Phylogenetics of the Paleartic model grass Brachypodium sylvaticum uncovers two divergent oriental and occidental micro-taxa lineages

Abstract

Brachypodium sylvaticum has been selected as a model for perennial grasses, and considerable genomic resources have been generated and a reference genome and several resequenced pangenome accessions are available for this species. Despite these genomic advances, the evolution and systematics of diploid B. sylvaticum s. l. is almost unknown. The B. sylvaticum complex is formed by up to seven taxonomically close micro-taxa which differentiate from typical B. sylvaticum s. s. based on a few morphological features. Moreover, some of them show some largely disjunct geographic distributions on both sides of their native Palearctic region. In this study, we used a phylogenomic approach including representative populations from the oriental and occidental distribution range of B. sylvaticum micro-taxa to elucidate their evolutionary relationships and assess the systematic value of the morphological features that separate them. A combined plastome and nuclear phylogenetic tree supports an early split and high divergence of the oriental lineage, showing the close relationship of the Himalayan B. sylvaticum var. breviglume lineages to the Pacific B. miserum / B. kurilense clade, and the contrasting large homogeneity and low divergence of the occidental European, N African and SW and C Asian lineage, with several B. sylvaticum s. s., B. spryginii, and B. glaucovirens samples showing identical or similar sequences. Divergence time estimate analysis suggests that the oriental lineage diverged from the common ancestor in the early Pleistocene (2.0 Ma), followed by subsequent colonization and isolations in the Himalayas (2.0 – 1.7 Ma) and the Far East (0.36 Ma) in more recent times, while the occidental lineage split in the Mid-Late Pleistocene (0.97 Ma), followed by rapid radiation and postglacial spread in the western Paleartic during the last thousand years.

Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis in Brachypodium model grasses

“…The striking large repeatome coverage of the recently evolved B. sylvaticum core-perennial diploid genome (34.2%) relative to other diploid (24.7%) and polyploid (<26%) core-perennial genomes sharing the same recently evolved karyotype x=9 ( Sancho et al., 2022 ) does not correlate with parallel differences in 1Cx genome sizes, which have similar values for B. sylvaticum -2x (456 Mbp) as for B. pinnatum -2x (401 Mbp) and other core-perennial 2x-4x-6x cytotypes (349-382 Mbp) ( Table 1 , Supplementary Tables S1, S3, S4 ). This unexpected result could be a consequence of a relatively recent polyploidization and subsequent diploidization of the wester lineage of B. sylvaticum from the Late Pliocene - Early Pleistocene (2.78 – 2.17 Ma; Figure 1 ; Catalán et al., 2023 ). B. sylvaticum samples showed a proliferation of Tekay retrotransposons (10%) compared to the other core perennial lineages (1-2%), and also higher proportions of Mutator, Ikeros and Angela elements ( Supplementary Tables S3, S4 ).…”

“…The cool seasonal genus Brachypodium , consisting of approximately 23 taxa ( Catalan et al., 2016 ; Catalán et al., 2023 ), has been selected as a model functional system for cereal and biofuel crops and to investigate the evolution of polyploidy in grasses. Annotated reference genomes and considerable genomic resources have been produced for its three annual species ( B. distachyon, B. stacei, B. hybridum ) ( Scholthof et al., 2018 ; Hasterok et al., 2022 ; Mu et al., 2023a , b ; Chen et al., 2024 ) and for the slender perennial B. sylvaticum ( Lei et al., 2024 ).…”