Genome size variation in Deschampsia cespitosa sensu lato (Poaceae) in Eurasia

The grass Deschampsia cespitosa is a variable taxon out of which many varieties, subspecies and endemic species have been separated. In this paper, the variation in genome size (GS) and ploidy of this grass including several of its subspecies and two related species in Eurasia was investigated by flow cytometric (FCM) measurements. GS and ploidy data were also related to specific environments and reproduction mode. Ploidy levels found by FCM were confirmed by chromosome counts of diploid (2n = 28) and tetraploid (2n = 52) samples. Seminiferous (seed bearing) D. cespitosa was mainly diploid (GS between 3.754 and 5.438 pg/1C). GS variation in diploids showed a geographic pattern with a significant difference (H = 41,441, P < 0.001) between European (median = 4.377 pg) and Asian (median = 4.881 pg) accessions. Genome size (1C) in tetraploids ranged from 7.9426 to 9.0399 pg. Tetraploid seminiferous D. cespitosa was found mostly in disturbed habitats in western and southern Europe, while tetraploids in Asia were registered in wet Arctic habitats. Genome size (1C between 8.3278 and 8.8603 pg) of the pseudoviviparous plants (spikelets produce plantlets asexually) of wet habitats in central and northern Europe indicated tetraploidy. A putative triploid (GS 6.6817 pg) was detected in Iceland. Summing up, we found a high variation in GS on the geographic scale with significant regional differences in diploid D. cespitosa. Among the tetraploids, the asexually reproducing plants were bound to specific habitats, while the seminiferous plants showed a habitat preference similar to the diploids.

Karyotype and genome size variation in white-flowered Eranthis sect. Shibateranthis (Ranunculaceae)

Comparative karyomorphological analyses of six out of the eight white-flowered species of Eranthis sect. Shibateranthis have been carried out. All studied specimens of E. byunsanensis, E. lobulata, E. pinnatifida, and E. stellata had a somatic chromosome number 2n = 16 with basic chromosome number x = 8. On the contrary, E. tanhoensis and E. sibirica had a basic chromosome number x = 7. The specimens of E. tanhoensis were diploid with 2n = 14, while the specimens of E. sibirica were polyploid with 2n = 42. Monoploid chromosome sets of the investigated diploid species had 4–5 metacentric chromosomes and 2–4 submetacentric/subtelocentric/acrocentric chromosomes. The highest level of interchromosomal asymmetry, estimated via CVCL, was found in E. byunsanensis and E. pinnatifida. The highest levels of intrachromosomal asymmetry (MCA) and heterogeneity in centromere position (CVCI) were found in E. lobulata and E. byunsanensis, while E. sibirica had the most symmetric karyotype. A multivariate PCoA analysis of basic karyotype parameters (2n, x, THL, CVCL, MCA, and CVCI) highlighted no overlap among species accessions, which was also confirmed by LDA. The average absolute monoploid DNA content (1Cx) of the 23 investigated samples of six Eranthis species varied from 9.26 ± 0.25 pg in E. sibirica to 15.93 ± 0.32 pg in E. stellata. Overall karyological affinity was highlighted between E. lobulata and E. stellata, on one side, and between E. byunsanensis and E. pinnatifida, on the other side. Interestingly, there was no significant correlation between total haploid (monoploid) chromosome length (THL) and 1Cx values in these species.

Genome size distributions in bacteria and archaea are strongly linked to phylogeny

The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses remain unclear. Moreover, statistical analyses on this topic have typically been limited to a narrow diversity of bacteria and archaea without considering the potential bias introduced by the shared recent ancestry of many lineages. In this study, we used a phylogenetic generalized least-squares (PGLS) analysis to evaluate the effect of different factors on the genome size of a broad diversity of bacteria and archaea. We used dN/dS to estimate the strength of purifying selection, and 16S copy number as a proxy for ecological strategy, which have both been postulated to play a role in shaping genome size. After model fit, Pagels lambda indicated a strong phylogenetic signal in genome size, suggesting that the diversification of this trait is strongly influenced by shared evolutionary histories. As a predictor variable, dN/dS showed a poor predictability and non-significance when phylogeny was considered, consistent with the view that genome reduction can occur under either weak or strong purifying selection depending on the ecological context. Copies of 16S rRNA showed poor predictability but maintained significance when accounting for non-independence in residuals, suggesting that ecological strategy as approximated from 16S rRNA copies might play a minor role in genome size variation. Altogether, our results indicate that genome size is a complex trait that is not driven by any singular underlying evolutionary force, but rather depends on lineage- and niche-specific factors that will vary widely across bacteria and archaea.

Measuring the invisible - The sequences causal of genome size differences in eyebrights (Euphrasia) revealed by k-mers

Genome size variation within plant (and other) taxa may be due to presence/absence variation in low-copy sequences or copy number variation in genomic repeats of various frequency classes. However, identifying the sequences underpinning genome size variation has been challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies miss low-copy number sequences. Here, we take a novel approach based on k-mers, short sub-sequences of equal length k, generated from whole genome sequencing data of diploid eyebrights (Euphrasia), a group of plants which have considerable genome size variation within a ploidy level. We compare k-mer inventories within and between closely related species, and quantify the contribution of different copy number classes to genome size differences. We further assign high-copy number k-mers to specific repeat types as retrieved from the RepeatExplorer2 pipeline. We find complex patterns of k-mer differences between samples. While all copy number classes contributed to genome size variation, the largest contribution came from repeats with 1000-10,000 genomic copies including the 45S rDNA satellite DNA and, unexpectedly, a repeat associated with an Angela transposable element. We also find size differences in the low-copy number class, likely indicating differences in gene space between our samples. In this study, we demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without use of a reference genome. Such sequences can serve as targets for future cytogenetic studies. We also show that studies of genome size variation should go beyond repeats and consider the whole genome. To allow future work with other taxonomic groups, we share our analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools.

It Is Just a Matter of Time: Balancing Homologous Recombination and Non-homologous End Joining at the rDNA Locus During Meiosis

Ribosomal RNA genes (rDNAs) are located in large domains of hundreds of rDNA units organized in a head-to-tail manner. The proper and stable inheritance of rDNA clusters is of paramount importance for survival. Yet, these highly repetitive elements pose a potential risk to the genome since they can undergo non-allelic exchanges. Here, we review the current knowledge of the organization of the rDNA clusters in Arabidopsis thaliana and their stability during meiosis. Recent findings suggest that during meiosis, all rDNA loci are embedded within the nucleolus favoring non-homologous end joining (NHEJ) as a repair mechanism, while DNA repair via homologous recombination (HR) appears to be a rare event. We propose a model where (1) frequent meiotic NHEJ events generate abundant single nucleotide polymorphisms and insertions/deletions within the rDNA, resulting in a heterogeneous population of rDNA units and (2) rare HR events dynamically change rDNA unit numbers, only to be observed in large populations over many generations. Based on the latest efforts to delineate the entire rDNA sequence in A. thaliana, we discuss evidence supporting this model. The results compiled so far draw a surprising picture of rDNA sequence heterogeneity between individual units. Furthermore, rDNA cluster sizes have been recognized as relatively stable when observing less than 10 generations, yet emerged as major determinant of genome size variation between different A. thaliana ecotypes. The sequencing efforts also revealed that transcripts from the diverse rDNA units yield heterogenous ribosome populations with potential functional implications. These findings strongly motivate further research to understand the mechanisms that maintain the metastable state of rDNA loci.

Diversity and Cytogenomic Characterization of Wild Carrots in the Macaronesian Islands

The Macaronesian islands constitute an enormous reservoir of genetic variation of wild carrots (subtribe Daucinae; Apiaceae), including 10 endemic species, but an accurate understanding of the diversification processes within these islands is still lacking. We conducted a review of the morphology, ecology, and conservation status of the Daucinae species and, on the basis of a comprehensive dataset, we estimated the genome size variation for 16 taxa (around 320 samples) occurring in different habitats across the Macaronesian islands in comparison to mainland specimens. Results showed that taxa with larger genomes (e.g., Daucus crinitus: 2.544 pg) were generally found in mainland regions, while the insular endemic taxa from Azores and Cabo Verde have smaller genomes. Melanoselinum decipiens and Monizia edulis, both endemic to Madeira Island, showed intermediate values. Positive correlations were found between mean genome size and some morphological traits (e.g., spiny or winged fruits) and also with habit (herbaceous or woody). Despite the great morphological variation found within the Cabo Verde endemic species, the 2C-values obtained were quite homogeneous between these taxa and the subspecies of Daucus carota, supporting the close relationship among these taxa. Overall, this study improved the global knowledge of DNA content for Macaronesian endemics and shed light into the mechanisms underpinning diversity patterns of wild carrots in the western Mediterranean region.

Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation

Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.

Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

Background Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied—despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population. Results Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Conclusions By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

Intragenomic Conflict between Knob Heterochromatin and B Chromosomes Is the Key to Understand Genome Size Variation along Altitudinal Clines in Maize

In maize, we studied the causes of genome size variation and their correlates with cultivation altitude that suggests the existence of adaptive clines. To discuss the biological role of the genome size variation, we focused on Bolivian maize landraces growing along a broad altitudinal range. These were analyzed together with previously studied populations from altitudinal clines of Northwestern Argentina (NWA). Bolivian populations exhibited numerical polymorphism for B chromosomes (Bs) (from 1 to 5), with frequencies varying from 16.6 to 81.8 and being positively correlated with cultivation altitude. The 2C values of individuals 0B (A-DNA) ranged between 4.73 and 7.71 pg, with 58.33% of variation. The heterochromatic knobs, detected by DAPI staining, were more numerous and larger in individuals 0B than in those with higher doses of Bs. Bolivian and NWA landraces exhibited the same pattern of A-DNA downsizing and fewer and smaller knobs with increasing cultivation altitude, suggesting a mechanistic link among heterochromatin, genome size and phenology. The negative association between the two types of supernumerary DNA (knob heterochromatin and Bs), mainly responsible for the genome size variation, may be considered as an example of intragenomic conflict. It could be postulated that the optimal nucleotype is the result of such conflict, where genome adjustment may lead to an appropriate length of the vegetative cycle for maize landraces growing across altitudinal clines.

Clandestinovirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis

For several decades, the vast world of DNA viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a giant virus named “clandestinovirus,” grown on the amoebal host Vermamoeba vermiformis. This virus was discovered in a mixed co-culture associated with another giant virus, Faustovirus ST1. Clandestinovirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinovirus is most closely related to Acanthamoeba castellanii medusavirus and was considered a member of the proposed Medusaviridae family. However, clandestinovirus genome is 65% larger than that of medusavirus, emphasizing the considerable genome size variation within this virus family. Functional annotation of the clandestinovirus genes suggests that the virus encodes four core histones. Furthermore, clandestinovirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinovirus to optimize the intracellular environment for efficient virus propagation.