Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors

Abstract

An allopolyploidization event formed allotetraploid Gossypium species from an A‐genome diploid species and a D‐genome diploid species. To explore the responses of transposable elements (TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes. Gypsy was the most abundant TE type and most TEs were located ∼500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24‐nt small interfering RNAs (siRNAs) that targeted TEs. TEs, particularly those targeted by 24‐nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co‐opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.

Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding

“…Data analysis indicated that the G. arboreum genome tended to harbor more LTRs inserted than G. raimondii genome during the last 0.5 million years (Cheng et al, 2019). G. arboreum genome had the greatest amount of repeat-containing sequences among sequenced cottons, and LTRs accounted for 95.12% of all repeat sequences (Cheng et al, 2019). In comparison to the G. raimondii genome, the G. arboreum genome had noticeable proliferation of Gorge elements.…”

“…They account up to 57% (441Mb) of the G. raimondii genome, mainly the gypsy and copia-like long terminal repeat (LTR), a type of retrotransposons, which explains much of the expansion of the G. raimondii genome. Data analysis indicated that the G. arboreum genome tended to harbor more LTRs inserted than G. raimondii genome during the last 0.5 million years (Cheng et al, 2019). G. arboreum genome had the greatest amount of repeat-containing sequences among sequenced cottons, and LTRs accounted for 95.12% of all repeat sequences (Cheng et al, 2019).…”

Evolutionary dynamics of transposable elements and satellite DNAs in polyploid Spartina species

“…Nevertheless, allopolyploids of different ages (i.e. recent to millions of years), show evidence for differential TE amplification and elimination [49][50][51][52][53]. It might be expected that genome redundancy in polyploids would buffer against the mutagenic impact of TE activity [19,26,40].…”

Plant polyploidy and evolution

“…Most TEs were located ∼500 bp away from genes and the highest fraction of unique match 24‐nt small interfering RNAs (siRNAs) that targeted TEs was detected in G. hirsutum . TEs were associated with reduced gene expression, particularly those TEs targeted by 24‐nt siRNAs (Cheng et al ). Ethylene is a key modulator of cotton fiber cell growth (Shi et al ).…”

“…Copia-like long terminal repeat-retrotransposable elements have maintained considerable activity in both G. arboreum and G. hirsutum. ChIP-qPCR (chromatin immunoprecipitation followed by quantitative polymerase chain reaction), using a copia-specific antibody, established that copia-like proteins primarily bind to the first exons of several protein-coding genes in cotton (Lin et al 2019). Using assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii, scientists analyzed different TE fractions and the effects of TEs on ortholog expression among Gossypium species.…”