Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

Sancho, Rubén; Inda, Luis A.; Díaz‐Pérez, Antonio; Des Marais, David L.; Gordon, Sean; Vogel, John P.; Lusinska, Joanna; Hasterok, Robert; Contreras‐Moreira, Bruno; Catalán, Pilar

doi:10.1111/tpj.15650

Title: Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

Journal Article · 23 December 2021 · The Plant Journal

DOI: https://doi.org/10.1111/tpj.15650 · OSTI ID:1982923

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University of Zaragoza (Spain); Spanish National Research Council (CSIC) (Spain)
University of Zaragoza (Spain)
University of Zaragoza (Spain); Central Univ. of Venezuela (Venezuela)
Harvard Univ., Boston, MA (United States). Arnold Arboretum
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
University of Silesia, Katowice (Poland)
Spanish National Research Council (CSIC) (Spain)

Unraveling the evolution of plant polyploids is a challenge when their diploid progenitor species are extinct or unknown or when genome sequences of known progenitors are unavailable. Existing subgenome identification methods cannot adequately infer the homeologous genomes that are present in the allopolyploids if they do not take into account the potential existence of unknown progenitors. We addressed this challenge in the widely distributed dysploid grass genus Brachypodium, which is a model genus for temperate cereals and biofuel grasses. We used a transcriptome-based phylogeny and newly designed subgenome detection algorithms coupled with a comparative chromosome barcoding analysis. Our phylogenomic subgenome detection pipeline was validated in Triticum allopolyploids, which have known progenitor genomes, and then used to infer the identities of three subgenomes derived from extant diploid species and four subgenomes derived from unknown diploid progenitors (ghost subgenomes) in six Brachypodium polyploids (B. mexicanum, B. boissieri, B. retusum, B. phoenicoides, B. rupestre and B. hybridum), of which five contain undescribed homeologous subgenomes. The existence of the seven Brachypodium progenitor genomes in the polyploids was confirmed by their karyotypic barcode profiles. Comparative phylogenomics of nuclear versus plastid trees allowed us to formulate hypothetical homoploid hybridizations and allo- and autopolyploidization scenarios that could have generated the six Brachypodium polyploids.

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Research Organization:: USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1982923

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Journal Issue: 6 Vol. 109; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Brachypodium
chromosomal barcodes
ghost progenitor genomes
phylogenomic subgenome detection pipeline
polyploids

Title: Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

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