Systematics of Xanthorrhoeaceae Sensu Lato, with an Emphasis on Bulbine

We provide here results of a combined analysis of plastid genes rbcL, matK, and ndhF for Xanthorrhoeaceae s.l., the Asphodelaceae/Xanthorrhoeaceae/Hemerocallidaceae clade, which are well supported by the DNA data. Xanthorrhoea (often treated as the sole member of Xanthorrhoeaceae) is sister to the hemerocallid clade (former Hemerocallidaceae); and the asphodelid clade (formerly Asphodelaceae) is sister to them both. For additional species of Bulbine and Jodrellia (both Asphodeloideae), we also collected rps16 intron and ITS nuclear ribosomal DNA sequences to better assess their relationships. Bulbine, with Jodrellia, embedded are sister to the collective genera of subfamily Alooideae in which all species are characterized by strongly bimodal and nearly identical karyotypes, whereas that of Bulbine is much more variable. Cytological studies have previously shown Bulbine to possess a range of karyotypes from graduated to clearly bimodal (although never exactly like the aloid genera) and point toward a lower level of bimodality in the Australian members, all of which are autotetraploid, than in the African members, all of which are diploid. Therefore, there have been two events of particular interest within Bulbine, a change in ploidy and a long-range dispersal event

Genome size expansion and the relationship between nuclear DNA content and spore size in the Asplenium monanthes fern complex (Aspleniaceae)

Background: Homosporous ferns are distinctive amongst the land plant lineages for their high chromosome numbers and enigmatic genomes. Genome size measurements are an under exploited tool in homosporous ferns and show great potential to provide an overview of the mechanisms that define genome evolution in these ferns. The aim of this study is to investigate the evolution of genome size and the relationship between genome size and spore size within the apomictic Asplenium monanthes fern complex and related lineages. Results: Comparative analyses to test for a relationship between spore size and genome size show that they are not correlated. The data do however provide evidence for marked genome size variation between species in this group. These results indicate that Asplenium monanthes has undergone a two-fold expansion in genome size. Conclusions: Our findings challenge the widely held assumption that spore size can be used to infer ploidy levels within apomictic fern complexes. We argue that the observed genome size variation is likely to have arisen via increases in both chromosome number due to polyploidy and chromosome size due to amplification of repetitive DNA (e.g. transposable elements, especially retrotransposons). However, to date the latter has not been considered to be an important process of genome evolution within homosporous ferns. We infer that genome evolution, at least in some homosporous fern lineages, is a more dynamic process than existing studies would suggest

The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights

Background and aims: Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. Methods: We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples. Key results: We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. Conclusions: We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.A.D.T. is supported by NERC research grants NE/L011336/1 and NE/N006739/1. The Royal Botanic Garden Edinburgh (RBGE) is supported by the Scottish Government’s Rural and Environment Science and Analytical Services Division. J.P. is supported by a Ramón y Cajal Fellowship (RYC-2017–2274) funded by the Ministerio de Ciencia y Tecnología (Gobierno de España).Issue Cover Volume 128Issue 5 8 October 2021 Article Contents Abstract INTRODUCTION METHODS The study system Population and species-level genome size variation Population sampling Genome size measurements Repeat content variation Sequence data generation Repeat content Statistical analyses Data availability RESULTS Population and species-level genome size variation Variation in genomic repeat content DISCUSSION Genome size variation mirrors population genetic patterns Genome size differences and genomic repeats Evolution of genome size variation SUPPLEMENTARY DATA ACKNOWLEDGEMENTS FUNDING LITERATURE CITED Supplementary dat

Biased retention of environment-responsive genes following genome fractionation.

The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements, have been postulated to shape genome-wide dominance and biased fractionation leading to a conserved least-fractionated (LF) and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. A chromosome-scale assembly of the alpine Buckler Mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is here coupled with transcriptional responses to heat, cold, drought and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of transposable elements in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the "turn a hobby into a job" model, about one third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally-expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased while others show high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.Thiswork was supported by the Natural Environment ResearchCouncil (grant no. NE/G017 24/1), the Czech Science Fou nda-tion (grant no. P501/12/G090), the AVCR (grant no.RVO:60077344) and a Beatriu de Pinos postdoctoral fellowshipto J.P. (grant no. 2011-A-00292; Catalan Government-E.U. 7thF.P.)

The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat "communities" are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat "community" composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat "communities".JP was supported by a Ramón y Cajal Fellowship (RYC-2017-2274) funded by MCIN/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’. SB was funded by a Garfield Weston Foundation postdoctoral fellowship. PN and JM were supported by the ELIXIR CZ Research Infrastructure Project (Czech Ministry of Education, Youth and Sports; grant no. LM2018131).IntroductionMaterials and Methods Plant material collection and genome size measurement Phylogenetic, environmental and genomic data collection Modelling relationships between genome size and environmental variables DNA repeat profiling Assessing repeat dynamics in palm genomesResults Palm genome size variation Aridity preferences of palm species help explain genome size variation Ecological metrics of palm repeat ‘communities’ vary with genome size Repeat abundances correlate with genome size Aridity preferences of palm species explain abundances of certain repeat lineagesDiscussion Palm genome size variation Aridity thresholds best explain palm genome size diversity The ‘community ecology’ of repeats correlates with genome size Repeat dynamics may be modulated by aridityConclusionsAcknowledgementsAuthor contributionsPeer reviewe

Genetic factors predict hybrid formation in the British flora

Natural hybridization can have a profound evolutionary impact, with consequences ranging from the extinction of rare taxa to the origin of new species. Natural hybridization is particularly common in plants; however, our understanding of the general factors that promote or prevent hybridization is hampered by the highly variable outcomes in different lineages. Here, we quantify the influence of different predictors on hybrid formation across species from an entire flora. We combine estimates of hybridization with ecological attributes and a new species-level phylogeny for over 1,100 UK flowering plant species. Our results show that genetic factors, particularly parental genetic distance, as well as phylogenetic position and ploidy, are key determinants of hybrid formation, whereas many other factors such as range overlap and genus size explain much less variation in hybrid formation. Overall, intrinsic genetic factors shape the evolutionary and ecological consequences of natural hybridization across species in a flora

Evolution of genome space occupation in ferns: linking genome diversity and species richness

Background and Aims:The dynamics of genome evolution caused by whole genome duplications and other processes are hypothesized to shape the diversification of plants and thus contribute to the astonishing variation in species richness among the main lineages of land plants. Ferns, the second most species rich lineages of land plants are highly suitable to test this hypothesis because of several unique features that distinguish fern genomes from those of seed plants. In this study, we tested the hypothesis that genome diversity and disparity shape fern species diversity by recording several parameters related to genome size and chromosome number.Methods:We conducted de novo measurement of DNA C-values across the fern phylogeny to reconstruct the phylogenetic history of the genome space occupation in ferns by integrating genomic parameters such as genome size, chromosome number, and average DNA amount per chromosome into a time-scaled phylogenetic framework. Using phylogenetic generalized least square methods, we determined correlations between chromosome number and genome size, species diversity and evolutionary rates of their transformation.Key ResultsThe measurements of DNA C-values for 233 species more than doubled the taxon coverage from ca. 2.2% in previous studies to 5.3% of extant diversity. The dataset documented not only substantial differences in the accumulation of genomic diversity and disparity among the major lineages of ferns but also recovered support the predicted correlation between species diversity and the dynamics of genome evolution.Conclusions:Our results demonstrated substantial genome disparity among different groups in ferns and supported the prediction that alterations of reproductive modes alter trends of genome evolution. Finally, we recovered evidence for a close link between the dynamics of genome evolution and species diversity in ferns for the first time.Fil: Fujiwara, Tao. Xishuangbanna Tropical Botanical Garden; ChinaFil: Liu, Hongmei. Xishuangbanna Tropical Botanical Garden; ChinaFil: Meza Torres, Esteban Ismael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Morero, Rita Ema. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Vega, Alvaro Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Liang, Yuehwei. Xishuangbanna Tropical Botanical Garden; ChinaFil: Ebihara, Atsushi. National Museum Of Nature And Sciences, Tsukuba, Japan; JapónFil: Leitch, Ilia J.. Royal Botanic Gardens; Reino UnidoFil: Schneider, Harald. Xishuangbanna Tropical Botanical Garden; Chin

Genome size diversity in angiosperms and its influence on gene space

Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C = 5.7 Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as ‘junk’ DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression

Eukaryotic genome size databases

Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (), the Animal Genome Size Database () and the Fungal Genome Size Database (). In total, these databases provide freely accessible genome size data for >10 000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs