Dynamics of mobile element activity in chalcone synthase loci in the common morning glory (Ipomoea purpurea)

Abstract

Mobile element dynamics in seven alleles of the chalcone synthase D locus (CHS-D) of the common morning glory (Ipomoea purpurea) are analyzed in the context of synonymous nucleotide sequence distances for CHS-D exons. By using a nucleotide sequence of CHS-D from the sister species Ipomoea nil (Japanese morning glory [Johzuka-Hisatomi, Y., Hoshino, A., Mori, T., Habu, Y. & Iida, S. (1999) Genes Genet. Syst. 74, 141-147], it is also possible to determine the relative frequency of insertion and loss of elements within the CHS-D locus between these two species. At least four different types of transposable elements exist upstream of the coding region, or within the single intron of the CHS-D locus in I. purpurea. There are three distinct families of miniature inverted-repeat transposable elements (MITES), and some recent transpositions of Activator/Dissociation (Ac/Ds)-like elements (Tip100), of some short interspersed repetitive elements (SINEs), and of an insertion sequence (InsIpCHSD) found in the neighborhood of this locus. The data provide no compelling evidence of the transposition of the mites since the separation of I. nil and I. purpurea roughly 8 million years ago. Finally, it is shown that the number and frequency of mobile elements are highly heterogeneous among different duplicate CHS loci, suggesting that the dynamics observed at CHS-D are locus-specific.

Figure 1

Unrooted neighbor-joining phylogram based on CHS-D coding sequences estimated by using the Kimura 2-parameter model. Numbers below nodes represent bootstrap percentages (1,000 replicates). Sequences for US1 and KKFR35N are identical.

Figure 2

An allele of CHS-D from I. nil (boxed) and alleles from individuals of I. purpurea collected from populations in the United States and Mexico are diagrammed showing insertion elements and conserved published regulatory elements. The previously published I. purpurea CHS-D allele is shown at Bottom (KKFR35N).

Figure 3

Distribution of Tip100 elements in alleles of CHS-D. Sequence data were not available for the KKVR40 CHS-D and KKWP3 CHS-D alleles and therefore were not included in the data analysis. In addition, sequence data were not available for the Tip100 elements in KKWP3.

Figure 4

Insertion elements in different I. purpurea CHS gene family members.