Identification of a genome-specific repetitive element in the Gossypium D genome

Abstract

The activity of genome-specific repetitive sequence is the main cause of the genome variation between Gossypium A and D genomes. Through the comparative analysis of the two genomes, we got a repetitive element (ICRd motif), which repeats massively in the diploid Gossypium raimondii (D5) genome while almost absent in the diploid Gossypium arboreum (A2) genome. We further explored the existence of ICRd motif in G. raimondii, G. arboreum, and two tetraploids (AADD) cotton G. hirsutum and G. barbadense by fluorescence in situ hybridization (FISH), and observed the ICRd motif exists in D5 and D-subgenomes but not in A2 and A-subgenome. The ICRd motif was investigated through its two constituents , a length variable tandem repeat region (TR) and a conservative sequence (CS), which highly repeat and evenly distribute in chromosomes of D5 genome. The ICRd motif was revealed as the common conservative region of ancient LTR-TEs. The identifications and investigation of the ICRd motif promote the study on the A and D genome differences, facilitate the research on the Gossypium genome evolution, and provide assistance to subgenome identification and genome assembling.

Chromosome Painting Based on Bulked Oligonucleotides in Cotton

“…Owing to the removal of repetitive sequences from the oligo sets, the two oligo probes produced clear signals without background noise on the chromosome 7 when hybridized to chromosomes of G. raimondii and its relative species (Figures 2A-D). At the same time, high proportions of repetitive sequences in the pericentromeric heterochromatic region of chromosomes (Liu et al, 2016;Lu et al, 2019) caused the disappearance of oligos in the middle region of the chromosome (Figure 1), which led to the signals of the oligo probes not diffusing the whole chromosome arms, and only appeared at the two end regions of chromosome (Figure 2). Moreover, the homoeologous chromosomes of G. raimondii chromosome 7 in allotetraploid cotton were unambiguously identified using the designed oligo probes (Figures 2G-I).…”