Additional file 1 of Homoeologous evolution of the allotetraploid genome of Poa annua L

Additional file 1: Supplementary Table 1. Features of the genome assemblies and annotations. Parental species, Poa infirma (PiA) and P. supina (PsB), relative to the subgenomes of P. annua (PaA and PaB). Values correspond to the seven pseudomolecules. BUSCOs are n=1,614. Supplementary Fig. 1. Linked density histograms of the Poa infirma and P. supina genomes. The Omni-C plot represents long-range cis information using proximity ligation and mapping position of paired-end data. Red indicates the number of read pair interactions within each bin. Supplementary Fig. 2. The homoeologous and orthologous sequences of Poa annua and its diploid parents, P. infirma and P. supina. (a) The evolutionary pathway and chromosomal relationships within and between the homologous sequences of P. annua and its diploid progenitors. (b) The distribution of sequence identity measured by the gap-compressed sequence identity of full-genome alignments. Percentages above violin plots indicate the median. (c) Chromosome lengths of the genome assemblies of all three species. Supplementary Fig. 3. Whole-genome sequence alignment depicts the primary mapping of parental chromosomes (PiA & PsB) to allotetraploid, Poa annua (PaA & PaB). The black arrow over Pa2B highlights 30 Mb of novel sequence in the tetraploid genome assembly, mostly composed of repetitive DNA (22.7Mb). Supplementary Fig. 4. The distribution of shared orthologous clusters (gene families) between the A and B genomes of Poa infirma (PiA), P. supina (PsB), and P. annua (PaA & PaB). Single-copy gene clusters are not depicted. Supplementary Fig. 5. Estimated molecular divergence of the PaA and PaB subgenomes of P. annua and the genomes of the diploid parents (PiA and PsB). Arrows and corresponding values highlight the peak density of synonymous substitutions. Supplementary Fig. 6. Sequence alignment of five model monocots spanning two whole-genome duplications. (a) A phylogenetic tree shows the species relationships. Pineapple (Ananas comosus) serves as outgroup because its speciation from the BOP and PACMAD clades of grasses predates the most recent of the ancestral Poaceae WGD events, rho (r). (b) Genomic alignment between monocots Ananas comosus, Brachypodium distachyon, Poa infirma, P. supina, and P. annua. Percentages in red show the ratio of 1:1 orthogroups relative to A. comosus. The syntenic block highlighted in green shows the colinear evolution of a cluster of genes. Supplementary Fig. 7. Retention of Poa annua ge