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Deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae)

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 extrem...

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Main Authors: Cai, Liming, Arnold, Brian J., Xi, Zhenxiang, Khost, Danielle E., Patel, Niki, Hartmann, Claire B., Manickam, Sugumaran, Sasirat, Sawitree, Nikolov, Lachezar A., Mathews, Sarah, Sackton, Timothy B., Davis, Charles C.
Format: Article
Published: Elsevier 2021
Subjects:
QK Botany
SB Plant culture
Online Access:http://eprints.um.edu.my/34491/
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spelling my.um.eprints.344912022-06-13T07:02:50Z http://eprints.um.edu.my/34491/ Deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae) Cai, Liming Arnold, Brian J. Xi, Zhenxiang Khost, Danielle E. Patel, Niki Hartmann, Claire B. Manickam, Sugumaran Sasirat, Sawitree Nikolov, Lachezar A. Mathews, Sarah Sackton, Timothy B. Davis, Charles C. QK Botany SB Plant culture 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 road map 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. Elsevier 2021-03-08 Article PeerReviewed Cai, Liming and Arnold, Brian J. and Xi, Zhenxiang and Khost, Danielle E. and Patel, Niki and Hartmann, Claire B. and Manickam, Sugumaran and Sasirat, Sawitree and Nikolov, Lachezar A. and Mathews, Sarah and Sackton, Timothy B. and Davis, Charles C. (2021) Deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae). Current Biology, 31 (5). ISSN 0960-9822, DOI https://doi.org/10.1016/j.cub.2020.12.045 <https://doi.org/10.1016/j.cub.2020.12.045>. 10.1016/j.cub.2020.12.045
institution Universiti Malaya
building UM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaya
content_source UM Research Repository
url_provider http://eprints.um.edu.my/
topic QK Botany
SB Plant culture
spellingShingle QK Botany
SB Plant culture
Cai, Liming
Arnold, Brian J.
Xi, Zhenxiang
Khost, Danielle E.
Patel, Niki
Hartmann, Claire B.
Manickam, Sugumaran
Sasirat, Sawitree
Nikolov, Lachezar A.
Mathews, Sarah
Sackton, Timothy B.
Davis, Charles C.
Deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae)
description 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 road map 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.
format Article
author Cai, Liming
Arnold, Brian J.
Xi, Zhenxiang
Khost, Danielle E.
Patel, Niki
Hartmann, Claire B.
Manickam, Sugumaran
Sasirat, Sawitree
Nikolov, Lachezar A.
Mathews, Sarah
Sackton, Timothy B.
Davis, Charles C.
author_facet Cai, Liming
Arnold, Brian J.
Xi, Zhenxiang
Khost, Danielle E.
Patel, Niki
Hartmann, Claire B.
Manickam, Sugumaran
Sasirat, Sawitree
Nikolov, Lachezar A.
Mathews, Sarah
Sackton, Timothy B.
Davis, Charles C.
author_sort Cai, Liming
title Deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae)
title_short Deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae)
title_full Deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae)
title_fullStr Deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae)
title_full_unstemmed Deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae)
title_sort deeply altered genome architecture in the endoparasitic flowering plant sapria himalayana griff. (rafflesiaceae)
publisher Elsevier
publishDate 2021
url http://eprints.um.edu.my/34491/
_version_ 1735570306080178176
score 13.211869

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