Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database.
Bottom Line: Transposable elements (TEs) are major components of plant genome and are reported to play significant roles in functional genome diversity and phenotypic variations.A total of 30,706 TEs were identified and classified as DNA transposons (24,386), full-length Copia type (1,038), partial or solo Copia type (10,118), full-length Gypsy type (1,570), partial or solo Gypsy type (23,293) and Long- and Short-Interspersed Nuclear Elements (3,659 and 53, respectively).A total of 134 Repeat Junction Markers were screened in 96 accessions of Setaria italica and 3 wild Setaria accessions of which 30 showed polymorphism.
Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.Show MeSH
Mentions: Retrotransposons were found to be transcriptionally active in all the four tissues, namely leaf, root, spica and stem (Fig. 2; Supplementary Tables S11–S15). A maximum of Copia-type TEs (∼80%) matched with RNA-HiSeq reads which revealed that Copia-type TEs were prevalently expressed in tissues of foxtail millet. Approximately 49% of Gypsy-type retrotransposons matched with RNA-HiSeq reads. Similarly, ∼10% LINEs, ∼15% SINEs and ∼16% DNA transposons matched with the expressed reads (Fig. 2; Supplementary Tables S11–S15).Figure 2.
Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.