Table 3

Insertion positions and names of the 71 genes harboring BRAMI-1 elements in intronic regions and list of their orthologous genes in Arabidopsis and NIPs in the triplicated blocks of the B. rapa genome
MITE No Chr No MITE start MITE end Ortholog from A. thaliana Triplicated blocks inB. rapaz
LF MF1 MF2
THREE COPY GENES 23 A01 8110084 8109821 At4g25050 Bra013859 Bra019193 Bra010475
83 A02 4177719 4177456 At5g17300 Bra008563 Bra006394 Bra023610
176 A03 5778627 5778365 At5g55050 Bra002937 Bra035549 Bra028994
188 A03 8910390 8910639 At2g37940 Bra005148 Bra017148 Bra000029
219 A03 17370042 17370087 At3g15820 Bra027205 Bra021138 Bra001607
220 A03 17370087 17370331 At3g15820 Bra027205 Bra021138 Bra001607
299 A04 13405505 13405756 At2g30110 Bra018338 Bra021611 Bra022779
303 A04 14136797 14136887 At2g31500 Bra018236 Bra021727 Bra022844
346 A05 7674854 7674713 At2g29980 Bra018348 Bra021599 Bra022767
347 A05 7674974 7675006 At2g29980 Bra018348 Bra021599 Bra022767
349 A05 8733844 8733992 At4g04640 Bra029511 Bra000802 Bra018503
368 A05 16917820 16918070 At3g20770 Bra035746 Bra023927 Bra001802
425 A06 14973843 14973752 At5g64740 Bra024324 Bra037793 Bra031904
443 A06 22195786 22196049 At3g28050 Bra025321 Bra033037 Bra039062
450 A06 24123977 24123793 At2g01430 Bra024888 Bra026666 Bra017451
452 A06 24666391 24666142 At5g46630 Bra025009 Bra022052 Bra017537
473 A07 8537339 8537527 At1g22340 Bra031388 Bra012324 Bra016424
474 A07 9114152 9114414 At1g20670 Bra025837 Bra012243 Bra016456
566 A08 20712404 20712596 At1g07920 Bra018669 Bra031602 Bra030707
654 A10 1570075 1569913 At1g06080 Bra015473 Bra032437 Bra030638
TWO COPY GENES 46 A01 18882651 18882770 At5g52140 Bra028293 Bra022579 -
55 A01 23626196 23626459 At3g16180 Bra027185 Bra021168 -
61 A01 25069244 25069502 At3g02180 - Bra021476 Bra001035
87 A02 5079784 5080047 At5g20540 - Bra006563 Bra020109
113 A02 9852697 9852644 At1g66370 Bra004162 Bra039763 -
153 A02 25486260 25486523 At5g23940 Bra009716 - Bra029388
168 A03 2298612 2298349 At5g12420 - Bra006160 Bra023377
200 A03 11193078 11192830 At2g47460 Bra004456 - Bra000453
234 A03 20936196 20936267 At5g23260 Bra013028 Bra026507 Bra029365
235 A03 20936271 20936494 At5g23260 Bra013028 Bra026507 Bra029365
249 A03 24785451 24785715 At4g22950 - Bra019343 Bra020826
319 A04 18584148 18584406 At2g45550 Bra004921 Bra039330 -
444 A06 22352521 22352784 At3g27640 Bra025293 - Bra039073
460 A07 1577014 1576769 At2g18230 Bra039627 - Bra037229
467 A07 6402416 6402153 At1g29120 - Bra030121 Bra010851
490 A07 12392864 12392917 At3g57530 Bra007334 - Bra003287
536 A08 12108300 12108552 At4g35150 - Bra017699 Bra034678
545 A08 15271728 15271631 At4g36760 Bra011704 - Bra010574
596 A09 8214071 8213980 At1g61890 Bra027073 Bra028379 -
597 A09 8214185 8214078 At1g61890 Bra027073 Bra028379 -
604 A09 16501688 16501868 At5g46350 Bra025021 Bra022033 Bra017561
605 A09 16667316 16667053 At5g46040 - Bra022016 Bra017582
606 A09 16682960 16683223 At5g46040 - Bra022016 Bra017582
608 A09 19871591 19871427 At1g32780 Bra023290 Bra010185 -
615 A09 24192808 24192545 At1g23380 Bra024593 - Bra016348
666 A10 8067999 8067852 At5g57655 Bra002710 Bra020426 -
670 A10 8789727 8789464 At5g59340 Bra002576 Bra020321 -
ONE COPY GENES 40 A01 14766344 14766081 - - - Bra029909
41 A01 14767003 14766741 - - - Bra029909
129 A02 16530545 16530808 At4g01590 - - Bra008554
178 A03 5992774 5992961 - - - Bra029035
223 A03 18448338 18448491 At3g20360 - - Bra001785
578 A09 3996947 3996684 At2g11810 - - Bra037199
266 A03 29733949 29734212 - - Bra017680 -
268 A03 30599723 30599787 At4g36940 - Bra017808 -
472 A07 7616363 7616100 - - Bra012436 -
49 A01 21397784 21397864 At3g19870 - Bra038237 -
120 A02 12485621 12485884 At1g72110 - Bra008008 -
128 A02 15935110 15935361 At1g80200 - Bra008487 -
148 A02 24005490 24005690 - - Bra020642 -
285 A04 7140471 7140542 - Bra028251 - -
378 A05 20048141 20048392 - Bra027271 - -
445 A06 22716443 22716194 At3g26610 Bra025216 - -
501 A07 16958538 16958801 At1g65590 Bra004121 - -
513 A07 20340243 20340188 At1g74790 Bra015893 - -
655 A10 4270200 4270396 At1g02390 Bra033323 - -
656 A10 4270415 4270484 At1g02390 Bra033323 - -
657 A10 4410198 4410053 - Bra033297 - -
672 A10 9364412 9364675 - Bra002467 - -
673 A10 9364744 9365007 - Bra002467 - -
677 A10 10858935 10858966 - Bra002214 - -

z The triplicated chromosome blocks are denoted according to the classification of the B. rapa genome annotation databases (BRAD) [25,31]. The triplicated chromosome blocks are classified as one least fractionized block (LF) and two moderately fractionized blocks (MF1, MF2). Genes with BRAMI-1 insertion in introns are denoted in bold and their NIPs are denoted in plain letters.

Sampath et al.

Sampath et al. BMC Plant Biology 2013 13:56   doi:10.1186/1471-2229-13-56

Open Data