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Retrotransposons contribute significantly to the size, organization, and genetic diversity of their host genomes. To characterize novel retrotransposon families in pigeonpea and develop retrotransposon-based sequence-specific amplification polymorphic markers, in silico homology sequence search was carried out against the whole genome shotgun sequence of pigeonpea variety Asha (ICPL87119). For homology searching, 5 copia-like retro elements belonging to soybean, common bean, mungbean, chickpea, and field pea were used as query sequences. Contigs with at least 80% query coverage and &gt;70% similarity were searched for retroelements using the long terminal repeat finder. A total of 28 copia-like retroelements were identified using this method. Multiple sequence alignment for the reverse transcriptase domain indicated conserved reverse transcriptase domains in all 28 elements compared with other reported elements. Phylogenetic analysis based on reverse transcriptase domains revealed 11 families. The copy number per family ranged from 1 (for B, J, and K family) to 8 (I). The sequence-specific amplification polymorphic marker-based insertion site profiling for one of the retrotransposon families (G) confirmed multiple insertions of this element across the pigeonpea genome. This study showed that our in silico homology search strategy was efficient for identifying and characterizing the Ty1/copia-like retrotransposon. The results of this study are useful for developing retrotransposon-based sequence-specific amplification polymorphic markers for pigeonpea crop improvement.

Characterization of Ty1/copia-like retrotransposon families from pigeonpea genome