Major recent and independent changes in levels and patterns of expression have occurred at the b gene, a regulatory locus in maize -- Data Supplement - -- Proceedings of the National Academy of Sciences

Supplementary material for Selinger and Chandler (1999) Proc. Natl. Acad. Sci. USA 96 (26), 15007-15012.

		`[Hb2`	`]`	`[`
`position`	`000000000000000`	`000000000000000`	`000011111111111`	`111111111111111`
`of`	`000122223334455`	`555666667778888`	`889900011111112`	`222222223333334`
`polymorphism`	`156723492790601`	`257234890131234`	`587845614567890`	`123456784567890`
`B-I`	`TAGAACTTTTTTC--`	`-CCGGTTTAAG----`	`-CGCTTCGGACTTTC`	`TCACAGCACTAAGGG`
`B-615`	`...............`	`...............`	`...............`	`...............`
`B-Mex7a`	`...............`	`...............`	`...............`	`...............`
`B-M106`	`...............`	`...............`	`...............`	`...............`
`B-Mex7b`	`...............`	`...............`	`...............`	`...............`
`B-Gua31`	`-..G.T.G.......`	`.....C.C..A....`	`.G...-.........`	`.....A.G....---`
`B-Marker`	`-..G.T.G.......`	`.....C.C..A....`	`.G...-.........`	`.....A.G....---`
`B-Mag466`	`-..G.T.G.......`	`.....C.C..A....`	`.G...-.........`	`.....A.G....---`
`B-M075`	`-..G.T.G.......`	`.....C.C..A....`	`.G...-.........`	`.....A.G....---`
`B-M046`	`-..G.T.G.......`	`.....C.C.......`	`.G...-.........`	`.....A.G....---`
`B-Peru`	`-..G.T.G.......`	`.....C.C..A....`	`.G...-T........`	`.....A.G....---`
`B-Bolivia`	`-..G.T.G.......`	`.....C.C..A....`	`.G...-T........`	`.....A.G....---`
`B-M092`	`...G.T.G....T..`	`.....C.C.......`	`.GTT.-T-..-----`	`---------------`
`B-M063`	`-...T.GG.....TC`	`AA...C----.....`	`.G...-.A.......`	`.....T.G....---`
`b-W23`	`-...T.GG.....TC`	`AA...C----.....`	`.G...-.A.......`	`.....T.G....---`
`B-bar`	`-...T.GG.....TC`	`AA...C----.....`	`.G...-.A.......`	`.....T.G....---`
`B-M031`	`..AGGT.GAG--...`	`..AA.C.C.......`	`.....-.A.G....T`	`.......G....---`
`B-M033`	`.TAGGT.G.......`	`....AC.C...CTTA`	`G...--..C......`	`...---.G....---`

	`Tourist-Zm23]`
`position`	`111111112222222`	`222222223333333`	`333333333333333`	`333333333333333`
`of`	`444444446666677`	`788889990011222`	`223334445556677`	`777788899999999`
`polymorphism`	`123456785678904`	`502360251413356`	`792340694571323`	`567804512345678`
`B-I`	`CCTGTTTGCTAAAGC`	`AACCT-GGATGCAGG`	`AGTTTGTCGAT-AAG`	`A-CTAGCTAGTTTTT`
`B-615`	`...............`	`...............`	`...............`	`...............`
`B-Mex7a`	`...............`	`...............`	`...............`	`...............`
`B-M106`	`T..............`	`...............`	`...............`	`...............`
`B-Mex7b`	`...............`	`...............`	`...............`	`...............`
`B-Gua31`	`------------.A.`	`C....T.......A.`	`..A...-..C..G.C`	`.....TT...C....`
`B-marker`	`------------.A.`	`C....T.......A.`	`..A...-..C..G.C`	`.....TT...C....`
`B-Mag466`	`------------.A.`	`C....T.......A.`	`..A...-..C..G.C`	`.....TT...C....`
`B-M075`	`------------.A.`	`C....T.......A.`	`..A...-..C..G.C`	`....GTT...C....`
`B-M046`	`------------.A.`	`C....T.......A.`	`..A...-..C..G.C`	`.....TT...C....`
`B-Mag466`	`------------.A.`	`C....T.A.....A.`	`..A...-..C..G.C`	`.....TT...C....`
`B-Bolivia`	`------------.A.`	`C....T.......A.`	`..A...-..C..G.C`	`.....TT...C....`
`B-M092`	`--------------.`	`CT...T.........`	`..C.........G.A`	`G.....T...C....`
`B-M063`	`------------.A.`	`C....T....A....`	`.AAA........G.C`	`...C..A...C....`
`b-W23`	`------------.A.`	`C.T..T....A....`	`.AA.........G.T`	`...C..A...C....`
`B-bar`	`------------.A.`	`C.T..T....A....`	`.AA.........G.T`	`...C..A...C....`
`B-M031`	`------------.AG`	`C....TA.G...G..`	`C...AA.TA.G.GGC`	`..T...T--------`
`B-M033`	`------------.A.`	`C..TCT...C.T..A`	`...........TG.C`	`.A....A...C....`

	`[ 359`	`bp insertion +`	`29bp del]`
`position`	`344444444444444`	`444444444444444`	`444444444444444`	`444444444444444`
`of`	`900000000001111`	`111111222222222`	`233333333334444`	`444444555555555`
`polymorphism`	`901234567890123`	`456789012345678`	`901234567890123`	`456789012345678`
`B-I`	`TCTCTCACAAAAACT`	`TTTT--CACGGCCAC`	`TGTATTACT------`	`---------------`
`B-615`	`...............`	`...............`	`...............`	`...............`
`B-Mex7a`	`...............`	`...............`	`...............`	`...............`
`B-M106`	`...............`	`...............`	`...............`	`...............`
`B-Mex7b`	`...............`	`...............`	`...............`	`...............`
`B-Gua31`	`C.....G...C....`	`....TT...C.....`	`A..CCA..CAAACAA`	`ATCTTATAG......`
`B-marker`	`C.....G...C....`	`....TT...C.T...`	`A..CCA..CAAACAA`	`ATCTTATAG......`
`B-Mag466`	`C.....G...C....`	`....TT...C.....`	`A..CCA..CAAACAA`	`ATCTTATAG......`
`B-M075`	`C.....G...C....`	`....TT...C.....`	`A..CCA..CAAACAA`	`ATCTTATAG......`
`B-M046`	`C.....G...C....`	`....TT...C.....`	`A..CCA..CAAACAA`	`ATCTTATAG......`
`B-Peru`	`C.....G...C....`	`....TT...C.T...`	`A..CCA..CAAACAA`	`ATCTTATAG......`
`B-Bolivia`	`C.....G...C....`	`....TT...C.....`	`A..CCA..CAAACAA`	`ATCTTATAG......`
`B-M092`	`C.G.......C....`	`....T.T.TC.....`	`A..TCA..CAAACAA`	`ATCTTATAT......`
`B-M063`	`C...C..T..C....`	`....T....A.....`	`A..CCA.T.AAATAG`	`ATCATAAAT......`
`b-W23`	`C...C..T..C....`	`....T....A....T`	`AA.CCA.T.AAATAG`	`AT...ATATCATAAA`
`B-bar`	`C...C..T..C....`	`....T....A....T`	`AA.CCA.T.AAATAG`	`AT...ATATCATAAA`
`B-M031`	`----------C..T.`	`....TT...A.....`	`AA..CA..CAAA...`	`...............`
`B-M033`	`C...C.....-----`	`----..---------`	`---------......`	`...............`

	`[ Mako ]`
`position`	`444444444444444`	`444444444444444`	`444444555555555`	`555555555566666`
`of`	`566666666667777`	`777777888888899`	`999999000001112`	`234455668800018`
`polymorphism`	`901234567890123`	`456789012678901`	`234589037890683`	`513518283434892`
`B-I`	`---------GTATAT`	`TTACGATCG------`	`----TACT----AAA`	`A-CACAGT-AGCCTC`
`B-615`	`...............`	`...............`	`...............`	`...............`
`B-Mex7a`	`...............`	`...............`	`...............`	`...............`
`B-M106`	`...............`	`...............`	`...............`	`...............`
`B-Mex7b`	`.GTATTACT......`	`...............`	`...............`	`............G..`
`B-Gua31`	`.............C.`	`.....C.T.......`	`...............`	`..TT.TC........`
`B-marker`	`.............C.`	`.....C.T.......`	`.............C.`	`..TT.TC........`
`B-Mag466`	`.............C.`	`.....C.T.......`	`...............`	`..TT.TC........`
`B-M075`	`.............C.`	`.....C.T.......`	`...............`	`..TT.TC........`
`B-M046`	`.............C.`	`.....C.T.......`	`...............`	`..TT.TC......G.`
`B-Peru`	`.............C.`	`.....C.T.......`	`...............`	`..TT.TCA..G....`
`B-Bolivia`	`.............C.`	`.....C.T.......`	`...............`	`..TT.TC........`
`B-M092`	`.............C.`	`.....C.T.......`	`...............`	`..TT.TC........`
`B-M063`	`.............C.`	`....AC.TATGACTC`	`GCGC.........C.`	`......C....A...`
`b-W23`	`T............C.`	`....AC.TATGACTC`	`GCGC.........C.`	`......C.GT.A...`
`B-bar`	`T............C.`	`....AC.TATGACTC`	`GCGC.........C.`	`......C.GT.A...`
`B-M031`	`.........------`	`---------......`	`....---A......G`	`.ATT.TC........`
`B-M033`	`.............CC`	`.....C.........`	`........TAATG..`	`T...G........GC`

	`[2500]`
`position`	`666667777777777`	`777777777777777`	`777777777777777`	`7888`
`of`	`899990034444444`	`444555555555566`	`666666788888888`	`9111`
`polymorphism`	`647890100123456`	`789012345678901`	`234567312345678`	`4038`
`B-I`	`T-----GTA------`	`---------------`	`------G--------`	`AGGC`
`B-615`	`...............`	`...............`	`...............`	`....`
`B-Mex7a`	`...............`	`...............`	`...............`	`....`
`B-M106`	`...............`	`...............`	`...............`	`....`
`B-Mex7b`	`...............`	`...............`	`.......AGTTGCAT`	`....`
`B-Gua31`	`.......C.......`	`TATATATA.......`	`...............`	`....`
`B-marker`	`.......C.......`	`TATATATATATA...`	`...............`	`....`
`B-Mag466`	`.......C.......`	`...............`	`...............`	`C.CT`
`B-M075`	`.......C.......`	`...............`	`...............`	`C.CT`
`B-M046`	`.......C.......`	`...............`	`...............`	`CACT`
`B-Peru`	`.......C..CTAGT`	`TATATAT........`	`..AGAA.........`	`C.CT`
`B-Bolivia`	`.......C..CTAGT`	`TATATAT.....AGA`	`ATAGAA.........`	`C.CT`
`B-M092`	`.......C.......`	`TA.............`	`...............`	`C.CT`
`B-M063`	`..GGTCAC.......`	`...............`	`...............`	`CACT`
`b-W23`	`..GGTCAC.......`	`...............`	`...............`	`CACT`
`B-bar`	`..GGTCAC.......`	`...............`	`...............`	`CACT`
`B-M031`	`.......C.......`	`TATA...........`	`...............`	`C.CT`
`B-M033`	`TC.....C--.....`	`...............`	`......A........`	`C.CT`

Fig. 6. Polymorphisms in the alignment of b allele sequences. The E-X PCR product from 18 alleles was cloned and sequenced, and the sequences from the E primer to the SacI site at the beginning of intron 1 were aligned. The CLUSTAL W alignment was adjusted by hand and imported in the SITES program (available from Jody Hey, Department of Genetics, Rutgers University, Piscataway, NJ). The polymorphism table from SITES was reformatted and annotated to generate this figure. The first three lines above each block of data (labeled "position of polymorphism") show the numerical position of the polymorphism (the numbers run vertically across the three columns). The data shown indicate only the polymorphic positions. We have indicated the large insertions by the use of square brackets enclosing the name of the element located above the position columns. Only a small portion of the Tourist-Zm23 insertion is shown here. Other than the 1-nt polymorphism shown, the sequence of this insertion is identical in all five alleles in clade III. The direct repeats flanking the Hb2 insertion in B-M033, the Mako insertion in B-Mex7b, and the 2,500-bp insertion in B-Peru and B-Bolivia are indicated; the sequence of these insertions was removed to prevent misalignment. The 29-bp deletion in B-M033 is shown. Along with the 29-bp deletion, this region of B-M033 contains 359 bp of sequence that is not found in any other allele.