Grzebelus Dariusz, Yau Yuan-Yeu, Simon Philipp W
Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, 31-425, Krakow, Poland.
Mol Genet Genomics. 2006 May;275(5):450-9. doi: 10.1007/s00438-006-0102-3. Epub 2006 Feb 16.
Members of a novel Master family of class II transposons were identified in the carrot genome. Two elements, 2.5 kb long DcMaster1 and 4.4 kb long DcMaster-a, are characterized by 22 bp imperfect terminal inverted repeats and by 3 bp target site duplications. GenBank search revealed that related elements are also present in Medicago truncatula, including a 5.1 kb element MtMaster-a. Both DcMaster-a and MtMaster-a contain open reading frames encoding for putative transposases with the complete DDE domain typical for plant class II transposable elements belonging to PIF/Harbinger superfamily, where the Master elements form a distinct group. Less than 10 copies of the DcMaster element containing the DDE domain are present in genomes of carrot and other Apiaceae, but more copies with internal deletions or insertions may occur. DcMaster elements were associated with putative coding regions in 8 of 14 identified insertion sites. PCR amplification of carrot genomic DNA using a primer complementary to TIRs of DcMaster gave products < 400 bp in size. We speculate that these may all represent a MITE-like family of transposable elements that we named Krak, present in the carrot genome in at least 3,600 copies.
在胡萝卜基因组中鉴定出了一个新型II类转座子的Master家族成员。两个元件,2.5 kb长的DcMaster1和4.4 kb长的DcMaster-a,其特征是具有22 bp的不完全末端反向重复序列和3 bp的靶位点重复序列。GenBank搜索显示,蒺藜苜蓿中也存在相关元件,包括一个5.1 kb的元件MtMaster-a。DcMaster-a和MtMaster-a都包含开放阅读框,编码推定的转座酶,具有属于PIF/Harbinger超家族的植物II类转座元件典型的完整DDE结构域,其中Master元件形成一个独特的群体。在胡萝卜和其他伞形科植物的基因组中,含有DDE结构域的DcMaster元件不到10个拷贝,但可能会出现更多有内部缺失或插入的拷贝。在14个已鉴定的插入位点中的8个位点,DcMaster元件与推定的编码区域相关联。使用与DcMaster的TIR互补的引物对胡萝卜基因组DNA进行PCR扩增,得到大小小于400 bp的产物。我们推测,这些可能都代表了一个类似微型反向重复转座元件(MITE)的转座元件家族,我们将其命名为Krak,在胡萝卜基因组中至少有3600个拷贝。