Abstract
The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.
Highlights
Repetitive DNA sequences are common in eukaryotic genomes, account for a huge fraction of the host genome (Ibarra-Laclette et al, 2013) and are highly correlated with the size of the host genome (Feschotte, 2008)
Manual inspection revealed the structure of the genome-specific sequence having two constituents, a tandem repeats array composed of 133 bp basic units, and an unknown conservative sequence (Figure 1)
Among the 72 ICRd motifs, the tandem repeat region (TR) are length-variable having a variety of the basic unit content that 2-20 basic units (Figure 2a), while the conservative sequence (CS) are stable and have an average size ~ 860 bp
Summary
Repetitive DNA sequences are common in eukaryotic genomes, account for a huge fraction of the host genome (Ibarra-Laclette et al, 2013) and are highly correlated with the size of the host genome (Feschotte, 2008). DNA can be divided into two major groups by their structures: tandem repeats and interspersed repeats (Jurka et al., 2005). The Interspersed repeats were called as transposable elements (TEs) or transposons. TEs play important roles in such as variations in intron size (Deutsch & Long, 1999; Zhang et al, 2011; Koonin, Csuros & Rogozin, 2013), segmental duplication (Del Pozo & Ramirez-Parra, 2015), transfer of organelle DNA to the nucleus Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer
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