"Deeply Altered Genome Architecture in the Endoparasitic Flowering Plan" by Liming Cai, Brian J. Arnold et al.

Faculty Publications

Title

Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)

Authors

Liming Cai, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
Brian J. Arnold, FAS Informatics Group, Harvard University, 38 Oxford Street, Cambridge, MA 02138, USA.
Zhenxiang Xi, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
Danielle E. Khost, FAS Informatics Group, Harvard University, 38 Oxford Street, Cambridge, MA 02138, USA.
Niki Patel, Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA.
Claire B. Hartmann, Bauer Core Facilities, Division of Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
Sugumaran Manickam, Rimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia.
Sawitree Sasirat, Queen Sirikit Botanic Garden, PO Box 7 Mae Rim, Chiang Mai 50180, Thailand.

Document Type

Article

Publication Date

3-8-2021

Abstract

Despite more than 2,000-fold variation in genome size, key features of genome architecture are largely conserved across angiosperms. Parasitic plants have elucidated the many ways in which genomes can be modified, yet we still lack comprehensive genome 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 eurosids are lost in Sapria, dwarfing previously reported levels of gene loss in vascular plants. These losses demonstrate remarkable functional convergence with other parasitic plants, suggesting a common genetic roadmap underlying the evolution of plant parasitism. Second, we identified extreme disparity in intron size among retained genes. This includes a category of genes with introns longer than any so far observed in angiosperms, nearing 100 kb in some cases, and a second category of genes with exceptionally short or absent introns. Finally, at least 1.2% of the Sapria genome, including both genic and intergenic content, is inferred to be derived from host-to-parasite horizontal gene transfers (HGTs) and includes genes potentially adaptive for parasitism. Focused phylogenomic reconstruction of HGTs reveals a hidden history of former host-parasite associations involving close relatives of Sapria's modern hosts in the grapevine family. Our findings offer a unique perspective into how deeply angiosperm genomes can be altered to fit an extreme form of plant parasitism and demonstrate the value of HGTs as DNA fossils to investigate extinct symbioses.

Publication Source (Journal or Book title)

Current biology : CB

First Page

1002

Last Page

1011.e9

Recommended Citation

Cai, L., Arnold, B. J., Xi, Z., Khost, D. E., Patel, N., Hartmann, C. B., Manickam, S., & Sasirat, S. (2021). Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae). Current biology : CB, 31 (5), 1002-1011.e9. https://doi.org/10.1016/j.cub.2020.12.045

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