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Decena Rodriguez, Maria Angeles [1], Sancho, Rubén [2], Inda Aramendia, Luis Angel [3], Pérez-Collazos, Ernesto [4], Catalan, Pilar [2].

Phylogenetics and evolution of the model grass genus Brachypodium based on different sources of genomic and cytogenetic data.

Brachypodium is a worldwide distributed genus nested in an intermediate evolutionary position within the Pooideae; it was selected as a functional model system for plant polyploidy and perenniality. Brachypodium contains ca. 20 species (3 annuals, 17 perennials) that show a complex evolutionary reticulate history and a remarkable dysploidy. However, the phylogenetic relations of the Brachypodium species and the identities of the subgenomes of the polyploid taxa are not well known, especially within the perennials. Cytogenetic studies of newly sampled accessions using chromosome counting, genome size and rDNA FISH analyses have validated previously neglected cytotypes and have detected new cytotypes that may correspond to cryptic species. We have used new high-throughput genome skimming sequence data to elucidate the evolutionary history of the perennial Brachypodium species and cytotypes. The genomes of 78 individuals corresponding to 18 perennial Brachypodium taxa and cytotypes were sequenced in the Illumina platform. Paired-end sequence reads from these samples were used to assemble and align their plastomes and nuclear rDNA 35S-cistron and 5S regions using de novo (Novoplasty) and reference-mapping (Geneious) approaches. Exploratory phylogenetic analysis performed through maximum likelihood (IQTREE) and Bayesian (Beast) searches recovered the same diploid skeleton tree in most cases and similar topologies for the nuclear rDNA loci. The rDNA cistron tree identified B. mexicanum-4x and B. boissieri-6x as the ancestral most lineages within Brachypodium, supporting previous findings based on transcriptomic data. The recent core perennial clade showed the earlier splits of Canarian B. arbuscula and Tropical African B. flexum/B. bolusii, followed by the divergence of B. retusum-6x and the interspersed placements of B. retusum-4x, B. phoenicoides-4x and 6x, and B. rupestre-4x and 6x among the B. glaucovirens, B. pinnatum, B. sylvaticum and B. genuense diploids, and a recent B. madagascariense/B. kawakamii plus East Asian-B. sylvaticum clade. The plastome tree supported the maternal ancestry of B. mexicanum and a B. distachyon-type plastome in
B. boissieri, a B. arbuscula-type in B. phoenicoides-6x and a B.pinnatum-type in B. retusum-4x. The B. rupestre-2x, B. glaucovirens-2x and B. sylvaticum-2x plastomes nested within the same clade. The data show an evolutionary convergence trend of rDNA 35S sequences towards their ancestral genomes and the maintenance of grass relict 35S copies in more recent
B. phoenicoides and B. rupestre polyploids. Our results throw insights on the identities of the potential progenitor genomes of some Brachypodium perennial polyploids.

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1 - University of Zaragoza, Agricultural and Environmental Sciences, High Polytechnic School of Huesca, Ctra. Cuarte, km 1, Huesca, Aragon, 22071, Spain
2 - University of Zaragoza: Universidad de Zaragoza, Agricultural and Environmental Sciences, High Polytechnic School of Huesca, Ctra. Cuarte km 1, Huesca, Aragón, 22071, Spain
3 - University of Zaragoza, Agricultural and Environmental Sciences, High Polytechnic School of Huesca, Crta. Cuarte Km 1, Huesca, Aragon, 22071, Spain
4 - High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spa, Department of Agricultural and Environmental Sciences, Carretera de Cuarte s/n., Huesca, Huesca, 220071, España

Brachypodium perennials
genome skimming
progenitor subgenomes
rDNA 35S and 5S loci.

Presentation Type: Poster
Session: P3, Phylogenomics Posters
Location: Virtual/Virtual
Date: Wednesday, July 21st, 2021
Time: 5:00 PM(EDT)
Number: P3PL009
Abstract ID:544
Candidate for Awards:None

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