 Chr5 64396828 64397613 -
Mal Mal1g6068 Chr1 139054376 139054721 -
Phco Phco2g00077 Chr2 712887 713562 -
Pumo Pumo9g00068 Chr9 1045240 1046409 -
Rops Rops9g02611 Chr9 48923282 48924005 +
Seca Seca4g00420 Chr4 6918494 6919477 +
Spst Spst8g02015 Chr8 27709159 27710535 +
Viun Viun8g00107 Chr8 621364 622312 -
Vivi Vivi3g00594 Chr3 9870458 9871239 -
Spst Spst8g02327 Chr8 34300106 34300669 -
Lasa Lasa5g04527 Chr5 670277322 670277840 -
Seca Seca4g00420 Chr4 6918494 6919477 +
Vivi Vivi3g00594 Chr3 9870458 9871239 -