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Table 2 PCR validation of PAV polymorphisms

From: High presence/absence gene variability in defense-related gene clusters of Cucumis melo

PAV gene Coordinates (v3.5)a Partially or fully absent (p/f) Varietiesb PAV gapsc
     Size (bp) Coordinates (v3.5)a Commentsd
4241 5,250,561-5,252,741 f IQ 6,225 5,246,795-5,253,019 C
CV
4260 5,508,406-5,509,772 p CV 498 5,508,275-5,508,772 C, SI (37 nt), E
4262 5,533,446-5,539,663 p IQ - - False PAV
CV
4278 5,683,128-5,692,676 p CV 1,308 5,684,308-5,686,215 C, I (partial)
4288 5,779,041-5,786,300 p IQ - - False PAV
CV
4289 5,801,121-5,806,330 f IQ 86,393 5,790,312-5,876,704 C, SI (3 kb)
p CV 739 5,802,779-5,803,517 C, I
4290 5,810,121-5,812,410 f IQ 86,393 5,790,312-5,876,704 C, SI (3 kb)
4291 5,840,867-5,843,162 f IQ 86,393 5,790,312-5,876,704 C, SI (3 kb)
p PI 57,737 5,843,353-5,901,089 SI (744 nt)
4292 5,855,171-5,860,831 f IQ 86,393 5,790,312-5,876,704 C, SI (3 kb)
p CV 532 5,857,419-5,857,950 C, E (partial), I (partial)
f PI 57,737 5,843,353-5,901,089 C, SI (744 nt)
4293 5,868,071-5,868,244 f IQ 86,393 5,790,312-5,876,704 C, SI (3 kb)
f PI 57,737 5,843,353-5,901,089 C, SI (744 nt)
4294 5,884,952-5,889,556 f CV 40,204 5,878,047-5,918,250 C, SI (3 kb)
f PI 57,737 5,843,353-5,901,089 C, SI (744 nt)
4295 5,893,422-5,893,773 f CV 40,204 5,878,047-5,918,250 C, SI (3 kb)
f PI 57,737 5,843,353-5,901,089 C, SI (744 nt)
4299 5,951,143-5,955,050 p IQ 525 5,953,236-5,953,760 I
p CV 525 5,953,236-5,953,760 I
p PI 524 5,953,237-5,953,760 I
4317 6,085,745-6,087,399 p PI - - False PAV
4318 6,111,948-6,113,580 f CV 149,716 6,088,767-6,238,482 C
4319 6,144,630-6,145,072 f CV 149,716 6,088,767-6,238,482 C
f PI 87,210 6,130,422-6,217,631 C
4320 6,158,620-6,160,417 f CV 149,716 6,088,767-6,238,482 CC
f PI 87,210 6,130,422-6,217,631 C
4321 6,180,382-6,182,596 f CV 149,716 6,088,767-6,238,482 C
f PI 87,210 6,130,422-6,217,631 C
4322 6,212,481-6,214,658 f CV 149,716 6,088,767-6,238,482 C
f PI 87,210 6,130,422-6,217,631 C
f IQ - - Not yet confirmed
4323 6,219,959-6,220,884 f CV 149,716 6,088,767-6,238,482 C
4324 6,232,683-6,236,414 p IQ 1,637 6,234,788-6,236,424 C, E (partial)
f CV 149,716 6,088,767-6,238,482 C
f PI 5,714 6,232-627-6,238,340 C
4326 6,251,955-6,252,158 f IQ 3005 6,250,865-6,253,869 C, SI (5.8 kb)
f CV 3588 6,250,865-6,254,452 C, SI (6 kb)
4331 6,306,224-6,307,985 f PI 6,370 6,306,115-6,312,484 C
5453 5,239,146-5,239,370 p IQ 0 5,239,342-5,239,343 C, SI (225 bp)
p CV 0 5,239,290-5,239,343
14632 4,629,508-4,646,365 p CV 7,278 4,628,501-4,635,778 C, E, I, SI (39 bp)
14633 4,655,610-4,656,362 f IQ 33,861 4,646,955-4,680,815 C, SI (7.5 kb)
f PI 33,861 4,646,955-4,680,815 C, SI (7.5 kb)
14634 4,658,485-4,659,820 f IQ 33,861 4,646,955-4,680,815 C, SI (7.5 kb)
f PI 33,861 4,646,955-4,680,815 C, SI (7,5 kb)
14635 4,676,224-4,677,197 f IQ 33,861 4,646,955-4,680,815 C, SI (7.5 kb)
f PI 33,861 4,646,955-4,680,815 C, SI (7,5 kb)
15015 1,061,280-1,061,542 f CV 28,011 1,038,039-1,066,049 C, SI (2,6 kb, transposon)
22141 1,707,299-1,710,539 p IQ - - False PAV
p PI
22145 1,728,890-1,744,072 p IQ 9,736 1,733,997-1,743,732 C, E, I, SI (6.5 kb)
p CV 9,736 1,733,997-1,743,732 C, E, I, SI (6.5 kb)
p PI 9,736 1,733,997- 1,743,732 C, E, I, SI (6.5 kb)
22153 1,815,300-1,819,596 p PI - - False PAV
22154 1,823,379-1,831,379 p CV - - False PAV
p PI
23276 756,768-760,353 f IQ 19,558 755,353-774,910 C, SI (445 bp)
f PS 19,558 755,353-774,910 C, SI (310 bp)
23277 765,000-765,855 f IQ 19,558 755,353-774,910 C, SI (445 bp)
f PS 19,558 755,353-774,910 C, SI (310 bp)
23278 766,024-767,842 f IQ 19,558 755,353-774,910 C, SI (445 bp)
f PS 19,558 755,353-774,910 C, SI (310 bp)
23577 1,518,347-1,521,271 p CV 2,191 1,519,298-1,521,488 C, E, I
24733 294,304-297,983 p CV 193 295,122-295,314 C,I,SI (234 bp, transposon)
24737 344,775-345,020 f CV 4,959 344,525-349,483 C
24743 468,195-469,071 p CV 726 468,516-469,241 C, E, I
  1. aCoordinates on the scaffold/contig that contains the gene.
  2. bCV: C-836, IQ: C-1012, PI: PI 161375, PS: T111.
  3. cDHL92 sequence fragment that contains the gene and is absent relative to the reference sequence.
  4. dC: PAV confirmed; E: Exon deletion; I: Intron deletion; SI: Sequence insertion relative to the reference.