The history and disposition of transposable elements in polyploidGossypium

Abstract

Transposable elements (TEs) are a major component of plant genomes. It is of particular interest to explore the potential activation of TE proliferation, especially in hybrids and polyploids, which often are associated with rapid genomic and epigenetic restructuring. Here we explore the consequences of genomic merger and doubling on copia and gypsy-like Gorge3 long terminal repeat (LTR) retrotransposons as well as on non-LTR long interspersed nuclear elements (LINEs) in allotetraploid cotton, Gossypium hirsutum. Using phylogenetic and quantitative methods, we describe the composition and genomic origin of TEs in polyploid Gossypium. In addition, we present information on ancient and recent transposition activities of the three TE types and demonstrate the absence of an impressive proliferation of TEs following polyploidization in Gossypium. Further, we provide evidence for present-day transcription of LINEs, a relatively minor component of Gossypium genomes, whereas the more abundant LTR retrotransposons display limited expression and only under stressed conditions.

A genome-wide identification and analysis of the DYW-deaminase genes in the pentatricopeptide repeat gene family in cotton (Gossypium spp.)

“…Allotetraploid Gossypium species evolved from two diploid cotton species through hybridizations and genome doubling that occurred 1–2 million years ago [11]. Therefore, diploid and allotetraploid cotton species are useful models for investigating the evolution of plants.…”

“…95% world cotton production) and G . barbadense [11]. The genomes of the two ancestral diploids (i.e., G .…”

Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant–hominin co-evolution back to the Pliocene

“…One approach to test the hypothesis of large amounts of small selective value change is to monitor transposable element composition of genomes over time, assuming that the majority of transposition events are of minor selective consequence. Cotton is an example of a crop in which the evolution of genome architecture can be studied in this way, because evidence from interspecific comparisons suggests that there have been recent significant expansions and contractions of TEs (Hawkins et al, 2006(Hawkins et al, , 2009Hu et al, 2010). Comparison of archaeological and modern samples of cotton shows a startling amount of change in TE composition in Gossypium herbaceum over a short period of time ( Fig.…”

Lessons from Natural and Artificial Polyploids in Higher Plants

“…Variation in the transposon complement between the A-and D-genomes might be predicted to cause hybrids to undergo the process of 'genomic shock' [McClintock, 1984], wherein merging 2 distinct genomes causes a general derepression of transposons and thus a transpositional burst. However, a survey of major LTR retrotransposon families in Gossypium [Hu et al, 2010] showed no evidence of a major burst in transposon activity since the formation of the allopolyploids. Transposon activity in allopolyploids is typically tied to alterations in DNA methylation and hence silencing, but here too, there is little in common between cotton and other allopolyploids such as Spartina or Brassica -use of MSAP shows that, as with structural rearrangement, there is no genome-wide effect in cotton.…”