Impact of mate availability, population size, and spatial aggregation of morphs on sexual reproduction in a distylous, aquatic plant

In distylous, self-incompatible plants, clonal propagation, unbalanced floral morph frequencies, and reduced population size can interfere with the functioning of distyly by compromising legitimate intermorph pollinations, resulting in reduced reproductive output. Here, we examined the mating system and the impact of mate availability, population size, and spatial aggregation of morphs on reproductive output in the distylous, clonal, aquatic plant Hottonia palustris. Controlled pollinations under greenhouse conditions detected no spontaneous selfing without the action of a pollen vector (autonomous autogamy) and demonstrated very low fruit and seed development after self-pollination. Intermorph (legitimate) crossings resulted in high reproductive output in both floral morphs (long- and short-styled individuals), whereas intramorph (illegitimate) crossings decreased fruit and seed development by more than 50%, indicating that the species has partial intramorph-incompatibility. In natural populations, small population size and increasing deviation of floral morph frequencies negatively affected reproductive outcome. Individuals of the majority morph type developed significantly fewer fruit and seeds than individuals of the minority morph type. This rapid decline in fecundity was symmetrical, indicating that regardless of which morph was in the majority, the same patterns of negative frequency-dependent mating occurred. Increasing spatial isolation between compatible morphs significantly reduced fruit and seed set in both morphs similarly. This study provides clear indications of frequency- and context-dependent mating in natural populations of a distylous plant species.     

Simplified method to obtain enhanced expression of tau protein from E. coli and one-step purification by direct boiling

Tau is an intrinsically disordered protein responsible for maintaining the structure and stability of axonal microtubules. However, in certain disease conditions including Alzheimer’s disease, tau protein may undergo biochemical and structural changes to form intracellular aggregates. Since tau is a proline- and arginine-rich eukaryotic protein, heterologous expression in Escherichia coli often results in poor yield and has been a major technical challenge. In the current work, we have improved the expressed yield of tau by overcoming codon bias problem and established a simplified protocol for efficient extraction. The reported method has two distinct features: (i) enhanced tau expression (upto eightfold) by supplementing deficient tRNAs that aid in rapid translation and (ii) direct boiling of expressed E. coli cells to extract tau with no separate cell lysis step. We further demonstrate that tau extracted by the direct boiling method is similar to tau purified by size-exclusion chromatography exhibiting similar structural and biophysical characteristics including aggregation propensity. Since morphologies and in vitro toxicity of fibrillar tau aggregates were also similar, tau extracted by the one-step direct boiling method can be used for tau aggregation assays without any additional purification.     

Expression and secretion of human bone morphogenetic protein-7 in pichia pastoris

The synonymous codons are used in a highly nonrandom manner in hosts of widely divergent species, which is termed ‘codon usage bias’. Several reports suggest that codon usage bias sometimes obstructs attempts to express high levels of exogenous genes. In this study, an attempt was made to express mature peptide of human bone morphogenetic protein-7 with optimized codons in P. pastoris expression system. Three low-usage ARG codons (CGG or CGA) in hBmp7 mature domain have been successfully transformed into P. pastoris-preferred ARG codons (AGA) with overlap extension PCR-based multiple-site-directed mutagenesis for a high level expression of hBMP7 mature peptide. The results of this study showed that the production level (25.45 mg/L) of a codon-optimized strain increased 4.6-fold in comparison with that (5.5 mg/L) of noncodon-optimized strain. A strain harboring multicopy of codon-optimized hbmp7 expression cassette showed an even higher expression level, which was about 2-fold compared with that of the single-copy one. These recombinant hBMP7 mature peptides were produced as 18-kD monomer proteins and were easily purified from culture supernatants using ion-exchange chromatography. Functional assay demonstrated that rhBMP7 could induce ectopic cartilage formation, although its inductive ability was much less active than that of CHO cell-derived hBMP7.     

Mating system shifts and transposable element evolution in the plant genus Capsella

Background

Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora.

Results

We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species.

Conclusion

Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-602) contains supplementary material, which is available to authorized users.     

Molecular evolution of the ent-kaurenoic acid oxidase gene in Oryzeae

We surveyed the substitution patterns in the ent-kaurenoic acid oxidase (KAO) gene in 11 species of Oryzeae with an outgroup in the Ehrhartoidaea. The synonymous and non-synonymous substitution rates showed a high positive correlation with each other, but were negatively correlated with codon usage bias and GC content at third codon positions. The substitution rate was heterogenous among lineages. Likelihood-ratio tests showed that the non-synonymous/synonymous rate ratio changed significantly among lineages. Site-specific models provided no evidence for positive selection of particular amino acid sites in any codon of the KAO gene. This finding suggested that the significant rate heterogeneity among some lineages may have been caused by variability in the relaxation of the selective constraint among lineages or by neutral processes.     

Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila

Natural selection influences synonymous mutations and synonymouscodon usage in many eukaryotes to improve the efficiency oftranslation in highly expressed genes. Recent studies of genecomposition in eukaryotes have shown that codon usage also variesindependently of expression levels, both among genes and atthe intragenic level. Here, we investigate rates of evolution(Ks) and intensity of selection (_s) on synonymous mutationsin two groups of genes that differ greatly in the length oftheir exons, but with equivalent levels of gene expression andrates of crossing-over in Drosophila melanogaster. We estimate_s using patterns of divergence and polymorphism in 50 Drosophilagenes (100 kb of coding sequence) to take into account possiblevariation in mutation trends across the genome, among genesor among codons. We show that genes with long exons exhibithigher Ks and reduced _s compared to genes with short exons.We also show that Ks and _s vary significantly across long exons,with higher Ks and reduced _s in the central region comparedto flanking regions of the same exons, hence indicating thatthe difference between genes with short and long exons can bemostly attributed to the central region of these long exons.Although amino acid composition can also play a significantrole when estimating Ks and _s, our analyses show that the differencesin Ks and _s between genes with short and long exons and acrosslong exons cannot be explained by differences in protein composition.All these results are consistent with the Interference Selection(IS) model that proposes that the Hill-Robertson (HR) effectcaused by many weakly selected mutations has detectable evolutionaryconsequences at the intragenic level in genomes with recombination.Under the IS model, exon size and exon-intron structure influencethe effectiveness of selection, with long exons showing reducedeffectiveness of selection when compared to small exons andthe central region of long exons showing reduced intensity ofselection compared to flanking coding regions. Finally, ourresults further stress the need to consider selection on synonymousmutations and its variation—among and across genes andexons—in studies of protein evolution.     

Under‐representation of avian studies in landscape genetics

Landscape genetics is a rapidly growing discipline that examines how heterogeneous landscapes and other environmental factors influence population genetic variation. We conducted a systematic review of the landscape genetic literature which demonstrates that birds are severely under‐represented relative to their species diversity and general publication prevalence. Most avian studies were on species that have relatively low dispersal ability, and we suggest that this reflects an assumed high vagility of birds that precludes spatial genetic variation relatable to landscape heterogeneity. However, spatial genetic variation exists in several bird species with very high dispersal ability, but this has not been considered in the context of landscape features. Genetic patterns may also relate to landscape due to breeding habitat selection and territorial behaviour, despite the fact that species may be able to move throughout different landscape elements with minimal movement costs. Habitat loss and fragmentation are continuing globally and are strongly related to declines in bird populations. Landscape genetic studies provide a means to understand, predict and mitigate the effects of anthropogenic landscape change on birds. This review promotes the need for landscape genetic studies of birds, such that a greater understanding of the drivers of their genetic structuring can be developed and generalizations can be made from landscape genetic studies that apply more broadly across taxa.     

Meta-analysis in applied ecology

This overview examines research synthesis in applied ecology and conservation. Vote counting and pooling unweighted averages are widespread despite the superiority of syntheses based on weighted combination of effects. Such analyses allow exploration of methodological uncertainty in addition to consistency of effects across species, space and time, but exploring heterogeneity remains controversial. Meta-analyses are required to generalize in ecology, and to inform evidence-based decision-making, but the more sophisticated statistical techniques and registers of research used in other disciplines must be employed in ecology to fully realize their benefits.     

Correspondence regarding October 31, 2003, Breakthroughs and Views by K. Brown and P.L. Carmichael

A. Fuglsang [Biochem. Biophys. Res. Commun. 317 (2004) 957-964] suggested that effective number of codons for individual amino acids (Nc-values) should be re-adjusted to the number of synonymous codons of those amino acids, in order to prevent the overestimation of the effective number of codons. Here, it is shown that re-adjustment at the level of individual amino acids results in loss of considerable amounts of information. Furthermore, we have shown that theoretical Nc-values are functions of GC3s (and GC1s); as a result, when an amino acid Nc-value exceeds the related theoretical Nc-value, the implication of re-adjustment depends on the GC composition of the gene.