An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

Advances in recent years have revolutionized our understanding of both the context and occurrence of polyploidy in plants. Molecular phylogenetics has vastly improved our understanding of plant relationships, enabling us to better understand trait and character evolution, including chromosome number changes. This, in turn, has allowed us to appreciate better the frequent occurrence and extent of polyploidy throughout the history of angiosperms, despite the occurrence of low chromosome numbers in some groups, such as in Arabidopsis (A. thaliana was the first plant genome to be sequenced and assembled). In tandem with an enhanced appreciation of phylogenetic relationships, the accumulation of genomic data has led to the conclusion that all angiosperms are palaeopolyploids, together with better estimates of the frequency and type of polyploidy in different angiosperm lineages. The focus therefore becomes when a lineage last underwent polyploidization, rather than simply whether a plant is ‘diploid’ or ‘polyploid’. This legacy of past polyploidization in plants is masked by large‐scale genome reorganization involving repetitive DNA loss, chromosome rearrangements (including fusions and fissions) and complex patterns of gene loss, a set of processes that are collectively termed ‘diploidization’. We argue here that it is the diploidization process that is responsible for the ‘lag phase’ between polyploidization events and lineage diversification. If so, diploidization is important in determining chromosome structure and gene content, and has therefore made a significant contribution to the evolutionary success of flowering plants. © 2015 The Authors. Botanical Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of Linnean Society of London, 2016, 180 , 1–5.     

Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait

Physiological novelties are often studied at macro‐evolutionary scales such that their micro‐evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C₄ photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C₄ and non‐C₄ genotypes, with some populations using laterally acquired C₄‐adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C₄ and non‐C₄ A. semialata individuals spanning the species’ range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C₄ components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally acquired genes for key C₄ functions were rapidly passed between populations with otherwise distinct genomic backgrounds. Thus, our intraspecific study of C₄‐related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations.     

Vessel-element dimensions and frequency within the most current growth increment along the length of Eucalyptus globulus stems

The mean number of vessels per unit area in the outer most growth increment at six percentage heights in individual trees, viewed in transverse section, showed an increasing trend from basal to apical regions. The highest frequency of vessels occurred at 90% of total tree height (23.58 mm^-2) while the lowest frequency (9.99 mm^-2) was recorded at 15% of total tree height from the base. Vessel elements were largest at 15% of total tree height and proceeded to decrease in size with increased stem height. Average radial measurements ranged between 111.27 µm and 160.0 µm while average tangential measurements ranged between 76.30 µm and 112.80 µm. There was variation seen at each percentage height between collection dates (i.e. individual trees); however, the trend of increasing vessel frequency from basal to apical regions existed regardless of between-tree variation in dimensions. Vessel-element dimensions showed a similar, but inverse trend to vessel-element frequency with the largest vessel elements located at 15% of total tree height and the smallest vessel elements located at 90% of total tree height.     

The distribution of a spliceosome protein in cereal (Triticeae) interphase nuclei from cells with different metabolic activities and through the cell cycle

A monoclonal antibody (mAb) KSm2 and three human Sm sere, which detect the ‘D’ polypeptide in mammals and is associated with the U1, U2, U4/U6, U5, U7, U9–U12 small nuclear RNAs, have been used in Western blotting to show that the antigen is conserved in wheat (Triticum aestivum cv. Beaver). Immunocytochemistry to wheat and a barley (Hordeum vulgare) suspension culture using the mAb KSm2 has shown that the ‘D’ polypeptide occurs in interphase nuclei as speckles and foci outside the nucleoli and as tracks. Nucleoli usually had at least one focus at their periphery. Immunocytochemistry at the electron microscope level of resolution has shown that the signal occurs between chromatin axes and predominantly in the outer domain of the nucleus. Analysis of the barley suspension culture demonstrated that there was a significant increase in antigen through G1, S to G2. In the wheat meristematic cells at prophase only the foci remained, and at metaphase the distribution of foci was asymmetrical with foci occurring either at one pole or on the metaphase plate. At telophase the foci appeared to decrease in size and were incorporated non-uniformly into the daughter nuclei because of their asymmetric distribution at metaphase. When wheat was grown at a range of temperatures, the root tip meristematic nuclei showed a number of different organization patterns. The average number of nucleoli increased and their size decreased. At the same time there was an increase in the average total area of foci as temperature increased from 4°, 10°, 25°, 34°, to 37°C. Thus the ‘D’ polypeptide distribution changes with metabolic activity and through the cell cycle.     

Improved gold chloride staining method for anatomical analysis of sensory nerve endings in the shoulder capsule and labrum as examples of loose and dense fibrous tissues

Consistency in gold chloride staining is essential for anatomical analysis of sensory nerve endings. The gold chloride stain for this purpose has been modified by many investigators, but often yields inconsistent staining, which makes it difficult to differentiate structures and to determine nerve ending distribution in large tissue samples. We introduce additional steps and major changes to the modified Gairns’ protocol. We controlled the temperature and mixing rate during tissue staining to achieve consistent staining and complete solution penetration. We subjected samples to sucrose dehydration to improve cutting efficiency. We then exposed samples to a solution containing lemon juice, formic acid and paraformaldehyde to produce optimal tissue transparency with minimal tissue deformity. We extended the time for gold chloride impregnation 1.5 fold. Gold chloride was reduced in the labrum using 25% formic acid in water for 18 h and in the capsule using 25% formic acid in citrate phosphate buffer for 2 h. Citrate binds gold nanoparticles, which minimizes aggregation in the tissue. We stored samples in fresh ultrapure water at 4° C to slow reduction and to maintain color contrast in the tissue. Tissue samples were embedded in Tissue Tek and sectioned at 80 and 100 μm instead of using glycerin and teasing the tissue apart as in Gairns’ modified gold chloride method. We attached sections directly to gelatin subbed slides after sectioning with a cryostat. The slides then were processed and coverslipped with Permount. Staining consistency was demonstrated throughout the tissue sections and neural structures were clearly identifiable.     

Genome size diversity in orchids: consequences and evolution

Background

The amount of DNA comprising the genome of an organism (its genome size) varies a remarkable 40 000-fold across eukaryotes, yet most groups are characterized by much narrower ranges (e.g. 14-fold in gymnosperms, 3- to 4-fold in mammals). Angiosperms stand out as one of the most variable groups with genome sizes varying nearly 2000-fold. Nevertheless within angiosperms the majority of families are characterized by genomes which are small and vary little. Species with large genomes are mostly restricted to a few monocots families including Orchidaceae.

Scope

A survey of the literature revealed that genome size data for Orchidaceae are comparatively rare representing just 327 species. Nevertheless they reveal that Orchidaceae are currently the most variable angiosperm family with genome sizes ranging 168-fold (1C = 0·33–55·4 pg). Analysing the data provided insights into the distribution, evolution and possible consequences to the plant of this genome size diversity.

Conclusions

Superimposing the data onto the increasingly robust phylogenetic tree of Orchidaceae revealed how different subfamilies were characterized by distinct genome size profiles. Epidendroideae possessed the greatest range of genome sizes, although the majority of species had small genomes. In contrast, the largest genomes were found in subfamilies Cypripedioideae and Vanilloideae. Genome size evolution within this subfamily was analysed as this is the only one with reasonable representation of data. This approach highlighted striking differences in genome size and karyotype evolution between the closely related Cypripedium, Paphiopedilum and Phragmipedium. As to the consequences of genome size diversity, various studies revealed that this has both practical (e.g. application of genetic fingerprinting techniques) and biological consequences (e.g. affecting where and when an orchid may grow) and emphasizes the importance of obtaining further genome size data given the considerable phylogenetic gaps which have been highlighted by the current study.Key words: AFLP, C-value, chromosome, evolution, genome size, guard cell size, Orchidaceae, Robertsonian fission, Robertsonian fusion