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BACKGROUND AND AIMS: The amount of DNA in an unreplicated gametic chromosome complement is known as the C-value and is a key biodiversity character of fundamental significance with many practical and predictive uses. Since 1976, Bennett and colleagues have assembled eight compilations of angiosperm C-values for reference purposes and subsequently these have been pooled into the Angiosperm DNA C-values Database (http://data.kew.org/cvalues/). Since the last compilation was published in 2005, a large amount of data on angiosperm genome size has been published. It is therefore timely to bring these data together into a ninth compilation of DNA amounts. SCOPE: The present work lists DNA C-values for 2221 species from 151 original sources (including first values for 1860 species not listed in previous compilations). Combining these data with those published previously shows that C-values are now available for 6287 angiosperm species. KEY FINDINGS: Analysis of the dataset, which is by far the largest of the nine compilations published since 1976, shows that angiosperm C-values are now being generated at the highest rate since the first genome sizes were estimated in the 1950s. The compilation includes new record holders for the smallest (1C = 0·0648 pg in Genlisea margaretae) and largest (1C = 152·23 pg in Paris japonica) genome sizes so far reported, extending the range encountered in angiosperms to nearly 2400-fold. A review of progress in meeting targets set at the Plant Genome Size meetings shows that although representation for genera, geographical regions and some plant life forms (e.g. island floras and parasitic plants) has improved, progress to increase familial representation is still slow. In terms of technique it is now clear that flow cytometry is soon likely to become the only method available for plant genome size estimations. Fortunately, this has been accompanied by numerous careful studies to improve the quality of data generated using this technique (e.g. design of new buffers, increased awareness and understanding of problems caused by cytosolic inhibitors). It is also clear that although the speed of DNA sequencing continues to rise dramatically with the advent of next-generation and third-generation sequencing technologies, 'complete genome sequencing' projects are still unable to generate accurate plant genome size estimates.

We studied the relationship between genome size and ploidy level variation and plant traits for the reed grass Phragmites australis . Using a common garden approach on a global collection of populations in Aarhus, Denmark, we investigated the influence of monoploid genome size and ploidy level on the expression of P. australis growth, nutrition and herbivore-defense traits and whether monoploid genome size and ploidy level play different roles in plant trait expression. We found that both monoploid genome size and latitude of origin contributed to variation in traits that we studied for P. australis , with latitude of origin being generally a better predictor of trait values and that ploidy level and its interaction with monoploid genome size and latitude of origin also contributed to trait variation. We also found that for four traits, tetraploids and octoploids had different relationships with the monoploid genome size. While for tetraploids stem height and leaf water content showed a positive relationship with monoploid genome size, octoploids had a negative relationship with monoploid genome size for stem height and no relationship for leaf water content. As genome size within octoploids increased, the number of aphids colonizing leaves decreased, whereas for tetraploids there was a quadratic, though non-significant, relationship. Generally we found that tetraploids were taller, chemically better defended, had a greater number of stems, higher leaf water content, and supported more aphids than octoploids. Our results suggest trade-offs among plant traits mediated by genome size and ploidy with respect to fitness and defense. We also found that the latitude of plant origin is a significant determinant of trait expression suggesting local adaptation. Global climate change may favor some genome size and ploidy variants that can tolerate stressful environments due to greater phenotypic plasticity and to fitness traits that vary with cytotype which may lead to changes in population genome sizes and/or ploidy structure, particularly at species’ range limits.

Recombinant proteins are extensively used for a growing number of fields in biology. However, microalgal species have not been widely adopted as cell factories for recombinant protein production. Unique metabolic properties, ease of cultivation, fast growth rates, and continuous progress in genetic engineering of microalgae have raised interest in the use of microalgae species for recombinant protein production. Here, we report an Agrobacterium-mediated genetic transformation system for the heterologous expression of a therapeutic protein, “erythropoietin,” in a nonmodel green microalga, Dictyosphaerium pulchellum. Hygromycin resistance gene (Hyg) was used as a selectable marker. The genetic transformation of D. pulchellum was performed in modified AF6 medium supplemented with 150 μM acetosyringone, co-cultivated for 48 h at 25 ± 2 °C and a light intensity of 18 ± 2 μmol photons m−2 s−1. Co-cultivation of D. pulchellum with Agrobacterium tumefaciens harboring the binary expression vector pCAMBIA1301-Hyg-EPO-Histag yielded hygromycin-resistant colonies on selective medium after 2–3 weeks. Gene integration into the D. pulchellum nuclear genome was confirmed by PCR amplification of T-DNA from the genomic DNA of hygromycin-resistant and wild-type strains. Interestingly, SDS-PAGE and subsequent Western blotting with His-tag monoclonal and anti-erythropoietin monoclonal antibodies revealed an EPO-specific signal slightly below 34 kDa. Furthermore, EPO gene expression and transgene copy numbers were estimated by quantitative real-time PCR. Approximately, 500 μg L−1 of extracellular recombinant erythropoietin protein was purified by His-tag affinity chromatography. The developed genetic transformation system would allow the metabolic engineering and a better alternative to produce recombinant therapeutic proteins from nonmodel freshwater microalgae species.

BACKGROUND AND AIMS: Brachypodium is a small genus of temperate grasses that comprises 12-15 species. Brachypodium distachyon is now well established as a model species for temperate cereals and forage grasses. In contrast to B. distachyon, other members of the genus have been poorly investigated at the chromosome level or not at all. METHODS: Twenty accessions comprising six species and two subspecies of Brachypodium were analysed cytogenetically. Measurements of nuclear genome size were made by flow cytometry. Chromosomal localization of 18-5·8-25S rDNA and 5S rDNA loci was performed by dual-colour fluorescence in situ hybridization (FISH) on enzymatically digested root-tip meristematic cells. For comparative phylogenetic analyses genomic in situ hybridization (GISH) applied to somatic chromosome preparations was used. KEY RESULTS: All Brachypodium species examined have rather small genomes and chromosomes. Their chromosome numbers and genome sizes vary from 2n = 10 and 0·631 pg/2C in B. distachyon to 2n = 38 and 2·57 pg/2C in B. retusum, respectively. Genotypes with 18 and 28 chromosomes were found among B. pinnatum accessions. GISH analysis revealed that B. pinnatum with 28 chromosomes is most likely an interspecific hybrid between B. distachyon (2n = 10) and B. pinnatum (2n = 18). Two other species, B. phoenicoides and B. retusum, are also allopolyploids and B. distachyon or a close relative seems to be one of their putative ancestral species. In chromosomes of all species examined the 45S rDNA loci are distally distributed whereas loci for 5S rDNA are pericentromeric. CONCLUSIONS: The increasing significance of B. distachyon as a model grass emphasizes the need to understand the evolutionary relationships in the genus Brachypodium and to ensure consistency in the biological nomenclature of its species. Modern molecular cytogenetic techniques such as FISH and GISH are suitable for comparative phylogenetic analyses and may provide informative chromosome- and/or genome-specific landmarks.

The DNA amount in the unreplicated haploid nucleus of an organism is known as its C-value. C-values differ about 1000-fold among angiosperms and are characteristic of taxa. The data are used in many biological fields, so they should be easily available. Values for 2802 angiosperm species (1%) were estimated during 1950–1997, and five collected lists of C-values were published for reference purposes during 1976–1997. Numbers of new angiosperm C-values published recently remained high, necessitating a further supplementary list. This paper lists DNA C-values for 807 angiosperm species from 70 original sources, including 520 (75.2%) from sources published after 1996, and 691 for species not included in any of the previous five lists. There is a continuing need to estimate accurate DNA C-values for plant taxa, as shown in a workshop on this biodiversity topic sponsored by Annals of Botany and held at Kew in 1997. Its key aim was to identify major gaps in our knowledge of plant DNA amounts and to recommend targets and priorities for new work to fill them. A target of estimating first C-values for the next 1% of angiosperm species in 5 years was set. The proportion of such C-values in the present work (85.6%) is very high; and the number being published (approx. 220 per annum) has never been exceeded. In 1997, C-values were still unknown for most (68%) families, so a target of complete coverage was set. This paper includes first C-values for 12 families, but as less than 2% of such values listed here targeted new families, the need to improve familial representation remains.

This study was mainly carried out to detect the quantitative trait loci (QTLs) located simultaneously in embryo and maternal plant nuclear genomes for beneficial fatty acid contents of rapeseed under different environments by using a mapping model and mapping populations from a cross of ‘Tapidor’ × ‘Ningyou7.’ Eight, three, six, seven and three QTLs respectively for palmitic, oleic, linoleic, linolenic and eicosenoic acid contents were identified and subsequently mapped on chromosomes A1, A3, A4, A6, A8, A9, C1, C3, C5, C7, C8 and C9. Among them, 12 QTLs were major ones that could respectively explain more than 10 % of phenotypic variation. Two specific genomic regions on A8 and C3 were associated with several QTLs relating to multiple fatty acid contents. Some of the markers such as HBr015 and JICB0633 showed tight linkage with the QTLs, which could be used for improving the fatty acid component(s) of rapeseed.

Background The endosymbiosis of the bacterial progenitors of the mitochondrion and the chloroplast are landmark events in the evolution of life on Earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of the genes found in living relatives of their ancestors. While many of the 95% of missing organellar genes have been discarded, others have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer. Results Here, we demonstrate that the difference in the per-cell copy number of the organellar and nuclear genomes presents an energetic incentive to the cell to either delete organellar genes or transfer them to the nuclear genome. We show that, for the majority of transferred organellar genes, the energy saved by nuclear transfer exceeds the costs incurred from importing the encoded protein into the organelle where it can provide its function. Finally, we show that the net energy saved by endosymbiotic gene transfer can constitute an appreciable proportion of total cellular energy budgets and is therefore sufficient to impart a selectable advantage to the cell. Conclusion Thus, reduced cellular cost and improved energy efficiency likely played a role in the reductive evolution of mitochondrial and chloroplast genomes and the transfer of organellar genes to the nuclear genome.

As the most common RNA cap in eukaryotes, the 7-methylguanosine (m⁷G) cap impacts nearly all processes that a messenger RNA undergoes, such as splicing, polyadenylation, nuclear export, translation, and degradation. The metabolite and redox agent, nicotinamide adenine diphosphate (NAD⁺), can be used as an initiating nucleotide in RNA synthesis to result in NAD⁺-capped RNAs. Such RNAs have been identified in bacteria, yeast, and human cells, but it is not known whether they exist in plant transcriptomes. The functions of the NAD⁺ cap in RNA metabolism or translation are still poorly understood. Here, through NAD captureSeq, we show that NAD⁺-capped RNAs are widespread in Arabidopsis thaliana. NAD⁺-capped RNAs are predominantly messenger RNAs encoded by the nuclear and mitochondrial genomes, but not the chloroplast genome. NAD⁺-capped transcripts from the nuclear genome appear to be spliced and polyadenylated. Furthermore, although NAD⁺-capped transcripts constitute a small proportion of the total transcript pool from any gene, they are enriched in the polysomal fraction and associate with translating ribosomes. Our findings implicate the existence of as yet unknown mechanisms whereby the RNA NAD⁺ cap interfaces with RNA metabolic processes as well as translation initiation. More importantly, our findings suggest that cellular metabolic and/or redox states may influence, or be regulated by, mRNA NAD⁺ capping.

Trailliaedoxa gracilis W. W. Smith et Forrest (Rubiaceae), a Chinese endemic monotypic genus belonging to the Alberteae (Rubiaceae), exhibits a narrow distribution in the dry valleys of the Jinsha River and Red River drainage area in southwestern China. The few sites at which T. gracilis occurs are fragmented and isolated, and several are highly vulnerable to human disturbance. As T. gracilis is a protected plant with a second-degree national priority, the genetic diversity and structure of the populations of this species should be investigated to determine the most suitable conservation strategy. In this study, two chloroplast regions and one nuclear region were used to investigate the genetic diversity, genetic structure, and demographic history of T. gracilis. We observed a high total genetic diversity (H T = 0.952 and 0.966) and low average within-population diversity (H S = 0.07 and 0.489) based on cpDNA and nDNA analyses. Thus, a strong genetic structure (F ST = 0.98049 and 0.59731) was detected. A phylogeographic structure was detected by nuclear DNA analysis (N ST > G ST, P < 0.05); however, the chloroplast data did not show a significant phylogeographic structure (N ST < G ST, P > 0.05). The Bayesian skyline plot and isolation with migration analysis were used to estimate the demographic history of T. gracilis. The results indicated that a marked bottleneck effect occurred during the glacial-interglacial of the Pleistocene. Among the extant populations of T. gracilis, the population found in ChunJiang, LuQuan, and YuXi showed the highest haplotype diversity based on cpDNA sequences and should be given priority for protection. According to the nDNA analysis, every population presented a high level of diversity and a high content of private haplotypes. Therefore, every population should be protected.

Microalgae have potential to help meet energy and food demands without exacerbating environmental problems. There is interest in the unicellular green alga Chromochloris zofingiensis, because it produces lipids for biofuels and a highly valuable carotenoid nutraceutical, astaxanthin. To advance understanding of its biology and facilitate commercial development, we present a C. zofingiensis chromosome-level nuclear genome, organelle genomes, and transcriptome from diverse growth conditions. The assembly, derived from a combination of short- and long-read sequencing in conjunction with optical mapping, revealed a compact genome of ∼58 Mbp distributed over 19 chromosomes containing 15,274 predicted protein-coding genes. The genome has uniform gene density over chromosomes, low repetitive sequence content (∼6%), and a high fraction of protein-coding sequence (∼39%) with relatively long coding exons and few coding introns. Functional annotation of gene models identified orthologous families for the majority (∼73%) of genes. Synteny analysis uncovered localized but scrambled blocks of genes in putative orthologous relationships with other green algae. Two genes encoding beta-ketolase (BKT), the key enzyme synthesizing astaxanthin, were found in the genome, and both were up-regulated by high light. Isolation and molecular analysis of astaxanthin-deficient mutants showed that BKT1 is required for the production of astaxanthin. Moreover, the transcriptome under high light exposure revealed candidate genes that could be involved in critical yet missing steps of astaxanthin biosynthesis, including ABC transporters, cytochrome P450 enzymes, and an acyltransferase. The high-quality genome and transcriptome provide insight into the green algal lineage and carotenoid production.