Evolutionary dynamics of genome size in a radiation of woody plants

From genome size to trait evolution during angiosperm radiation

Angiosperm diversity arises from trait flexibility and repeated evolutionary radiations, but the role of genomic characters in these radiations remains unclear. In this opinion article, we discuss how genome size can influence angiosperm diversification via its intricate link with cell size, tissue packing, and physiological processes which, in turn, influence the macroevolution of functional traits. We propose that integrating genome size, functional traits, and phylogenetic data across a wide range of lineages allows us to test whether genome size decrease consistently leads to increased trait flexibility, while genome size increase constrains trait evolution. Combining theories from molecular biology, functional ecology and macroevolution, we provide a framework to better understand the role of genome size in trait evolution, evolutionary radiations, and the global distribution of angiosperms.

A set of SSR markers to characterize genetic diversity in all Viburnum species

About 160 species are classified within the Viburnum genus and many of these are cultivated for horticultural purposes. The vast dispersal of Viburnum makes the genus a useful model for studying evolutionary history and inferring how species expanded into their current distributions. Simple sequence repeat (SSR) markers were previously developed for five Viburnum species that were classified within the four major clades (Laminotinus, Crenotinus, Valvatotinus, and Porphyrotinus). The ability of some of these markers to cross-amplify in Viburnum species has been scantly evaluated, but there has not been any genus-wide assessment for the markers. We evaluated a collection of 49 SSR markers for the ability to cross-amplify in 224 samples, including 46 Viburnum species, representing all 16 subclades, and five additional species in the Viburnaceae and Caprifoliaceae. A subset of 14 potentially comprehensive markers for Viburnum species was identified and evaluated for the ability to detect polymorphisms in species outside of their respective clades. The 49 markers had overall amplification success in 52% of the samples, including a 60% success rate within the Viburnum genus and 14% in other genera. The comprehensive marker set amplified alleles in 74% of all samples tested, including 85% of Viburnum samples and 19% of outgroup samples. To the best of our knowledge, this is the first comprehensive set of markers able to characterize species across an entire genus. This set of markers can be used to assess the genetic diversity and population structure of most Viburnum species and closely allied species.

De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids

Gentiana macrophylla is a perennial herb in the Gentianaceae family, whose dried roots are used in traditional Chinese medicine. Here, we assembled a chromosome-level genome of G. macrophylla using a combination of Nanopore, Illumina, and Hi-C scaffolding approaches. The final genome size was ~1.79 Gb (contig N50 = 720.804 kb), and 98.89% of the genome sequences were anchored on 13 pseudochromosomes (scaffold N50 = 122.73 Mb). The genome contained 55,337 protein-coding genes, and 73.47% of the assemblies were repetitive sequences. Genome evolution analysis indicated that G. macrophylla underwent two rounds of whole-genome duplication after the core eudicot γ genome triplication event. We further identified candidate genes related to the biosynthesis of iridoids, and the corresponding gene families mostly expanded in G. macrophylla. In addition, we found that root-specific genes are enriched in pathways involved in defense responses, which may greatly improve the biological adaptability of G. macrophylla. Phylogenomic analyses showed a sister relationship of asterids and rosids, and all Gentianales species formed a monophyletic group. Our study contributes to the understanding of genome evolution and active component biosynthesis in G. macrophylla and provides important genomic resource for the genetic improvement and breeding of G. macrophylla.

No Consistent Shift in Leaf Dry Mass per Area Across the Cretaceous-Paleogene Boundary

The Chicxulub bolide impact has been linked to a mass extinction of plants at the Cretaceous-Paleogene boundary (KPB; ∼66 Ma), but how this extinction affected plant ecological strategies remains understudied. Previous work in the Williston Basin, North Dakota, indicates that plants pursuing strategies with a slow return-on-investment of nutrients abruptly vanished after the KPB, consistent with a hypothesis of selection against evergreen species during the globally cold and dark impact winter that followed the bolide impact. To test whether this was a widespread pattern we studied 1,303 fossil leaves from KPB-spanning sediments in the Denver Basin, Colorado. We used the relationship between petiole width and leaf mass to estimate leaf dry mass per area (LMA), a leaf functional trait negatively correlated with rate of return-on-investment. We found no evidence for a shift in this leaf-economic trait across the KPB: LMA remained consistent in both its median and overall distribution from approximately 67 to 65 Ma. However, we did find spatio-temporal patterns in LMA, where fossil localities with low LMA occurred more frequently near the western margin of the basin. These western margin localities are proximal to the Colorado Front Range of the Rocky Mountains, where an orographically driven high precipitation regime is thought to have developed during the early Paleocene. Among these western Denver Basin localities, LMA and estimated mean annual precipitation were inversely correlated, a pattern consistent with observations of both fossil and extant plants. In the Denver Basin, local environmental conditions over time appeared to play a larger role in determining viable leaf-economic strategies than any potential global signal associated with the Chicxulub bolide impact.

Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View

Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.

Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights

PREMISE

Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb-Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times.

METHODS

Sampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off-target reads, and 10 fossils were used to calibrate dated trees.

RESULTS

Varying numbers of targeted loci and off-target plastomes were recovered from most taxa. Nuclear and plastid data confidently place Heptacodium with Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement of Zabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm-wide dating analyses, but many major splitting events date to the Eocene.

CONCLUSIONS

The Angiosperms353 probe set facilitated the assembly of a large, single-copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades.

Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem

The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.