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.Further, 20,278 TE-based markers were developed, namely Retrotransposon-Based Insertion Polymorphisms (4,801, ∼24%), Inter-Retrotransposon Amplified Polymorphisms (3,239, ∼16%), Repeat Junction Markers (4,451, ∼22%), Repeat Junction-Junction Markers (329, ∼2%), Insertion-Site-Based Polymorphisms (7,401, ∼36%) and Retrotransposon-Microsatellite Amplified Polymorphisms (57, 0.2%).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: TEs are reported to play a crucial role in gene evolution by disrupting the genes. Upon getting integrated into the genome, TEs mediate chromosomal rearrangements, leading to accumulation of mutations and ultimately become transpositionally inactive. The presence of TEs was searched in the introns of 45,735 protein-coding genes of foxtail millet. Approximately 12% genes of foxtail millet were found to be integrated with TEs, of which ∼0.75% genes had Copia-type retrotransposons, ∼1% genes had Gypsy type, ∼3% genes had LINEs and ∼6% genes were interrupted with DNA transposons (Table 1). LINEs (1,497 interrupted genes) and DNA transposons (830 genes with PIF-Harbinger and 635 genes with TcMar-Stowaway) were observed to be predominantly integrated within genic region. Similar phenomenon of TE insertion in intronic region was also observed in sorghum, maize, rice and Brachypodium (Fig. 5; Table 1). Further, the patterns of the nested TEs (the insertion of TEs into pre-existing TEs) for all the types of retrotransposons were analysed. A total of 4,927 inserted TEs were found to be inserted within 2,078 host TEs, thus revealing that >1 TE inserted into a single host TE. Of the total inserted TEs, 6.3% (308) was found to be inserted in RC/Helitron, 13.66% (673) in DNA/CMC-EnSpm, 11.26% (555) in DNA/En-Spm, 0.37% (18) in DNA/hAT-Ac, 0.30% (15) in DNA/MULE-MuDR, 0.41% (20) in DNA/TcMar-Stowaway, 3.75% (185) in DNA/PIF-Harbinger, 0.26%, (13) in DNA/Tourist, 0.52% (26) in LINE/L1, 26.91% (1,326) in Copia and 36.28% (1,788) in Gypsy (Supplementary Fig. S8). It has been reported that the movement of TEs in genomes results in the occurrence of nested TEs.43 These nested TEs in foxtail millet genome may negatively influence genome expansion and enrich the diversity of gene expression or regulation.Table 1.
Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.