The origin of the peanut

Peanuts or groundnuts (Arachis hypogaea) originate from South America but are now a major food crop world wide, with an annual production of around 38 million tonnes. They are grown throughout the tropics and sub-tropics, but are most important in Asia and Africa. Within the Papilionoid legumes, peanut belongs to the Dalbergioids, a clade separated from most other economically important legumes (peas and beans) by an estimated 55 million years of evolution. They have 2n = 20 as an ancestral chromosome number and most Arachis species have 2n = 2x = 20 chromosomes, but A. hypogaea is an exception in having 40 chromosomes. It is a recent allotetraploid, most probably resulting from the hybridization of two wild species followed by natural chromosome duplication.

A recent paper in Annals of Botany examines the evolution of the A. hypogaea genome, focusing on its highly repetitive component. The authors find that a substantial proportion of the repetitive content appears to be accounted for by relatively few long terminal repeat (LTR) retrotransposons and their truncated copies. The retrotransposons described are all transcribed, although levels are low. They conclude that the activity of these retrotransposons has been a very significant driver of genome evolution since the divergence of the peanut A and B genomes.

It is an intriguing feature of eukaryotic genomes that genes which have the greatest functional significance occupy only a small fraction of the whole; repetitive DNA occupies most of the genome and determines the large-scale structure of the chromosomes. The repetitive fraction of plant genomes has perhaps been most studied in cereal genomes, where retrotransposon activity has resulted in variation of cereal genome sizes. Previously work estimated that the peanut A and B genomes diverged about 3–3·5 Mya. Only very recently were they bought together by a polyploidy event, probably in pre-historical times. This study shows that a substantial proportion of the highly repetitive component of the A genome of peanut is accounted for by relatively few LTR retrotransposons. Three of the most abundant elements are non-autonomous, and two of these appear to harbour ‘hitchhiking’ ORFs, in one case with retrotransposon-related function, and in the other with a biological function that remains to be identified. Retrotransposons and other repetitive DNAs have played an important part in genome remodelling, especially in intergenic regions, over evolutionary time.