Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization

Abstract

Mobile elements constitute a considerable part of the eukaryotic genome. This work is focused on the distribution and evolution of DNA-transposons in the genomes of diploid and allopolyploid Triticeae species and their role in the formation of functionally important chromosomal subtelomeric regions. The Caspar family is among the most abundant of CACTA DNA-transposons in Triticeae. To study the evolution of Caspar-like elements in Triticeae genomes, we analyzed their sequences and distribution in chromosomes by in situ hybridization. In total, 46 Caspar-like elements from the wheat and barley Caspar, Clifford, and Donald families were analyzed after being extracted from databases using the transposase consensus sequence. Sequence alignment and subsequent phylogenetic analyses revealed that the transposase DNA sequences formed three major distinct groups: (1) Clifford, (2) Caspar_Triticinae, and (3) Caspar_Hordeinae. Additionally, in situ hybridization demonstrated that Caspar_Triticinae transposons are predominantly compartmentalized in the subtelomeric chromosomal regions of wheat and its progenitors. Analysis of data suggested that compartmentalization in the subtelomeric chromosomal region was a characteristic feature of all the main groups of Caspar-like elements. Furthermore, a dot plot analysis of the terminal repeats demonstrated that the divergence of these repeats strictly correlated with the divergence of Caspar coding sequences. A clear distinction in the Caspar DNA sequences among the species Triticum/Aegilops (Caspar_Triticinae), Hordeum (Caspar_Hordeinae), and different distributions in individual hexaploid wheat genomes (A/B and D) suggest an independent proliferation of these elements in wheat (or its progenitors) and barley genomes. Thus, Caspar-like transposons can significantly contribute to the formation and differentiation of subtelomeric regions in Triticeae species.

Repetitive DNA: A Versatile Tool for Karyotyping in<b><i> Festuca pratensis</i></b> Huds.

“…In this work, most of the mobile DNA elements were dispersed along all fescue chromosomes. This agrees with previous reports in other plant species [Wicker et al, 2003;Hřibová et al, 2010;Sergeeva et al, 2010;Akiyarma et al, 2012]. The strongest hybridization signals were obtained for the Athila retroelement (CL6) from the Ty3/gypsy family, indicating that it is the most abundant DNA repeat in the meadow fescue genome.…”

“…Caspar -like elements, members of the CACTA family of DNA transposons, were identified in high copy number in different Triticeae genomes including Hordeum sp., Triticum spp., Aegilops spp., and Secale sp. [Wicker et al, 2003[Wicker et al, , 2009Zhang et al, 2004;Sergeeva et al, 2010]. While several CACTA DNA transposons are dispersed in Triticeae chromosomes [Raskina et al, 2004;Altinkut et al, 2006], Caspar elements predominantly localize in subtelomeric regions [Sergeeva et al, 2010].…”

“…[Wicker et al, 2003[Wicker et al, , 2009Zhang et al, 2004;Sergeeva et al, 2010]. While several CACTA DNA transposons are dispersed in Triticeae chromosomes [Raskina et al, 2004;Altinkut et al, 2006], Caspar elements predominantly localize in subtelomeric regions [Sergeeva et al, 2010]. An active utilization of recombination processes for transposition was proposed as the most probable mechanism responsible for the increased abundancy of the Caspar element in subtelomeric regions of Triticeae genomes [Sergeeva et al, 2010].…”

“…While several CACTA DNA transposons are dispersed in Triticeae chromosomes [Raskina et al, 2004;Altinkut et al, 2006], Caspar elements predominantly localize in subtelomeric regions [Sergeeva et al, 2010]. An active utilization of recombination processes for transposition was proposed as the most probable mechanism responsible for the increased abundancy of the Caspar element in subtelomeric regions of Triticeae genomes [Sergeeva et al, 2010]. In contrast to the Caspar -like element, one putative LTR element identified previously in 4F sequence data [Kopecký et al, 2013] preferentially localized to centromeric regions.…”

New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents

“…The diverse sites of the TEs in the Triticeae chromosomes have enabled the identification of wheat and related species by in situ hybridization (Li et al 2004;Stein 2007). Sergeeva et al (2010) isolated the Caspar family among the most abundant of CACTA DNA-transposons in wheat, which significantly contributed to the formation and differentiation of subtelomeric regions in Triticeae species revealed by FISH. We noted that the Conan and Clifford family of CACTA TEs was most abundant in Ps.…”