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Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance

Abstract (Expand)

Polyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids … often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being “dominant.” Such “genome dominance” can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k‐mer–based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans‐acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent‐specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.

Authors: Marek Glombik, Dario Copetti, Jan Bartos, Stepan Stoces, Zbigniew Zwierzykowski, Tom Ruttink, Jonathan F. Wendel, Martin Duchoslav, Jaroslav Dolezel, Bruno Studer, David Kopecky

Date Published: 4th Aug 2021

Publication Type: Journal

Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.

Abstract (Expand)

The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. … However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.

Authors: M. Montoliu-Nerin, M. Sanchez-Garcia, C. Bergin, M. Grabherr, B. Ellis, V. E. Kutschera, M. Kierczak, H. Johannesson, A. Rosling

Date Published: 28th Jan 2020

Publication Type: Journal

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