Supplemental text
Transposon structure of bz haplotypes
We use either sequence names or a combination of generic TE type and number
to designate the TE insertions. Seventeen new LTR-retrotransposons, four in
Tripsacum, eight in Coix, one in Zea diploperennis and four in Sorghum, were identified.
Zea mays, ssp. mays KYS inbred. Two Helitrons are inserted in the tac6058
gene, whose transcript is probably a noncoding RNA (Fu et al. 2001): the 469-bp Hel1-4
is shared with A188 and mexicana haplotype 2 and the 5.5-kb Hel1-7, named
sequentially after other bz region Helitrons (Wang and Dooner 2006), carries fragments
from two different genes. Seven different large elements have inserted in the
hypervariable hypro1-znf intergenic region. Starting from the proximal (left) side, these
are: a 17.2-kb Huck2-Ruda double-decker retroelement (RE) cluster; a 1.3-kb Ji1 soloLTR; a 1.9-kb hAT DNA transposon; a 1-kb Hel1-5 Helitron; an ancient Hopscotch gagpol fragment, reduced to variable extents in the different Zea species that retain this
region; an 18-kb insertion consisting of a 12-kb Huck2 LTR RE piggybacked on a 6-kb
LINE nonLTR RE; and a 3.6-kb Milt RE. KYS shares with several other lines the single
12.4-kb Grande1 element between the znf and tac7077 genes.
Zea mays, ssp. mexicana haplotypes 1 and 2. The two haplotypes share only
the conserved Hopscotch gag-pol fragment in the hypro1-znf intergenic region and the 1
Myr-old Grande1 RE in the znf-tac7077 intergenic region, but these old insertions are
differentially interrupted by more recent RE insertions in each haplotype (LTR RE
insertion dates in Supplemental Table S1): the former by an Opie2 RE in haplotype 2
and the latter by an Opie3 RE in haplotype 1 and a Xilon RE in haplotype 2. Many
unique insertions not previously found in any of the 9 maize bz haplotypes analyzed so
far are present in the Chalco teosinte haplotypes. Haplotype 1 has a 0.4-kb hAT
element in the bz-stc1 intergenic region; two single Elote2 REs, one inserted in the third
intron of rpl35A, from where it is probably spliced out, and another in the znf-tac7077
intergenic region; a 4.97-kb PIF DNA transposon in the last exon of the tac6058 gene;
and two complex additional insertions in the hypro1-znf intergenic region: a 15.2-kb
double-decker Ji3-Ruda retrocluster and a 3.7-kb Hel1-8 Helitron carrying several gene
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fragments. Haplotype 2 has two small hAT elements in the bz-stc1 intergenic region,
one of which is shared with haplotype 1; two agenic Helitrons, a 625-bp Hel1-9 in the
bz-stc1 intergenic region and the Hel1-4 in tac6058 shared with KYS; a TAFT1 element
in the hypro1-znf intergenic region, previously reported in the CIMMYT line CML258
(Wang and Dooner 2006); a 30-kb retrocluster with a Huck1 RE in the first layer
disrupted by insertions of Opie3 and Ji4 REs in the second layer, and two short hAT
elements in different introns of the uce2 gene.
Zea luxurians. Five different insertions lie in the 80-kb bz-stc1 intergenic region.
From proximal to distal end, these are a 3.5-kb hAT element; a 13.3-kb Huck2 RE; a
22.1-kb Tekay-Tekay double-decker retrocluster, missing the 3’-LTR of the upper-level
element; an 8.1-kb Opie1 RE; and a 30-kb RE cluster with Prem1r4 at the base and Ji4
and Opie1 at the top.
Zea diploperennis. All the LTR REs, as well as the DNA elements, have
counterparts in maize. The 31-kb bz-stc1 intergenic region has two large insertions: a
9.4-kb Ji4 RE and an 8.4-kb gene-fragment-bearing Helitron, Hel1-10, that also carries
a 12.9-kb Xilon RE. The hypro1-znf intergenic region contains a novel 15.5-kb Hel1-11
element and just 250 bp of the Hopscotch gag-pol fragment. Interestingly, Hel1-11 is
inserted into the same stretch of TA repeats as is TAFT1 in mexicana haplotype 2 and
other haplotypes, indicating that some host sequences may be prone to visitation by
TEs of different superfamilies. Hel1-11 carries three different gene fragments, the last
of which bears a 9-kb Opie1 RE. The ends of Hel1-11 are most closely related to those
of the Helitron element in the ba-1R mutation (Gupta et al. 2005). They are 82%
identical over the 3’ terminal 115 bp and 65% identical over the 5’ terminal 53 bp.
However, the two Helitrons have captured different gene fragments. A 53.6-kb
branched, multilayered transposon tree is inserted between znf and tac7077. The tree
has a doubly branched Elote2 element at its base. The 16.9-kb proximal branch
contains a CACTA DNA element in the second layer interrupted by a Ji4 RE in the third
layer. The 30.8-kb distal branch contains a Cocopi (Nahuatl for teosinte) RE, distantly
related to Huck1, in the second layer and an Opie1 and Ji4 element in the third layer.
Tripsacum dactyloides. Flanking bz on the proximal side of the T. dactyloidesBz BAC clone (not shown in Fig. 2) is a 12-kb intact TDRE1 (Tripsacum dactyloides
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retroelement). A note on RE nomenclature is warranted here. All the LTR sequences
of Tripsacum retrotransposons differ from those in maize by more than the 20% identity
criterion recently recommended for naming LTR retrotransposons families (Wicker et al.
2007). However, in order to indicate obvious relationships between REs of the sister
genera Zea and Tripsacum, we have applied in this instance the less stringent criterion
of 50% identity originally suggested for maize (SanMiguel and Bennetzen 1998). New
REs were named TDRE1 to TDRE4 and related REs were named after those in maize.
Flanking the fractured stc1 gene on the distal side is a 14.5-kb intact TDRE2. In the
distal T. dactyloides-tac7077 Not I BAC clone, the 42-kb uce2–pme intergenic region
(not shown in Fig. 2, but available in GenBank) contains a 3.4-kb Mu-like DNA
transposon and a 32.4-kb three-layer retrocluster containing a TDRE3 element in the
first, a TDRE4 element in the second, and two different REs with LTRs more closely
related to those in Zea in the third: a 7.7-kb Prem-like element and an 8.2-kb Opie-like
element.
Coix lacryma-jobi. Several LTR-RE insertions are present in the two BACs,
which we have named CLREs. The 102.9-kb bz-stc1 intergenic region in the Bz BAC,
the largest so far sequenced, has five different simple and compound CLREs: a 9.5-kb
CLRE1; a 22.9-kb CLRE2-CLRE3 double-decker retrocluster, with a solo-LTR inserted
in the 3’-LTR of CLRE3; a 32-kb CLRE4; a 10-kb CLRE5; and a 5.4-kb CLRE6. The
5.6-kb CLRE7 in the fifth intron of stc1 is the only Coix retroelement inserted in a gene.
In the tac7077 BAC clone, there are two insertions: a 14.2-kb CLRE8 in the znf-tac7077
intergenic region, and a 1.1-kb CLDE1, a Coix unclassified DNA element (DE), in the
last intron of uce2 gene.
Sorghum propinquum. There are fewer transposons in S. propinquum than in
any of the other species examined so far. A 5-kb RE named SPRE1 is inserted in the
hypro1-meiosis5 intergenic region, an 8-kb SPRE2 RE in the meiosis5–znf intergenic
region, and a 1.9-kb solo-LTR in the znf-tac7077 intergenic region. We also identified
two DNA elements, an 8.2-kb MULE in the znf-tac7077 intergenic region and a 3-kb
unclassified DNA element, SPDE1, in the tac7077-uce2 intergenic region.
Sorghum bicolor. The same genes are present in S. propinquum and S.
bicolor, but the transposons differ. There are two single LTR-retrotransposons in S.
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bicolor, both inserted in introns: a 14.6-kb SBRE1 RE and a 5.3-kb SBRE2 RE. No DEs
other than small insertions were identified in the S. bicolor bz region.
REFERENCES
Fu, H., Park, W., Yan, X., Zheng, Z., Shen, B. and Dooner, H.K. (2001) The highly
recombinogenic bz locus lies in an unusually gene-rich region of the maize
genome. Proc. Natl. Acad. Sci. USA, 98, 8903-8908.
Gupta, S., Gallavotti, A., Stryker, G.A., Schmidt, R.J. and Lal, S.K. (2005) A novel
class of Helitron-related transposable elements in maize contain portions of
multiple pseudogenes. Plant Mol. Bio., 57, 115-127.
SanMiguel, P. and Bennetzen, J.L. (1998) Evidence that a recent increase in maize
genome size was caused by the massive amplification of intergene
retrotransposons. Ann. Botany, 82, 37-44.
Wang, Q. and Dooner, H.K. (2006) Remarkable variation in maize genome structure
inferred from haplotype diversity at the bz locus. Proc. Natl. Acad. Sci. USA, 103,
17644-17649.
Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell,
A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P. and
Schulman, A.H. (2007) A unified classification system for eukaryotic
transposable elements. Nat Rev Genet, 8, 973-982.
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