Analysis of Brachypodium genomes with genome-wide optical maps

Abstract

Brachypodium distachyon (n = 5) is a diploid and has been widely used as a genetic model. Brachypodium stacei (n = 10) and B. hybridum (n = 15) are species that are related to B. distachyon, leading to an hypothesis that they are part of a polyploid series based on x = 5. Several lines of evidence suggest that this hypothesis is incorrect and that the genomes of the three taxa may have evolved by a more complex process. We constructed an optical whole-genome BioNano genome (BNG) map for each species and did pairwise alignment of the BNG maps. The maps showed that B. distachyon and B. stacei are both diploid, in spite of B. stacei having twice as many chromosomes as B. distachyon, and that B. hybridum is an allopolyploid formed from hybridization between B. distachyon and B. stacei. This study also demonstrated the use of BNG maps in the detection and quantification of structural variants among the genomes.

Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species

“…Contigs or scaffolds assembled from long-reads are sufficiently long to be aligned on genome-wide optical maps, which can be assembled with very high accuracy, even for large or polyploid plant genomes 14,15 . Alignments of the optical maps of a hybrid onto the optical maps of its parents will assign contigs to parental genomes 16 , while also serving as an assembly quality control 14 .…”

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

“…Therefore, we use a model grass polyploid system consisting of the diploids Brachypodium distachyon and B. stacei, and their derived allotetraploid B. hybridum. B. distachyon has emerged as a powerful model to study grass biology, and numerous experimental resources have been developed for it 19,20 . Historically, B. distachyon included the current B. distachyon, as well as B. stacei and B. hybridum.…”

Procedurally Generated Artworks Based on Multiple Sequence Alignment of Orthologous Gene Copies

“…Multiple sequence alignment for CDS derived from VRN1 orthologous gene copies in Brachypodium stacei (Brast06G240300.1 and Brast02G311100.1), Brachypodium distachyon (Bradi1g08340.1), rice (LOC_Os03g54160.1) and maize (GRMSM2G553379_T07 and GRMZM2G032339_T02), respectively. Because Brachypodium stacei and maize underwent an additional round of whole genome duplication relative to Brachypodium distachyon and rice, respectively [35,36], they harbor two gene copies each (homeologous copies), constituting six CDS considered in this study instead of four. (© Martin Calvino) CDS; thus it was practically convenient to use them as proof of concept.…”