Abundant retrotransposons in the onion and asparagus genomes

Monocotyledonous plants are divided into 11 orders: Acorales, Alismatales, Petrosaviales, Dioscoreales, Pandanales, Liliales, Asparagales, Arecales, Poales, Commelinales and Zingiberales, the last four being grouped into the Commelinid clade. Among these, the Asparagales may be the second most important for agriculture and horticulture after the Poales (grasses). The Asparagales includes the Orchidaceae with >30,000 species, but also includes important crops such as aloe (Aloe vera), agave (Agave tequilana), asparagus (Asparagus officinalis), garlic (Allium sativum), leek (Allium ampeloprasum), onion (Allium cepa) and vanilla (Vanilla planifolia), as well as ornamental plants such as yuccas, amarylids, daffodils, irises. With an annual world production of >95 Mt, it is the third most cultivated group for vegetable production in the world after the Solanales (including potato, tomato, pepper and aubergine) and the Cucurbitales (including melons, cucumbers and gourds).

To extend our understanding of genome evolution in the monocots, a recent paper in Annals of Botany examines the asparagus and onion genomes, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons. The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Some families have become particularly abundant, as high as 4–5 % (asparagus) or 3–4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize. Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, these results show that this was largely due to the methodology used. In contrast, this work indicates an ensemble of genomic features similar to those observed in the Poaceae.