Computational prediction and molecular confirmation of Helitron transposons in the maize genome

BMC Genomics

Table 2 Molecular Verification of Helitrons

Germplasm	Silico 1	Silico 2	Silico 3	Silico4
4Co63	Vacant	Occupied	x	Vacant
A188	x	x	x	Vacant
A636	Vacant	Occupied	Occupied	Vacant
B73	Vacant	Occupied	Occupied	Vacant
BSSS53	Occupied	x	x	Vacant
McC	Vacant	Occupied	Vacant	Occupied
H99	Vacant	Vacant	x	Vacant
M14	Vacant	Occupied	x	Occupied
Mo17	Vacant	Vacant	x	Vacant
W22	Vacant	Occupied	Vacant	x
W23	Occupied	x	Vacant	Occupied
CML139			x	Vacant
I137 TN			x	Vacant
Ki3			x	x
bz-R			Vacant	Vacant

Silico 1, Silico 2, Silico 3, and Silico 4 are Helitron candidates predicted by the HelitronFinder program. 4Co63, A188, A636, B73, BSSS53, H99, M14, Mo17, W22, W23, CML139, I137 TN, and Ki3 are inbred lines. McC and bz-R are genetic lines. Vacant: amplified PCR product lacks a Helitron.
Occupied: amplified PCR product contains a Helitron, which was confirmed by sequencing.
X: no PCR product detected.
Blank: line not tested for the corresponding Helitron candidate.
The PCR products highlighted in yellow have been cloned and sequenced for further confirmation.

ISSN: 1471-2164