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Background  Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5′-‘TG’–‘CA’-3′ motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of their structures and evolutionary history.    Results  Here, we report two new LTR-RT subfamilies ( TGTT  and  AACA ) with atypical dinucleotide ends of 5′-‘TG’–‘TT’-3′, and 5′-‘AA’–‘CA’-3′ in pear, apple, peach and mei. In total, 91 intact LTR-RTs were identified and classified into four  TGTT  and four  AACA  families. A structural annotation analysis showed that the four  TGTT  families, together with  AACA1  and  AACA2 , belong to the  Copia -like superfamily, whereas  AACA3  and  AACA4  appeared to be TRIM elements. The average amplification time frames for the eight families ranged from 0.05 to 2.32 million years. Phylogenetics coupled with sequence analyses revealed that the  TGTT1  elements of peach were horizontally transferred from apple. In addition, 32 elements from two  TGTT  and three  AACA  families had detectable transcriptional activation, and a qRT-PCR analysis indicated that their expression levels varied dramatically in different species, organs and stress treatments.    Conclusions  Two novel LTR-RT subfamilies that terminated with non-palindromic dinucleotides at the ends of their LTRs were identified in four Rosaceae species, and a deep analysis showed their recent activity, horizontal transfer and varied transcriptional levels in different species, organs and stress treatments. This work enhances our understanding of the structural variation and evolutionary history of LTR-RTs in plants and also provides a valuable resource for future investigations of LTR-RTs having specific structures in other species.    Electronic supplementary material  The online version of this article (10.1186/s13100-017-0098-8) contains supplementary material, which is available to authorized users.

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TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species