Abstract Detail

Comparative Genomics/Transcriptomics

Cai, Liming [1], Arnold, Brian [2], Xi, Zhenxiang [3], Khost, Danielle E. [4], Patel, Nikisha [5], Hartmann, Claire B. [6], Manickam, Sugumaran [7], Sasirat, Sawitree [8], Nikolov, Lachezar [9], Mathews, Sarah [10], Sackton, Timothy B. [4], Davis, Charles [11].

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 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.

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Article

1 - Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA, 02138, United States
2 - Harvard University, Organismic And Evolutionary Biology, 8 Plympton St, Apt 38, Cambridge, MA, 02138, United States
3 - Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Chengdu, Sichuan, China
4 - Harvard University, FAS Informatics Group, Cambridge, MA, 02138, USA
5 - University of Connecticut, Department of Ecology and Evolutionary Biology, Storrs, CT, 06269, USA
6 - Harvard University, Bauer Core Facilities, Division of Science, Cambridge, MA, 02138, USA
7 - University of Malaya, Rimba Ilmu Botanic Garden, Institute of Biological Sciences, Kuala Lumpur, Malaysia
8 - Queen Sirikit Botanic Garden, Chiang Mai , Thailand
9 - UCLA, Molecular, Cell And Developmental Biology, 610 Charles E Young Dr East, 4018 TLSB Terasaki Life Sciences Building, Los Angeles, CA, 90095, United States
10 - Louisiana State University, Biological Sciences, 202 Life Sciences Building, Baton Rouge, LA, 70803, United States
11 - Harvard University, 22 Divinity Avenue, 22 Divinity Avenue, Cambridge, MA, 02138, United States

Keywords:
horizontal gene transfer
gene loss
codon bias
transposable elements
intron loss.

Presentation Type: Oral Paper
Session: CGT3, Comparative Genomics/Transcriptomics III
Location: /
Date: Tuesday, July 20th, 2021
Time: 4:15 PM(EDT)
Number: CGT3006
Abstract ID:164
Candidate for Awards:Margaret Menzel Award