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Angiosperms present an astonishing diversity of genome sizes that can vary intra‐ or interspecifically. The remarkable new cytogenomic data shed some light on our understanding of evolution, but few studies were performed with insular and mainland populations to test possible correlations with dispersal, speciation, and adaptations to insular environments. Here, patterns of cytogenomic diversity were assessed among geographic samples (ca. 114) of Crithmum maritimum (Apiaceae), collected across the Azores and Madeira archipelagos, as well as in adjacent continental areas of Portugal. Using flow cytometry, the results indicated a significant intraspecific genome size variation, spanning from reduced sizes in the insular populations to larger ones in the mainland populations. Moreover, there was a tendency for an increase in genome size along the mainland populations, associated with lower temperatures, higher precipitation, and lower precipitation seasonality. However, this gradient might be the result of historic phylogeographical events associated with previous dispersal and extinction of local populations. Overall, our findings provided evidence that smaller genome sizes might play a critical role in the colonization of islands, corroborating other studies that argue that organisms with smaller genomes use fewer resources, having a selective advantage under insular environments. Although further studies are needed to improve our understanding of the mechanisms underlying genome size evolution on islands, conservation strategies must be promoted to protect the rich cytogenomic diversity found among C. maritimum populations, which occur in coastal areas that are particularly threatened by human activity, pollution, invasive species, and climate changes. [ABSTRACT FROM AUTHOR]

Synteny, the ordering of sequences within homologous chromosomes, must be maintained within the genomes of sexually reproducing species for the sharing of alleles and production of viable, reproducing offspring. However, when the genomes of closely related species are compared, a loss of synteny is often observed. Unequal homologous recombination is the primary mechanism behind synteny loss, occurring more often in transposon rich regions, and resulting in the formation of chromosomal rearrangements. To examine patterns of synteny among three closely related, interbreeding, and wild Eucalyptus species, we assembled their genomes using long‐read DNA sequencing and de novo assembly. We identify syntenic and rearranged regions between these genomes and estimate that ~48% of our genomes remain syntenic while ~36% is rearranged. We observed that rearrangements highly fragment microsynteny. Our results suggest that synteny between these species is primarily lost through small‐scale rearrangements, not through sequence loss, gain, or sequence divergence. Further examination of identified rearrangements suggests that rearrangements may be altering the phenotypes of Eucalyptus species. Our study also underscores that the use of single reference genomes in genomic variation studies could lead to reference bias, especially given the scale at which we show potentially adaptive loci have highly diverged, deleted, duplicated and/or rearranged. This study provides an unbiased framework to look at potential speciation and adaptive loci among a rapidly radiating foundation species of woodland trees that are free from selective breeding seen in most crop species. [ABSTRACT FROM AUTHOR]

SUMMARY: Self‐incompatibility in the Brassicaceae family is governed by SRK and SCR, which are two highly polymorphic genes located at the S‐locus. Previously, the Arabidopsis lyrata SRK and SCR genes were introduced into Arabidopsis thaliana to generate self‐incompatible lines. However, there are no reports showing that Brassica SRK and SCR genes confer self‐incompatibility in A. thaliana. Doing so would further advance the mechanistic understanding of self‐incompatibility in Brassicaceae. Therefore, we attempted to generate A. thaliana transformants showing the self‐recognition activity of Brassica rapa by introducing BrSCR along with a chimeric BrSRK (BrSRK chimera, in which the kinase domain of BrSRK was replaced with that of AlSKR‐b). We found that the BrSRK chimera and BrSCR of B. rapa S‐9 and S‐46 haplotypes, but not those of S‐29, S‐44, and S‐60 haplotypes, conferred self‐recognition activity in A. thaliana. Analyses of A. thaliana transformants expressing mutant variants of the BrSRK‐9 chimera and BrSCR‐9 revealed that mutations at the amino acid residues involved in BrSRK9–BrSCR9 interaction caused defects in the self‐incompatibility response. The method developed in this study for generating self‐incompatible A. thaliana transformants showing B. rapa self‐recognition activity will be useful for analysis of self‐recognition mechanisms in Brassicaceae. Significance Statement: Although self‐incompatible A. thaliana was constructed by introducing SRK and SCR of A. lyrata, it has not been reported that Brassica SRK and SCR genes confer self‐incompatibility in A. thaliana. We generated A. thaliana transformants showing the self‐recognition activity of B. rapa by introducing BrSCR with a BrSRK chimera, in which the kinase domain of BrSRK was replaced with that of AlSKR‐b. Our finding will be useful for analysis of self‐recognition mechanisms in Brassicaceae. [ABSTRACT FROM AUTHOR]

Summary: This study explores how allopolyploidization reshapes the biased expression and asymmetric epigenetic modification of homoeologous gene pairs, and examines the regulation types and epigenetic basis of expression bias.We analyzed the gene expression and four epigenetic modifications (DNA methylation, H3K4me3, H3K27me3 and H3K27ac) of 29 976 homoeologous gene pairs in resynthesized, natural allopolyploid Brassica napus and an in silico 'hybrid'.We comprehensively elucidated the biased gene expression, asymmetric epigenetic modifications and the generational transmission characteristics of these homoeologous gene pairs in B. napus. We analyzed cis/trans effects and the epigenetic basis of homoeolog expression bias. There was a significant positive correlation between two active histone modifications and biased gene expression.We revealed that parental legacy was the dominant principle in the remodeling of homoeolog expression bias and asymmetric epigenetic modifications in B. napus, and further clarified that this depends on whether there were differences in the expression/epigenetic modifications of gene pairs in parents/progenitors. The maternal genome was dominant in the homoeolog expression bias of resynthesized B. napus, and this phenomenon was attenuated in natural B. napus. Furthermore, cis rather than trans effects were dominant when epigenetic modifications potentially affected biased expression of gene pairs in B. napus. [ABSTRACT FROM AUTHOR]

Summary: Allopolyploids have globally higher fitness than their diploid progenitors; however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success.Using the Brassica model, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploid Brassica napus and systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors, and polyploid formation type. We evaluated the evolution of meiotic behavior and fertility and identified rearrangements in S1 to S9 lineages to explore the positive consequences of euploid selection on B. napus genome stability.Recurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a decrease in number of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number depended strongly on the genetic background and cytoplasm donor.The combined use of both self‐fertilization and recurrent euploid selection allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explain B. napus speciation success. [ABSTRACT FROM AUTHOR]

Summary: Allopolyploidisation merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is 'dominant' over the other subgenome, often being more highly expressed.Here, we 'replayed the evolutionary tape' with six isogenic resynthesised Brassica napus allopolyploid lines and investigated subgenome dominance patterns over the first 10 generations postpolyploidisation.We found that the same subgenome was consistently more dominantly expressed in all lines and generations and that >70% of biased gene pairs showed the same dominance patterns across all lines and an in silico hybrid of the parents. Gene network analyses indicated an enrichment for network interactions and several biological functions for the Brassica oleracea subgenome biased pairs, but no enrichment was identified for Brassica rapa subgenome biased pairs. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the dominant subgenome in all lines and generations. Many of these differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting that subgenome dominance is partly related to parental genome differences rather than just a byproduct of allopolyploidisation.These findings demonstrate that 'replaying the evolutionary tape' in an allopolyploid results in largely repeatable and predictable subgenome expression dominance patterns. [ABSTRACT FROM AUTHOR]