A profoundly altered genome architecture in the endoparasitic flowering plant Sapria himalayana Griff. (Rafflesiaceae)

This article was originally published here

Curr Biol. 2021 Jan 23: S0960-9822 (20) 31897-2. doi: 10.1016 / j.cub.2020.12.045. Online before printing.

SUMMARY

Despite more than a 2000-fold variation in genome size, major features of genome architecture are largely preserved through angiosperms. Parasitic plants have elucidated the many ways to modify genomes, yet we still lack comprehensive genomic data for species that represent the most extreme form of parasitism. Here we present the highly modified genome of the iconic endophytic parasite Sapria himalayana Griff. (Rafflesiaceae), which lacks a typical plant body. First, 44% of the genes conserved in eurids are lost in Sapria, dwarf previously reported levels of gene loss in vascular plants. These losses show remarkable functional convergence with other parasitic plants, suggesting a common genetic roadmap under the development of plant parasitism. Second, we identified extreme inequality in intron size between retained genes. This includes a category of genes with introns longer than some hitherto observed in angiosperms, nearly 100 kb in some cases, and a second category of genes with exceptionally short or absent introns. Finally, at least 1.2% of the genus Sapria, including both gene and intergenic content, is concluded to be derived from host to parasite horizontal gene transfers (HGTs) and include genes potentially adaptive for parasitism. A focused phylogenomic reconstruction of HGTs reveals a hidden history of former host-parasitic associations involving close relatives of the modern hosts of Sapria in the vine family. Our findings offer a unique perspective on how deeply angiosperm genomes can be altered to match an extreme form of plant parasitism and demonstrate the value of HGT as DNA fossils to investigate extinct symbioses.

PMID: 33485466 | DOI: 10.1016 / j.cub.2020.12.045

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