The distribution of sexual function in the flowering plant: from monoecy to dioecy

In flowering plants, male and female functions are usually closely associated in the same flowers, as predicted by resource allocation theory. However, the benefits of outbreeding can lead to unisexual flowers and the physiological control of their distribution across the plant (monoecy). Monoecy is thought to be a major route to dioecy (separation of sexual function of different individuals). The developmental and functional problems associated with unisexual flowers may thus be solved at the level of the evolution of monoecy. Consequently, the evolution of dioecy from monoecy requires mutations in only a single gene. Here various scenarios (conceptual models) are presented for the evolution of monoecy and dioecy, including scenarios consistent with known cases of single-gene control of dioecy, such as in Populus, and the artificial breeding of dioecy from monoecy experimentally achieved in Zea and Cucumis. Attention is also drawn here to the phenomenon of pleogamy, the minor or occasional occurrence of additional sex morphs within a species, which may provide important information about the genetic and developmental control of various sexual systems. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.

Some sexual consequences of being a plant

Plants have characteristic features that affect the expression of sexual function, notably the existence of a haploid organism in the life cycle, and in their development, which is modular, iterative and environmentally reactive. For instance, primary selection (the first filtering of the products of meiosis) is via gametes in diplontic animals, but via gametophyte organisms in plants. Intragametophytic selfing produces double haploid sporophytes which is in effect a form of clonal reproduction mediated by sexual mechanisms. In homosporous plants, the diploid sporophyte is sexless, sex being only expressed in the haploid gametophyte. However, in seed plants, the timing and location of gamete production is determined by the sporophyte, which therefore has a sexual role, and in dioecious plants has genetic sex, while the seed plant gametophyte has lost genetic sex. This evolutionary transition is one that E.J.H. Corner called 'the transference of sexuality'. The iterative development characteristic of plants can lead to a wide variety of patterns in the distribution of sexual function, and in dioecious plants poor canalization of reproductive development can lead to intrasexual mating and the production of YY supermales or WW superfemales. Finally, plant modes of asexual reproduction (agamospermy/apogamy) are also distinctive by subverting gametophytic processes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.

Whole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility

Whole‐genome sequencing of non‐model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data‐handling. Three such regions are the major histocompatibility complex (MHC), sex‐determining regions (SDRs) and the plant self‐incompatibility locus (S‐locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short‐read sequences against multiple alternative references improves genotyping comprehensiveness at the S‐locus thereby contributing to more accurate assessments of allelic frequencies. Long‐read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S‐locus haplotypes. These advances are adding value to short‐read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.

Functional Characterization of Terpene Synthases Accounting for the Volatilized-Terpene Heterogeneity in Lathyrus odoratus Cultivar Flowers

Lathyrus odoratus (sweet pea) is an ornamental plant with exceptional floral scent, previously used as an experimental organism in the early development of Mendelian genetics. However, its terpene synthases (TPSs), which act as metabolic gatekeepers in the biosynthesis of volatile terpenoids, remain to be characterized. Auto-Headspace Solid-phase Microextraction/Gas chromatography-mass spectrometry analysis of floral volatile terpene constituents from seven sweet pea cultivars identified α-bergamotene, linalool, (-)-α-cubebene, geraniol, β-caryophyllene and β-sesquiphellandrene as the dominant compounds. RNA sequencing was performed to profile the transcriptome of L. odoratus flowers. Bioinformatic analysis identified eight TPS genes (acronymed as LoTPS) that were successfully cloned, heterologously expressed and functionally analyzed. LoTPS4 and LoTPS7, belonging to the TPS-b clade, biochemically catalyzed the formation of monoterpenes and sesquiterpenes. LoTPS3 and LoTPS8, placed in the TPS-a clade, also generated monoterpenes and sesquiterpenes, while LoTPS12 belonging to the TPS-g clade showed linalool/nerolidol synthase activity. Notably, biochemical assays of the recombinant LoTPS proteins revealed their catalytic promiscuity, and the enzymatic products were basically consistent with major volatile compounds released from sweet pea flowers. The data from our study lay the foundation for the chemical ecology, molecular genetics and biotechnological improvement of sweet pea and other legumes (Fabaceae).

Salix transect of Europe: records of willow-associated weevils (Coleoptera: Curculionoidea) from Greece to Arctic Norway, with insights from DNA barcoding

Background

Curculionid beetles associated with willow (Salix spp.) were surveyed at 42 sites across Europe, from Greece (lat. 38.8 °N) to arctic Norway (lat. 69.7 °N). DNA sequence data provide additional verification of identifications and geographic clustering.

New information

In all, 73 curculionid species were collected from willows, of which seven were particularly abundant. The most widespread species were: Acalyptuscarpini Fabricius, 1793 at 15 sites; Tachyergesstigma Germar, 1821 at 13 sites; Phyllobiusoblongus (Linnaeus, 1758) at 11 sites; Phyllobiusmaculicornis Germar, 1824 at 10 sites; and Archariussalicivorus (Paykull, 1792), Melanapionminimum (Herbst, 1797), and Phyllobiuscf.pyri (Linnaeus, 1758) all at nine sites. The mean number of curculionid species collected on willow at each site was 5.5 (range 0-14). Compared to chrysomelids, curculionids were richer in species but the species had relatively low average abundance. Widespread curculionid species appear to have scattered and patchy observed distributions with limited geographical structuring in our data. However, deeper sampling (e.g. over multiple seasons and years), would give a better indication of distribution, and may increase apparent geographical structuring. There is some site-to-site variation in colour in a few taxa, but little notable size variation. DNA barcoding, performed on some of the more common species, provides clear species clusters and definitive separation of the taxonomically more challenging species, as well as some interesting geographic insights. Our northernmost sample of Phyllobiusoblongus is unique in clustering with Canadian samples of this species. On the other hand, our samples of Acalyptuscarpini cluster with European samples and are distinct from a separate Canadian cluster of this species. We provide the first available DNA sequences for Phyllobiusthalassinus Gyllenhal, 1834 (Hungary).

A single gene underlies the dynamic evolution of poplar sex determination

Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive¹. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR-Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes.

Gene expression trajectories during male and female reproductive development in balsam poplar (Populus balsamifera L.)

Plant reproductive development from the first appearance of reproductively committed axes through to floral maturation requires massive and rapid remarshalling of gene expression. In dioecious species such as poplar this is further complicated by divergent male and female developmental programs. We used seven time points in male and female balsam poplar (Populus balsamifera L.) buds and catkins representing the full annual flowering cycle, to elucidate the effects of time and sex on gene expression during reproductive development. Time (developmental stage) is dominant in patterning gene expression with the effect of sex nested within this. Here, we find (1) evidence for five successive waves of alterations to the chromatin landscape which may be important in setting the overall reproductive trajectory, regardless of sex. (2) Each individual developmental stage is further characterized by marked sex-differential gene expression. (3) Consistent sexually differentiated gene expression regardless of developmental stage reveal candidates for high-level regulators of sex and include the female-specific poplar ARR17 homologue. There is also consistent male-biased expression of the MADS-box genes PISTILLATA and APETALA3. Our work provides insights into expression trajectories shaping reproductive development, its potential underlying mechanisms, and sex-specific translation of the genome information into reproductive structures in balsam poplar.

Moth versus fly: a preliminary study of the pollination mode of two species of endemic Asteraceae from St Helena (Commidendrum robustum and C. rugosum) and its conservation implications

Commidendrumrobustum (Roxb.) DC. (St Helena gumwood) and C.rugosum (Dryand.) DC. (St Helena scrubwood) are ecologically important, endemic woody Asteraceae from the isolated South Atlantic island of St Helena. Once very abundant, they now exist in sparse fragmented populations due to 500 years of environmental destruction. They are sister taxa that evolved on the island and are reported to hybridise. Commidendrumrugosum has a saucer-like erect capitulum, whereas C.robustum has a somewhat globular hanging capitulum. Using daytime timelapse photography to follow capitula through their life cycle, we found that C.rugosum appears to be myophilous, visited largely by flies (including the endemic syrphid, Sphaerophoriabeattiei Doesburg & Doesburg) and occasionally by Lepidoptera. Commidendrumrobustum, on the other hand, although visited by flies, strongly attracts moths (especially noted at the Millennium Forest site). Our data suggest that moth visits may reduce visits from flies due to the sensitivity of flies to interference by other insects. We conclude that C.robustum may have a mixed syndrome of myophily/phalaenophily and that there is apparently some divergence of the pollination niche between the two species. Its potential in attracting moths, coupled with its former abundance, suggests that it may have been a major food source for adults of the numerous endemic moths. Pollinator activity was measured by insect visitation rates (mean visits per capitulum per day, V) and insect residence time (mean pollinator kiloseconds per capitulum per day, R). Both are higher for C.robustum (C.rugosum, V = 16.4, R = 3.101; C.robustum, V = 34.0, R = 8.274), reflecting the abundance of moths on the capitula at the Millennium Forest site. The conservation implications of the pollination mode are that: (1) there is considerable pollinator activity on the capitula and pollination is not currently a limiting factor for plant reproduction; (2) gene exchange between geographically-isolated populations of C.rugosum is likely to be minimal due to the apparent reliance of the species for pollination on small flies (especially Sphaerophoriabeattiei), which are believed to be not effective as pollinators over long distances (> 1 km). A possible exception is the strong-flying drone-fly, Eristalistenax Linn. which, although not as abundant as Sphaerophoria, does visit the flowers; (3) there is considerable overlap between the two species in flower visitors and interspecific pollen transfer is possible where the two species grow intermixed (which has potential positive and negative implications for species survival).

Salix transect of Europe: patterns in the distribution of willow-feeding psyllids (Hemiptera: Psylloidea) from Greece to arctic Norway

Background Psyllids are oligophagous phytophagous insects with many specialist willow (Salix spp.) feeding species in two genera (Cacopsylla and Bactericera). We examine the patterns of distribution and co-occurrence of willow-feeding species at 42 willow sites across Europe forming a transect from Greece (lat. 38.8 °N) to arctic Norway (lat. 70.6 °N). The transect and sites have been described in previous papers. New information A total of 1245 individual psyllids were examined from 23 species of willow over the transect, representing 17 willow-feeding species (11 Cacopsylla and 6 Bactericera). Numerous species were very widely distributed, with two species, Bactericera albiventris (Foerster, 1848) and Cacopsylla pulchra (Zetterstedt, 1840), occurring from Greece to Finland. Other widespread species (Romania to Finland) were Cacopsylla ambigua (Foerster, 1848) and Bactericera curvatinervis (Foerster, 1848). The mean number of psyllid species per site was 2.4 (1.3 Cacopsylla, 1.1 Bactericera).

Default Sex and Single Gene Sex Determination in Dioecious Plants

A well-established hypothesis for the evolution of dioecy involves two genes linked at a sex-determining region (SDR). Recently there has been increased interest in possible single gene sex determination. Work in Populus has finally provided direct experimental evidence for single gene sex determination in plants using CRISPR-Cas9 to knock out a single gene and convert individuals from female to male. In poplar, the feminizing factor popARR17 acts as a "master regulator", analogous to the mammalian masculinizing factor SRY. The production of fully functional males from females by a simple single gene knockout is experimental evidence that an antagonistic male-determining factor does not exist in Populus. Mammals have a "default sex" (female), as do poplar trees (Populus), although the default sex in poplars is male. The occurrence of single gene sex determination with a default sex may be much commoner in plants than hitherto expected, especially when dioecy evolved via monoecy. The master regulator does not even need to be at the SDR (although it may be). In most poplars the feminizing factor popARR17 is not at the SDR, but instead a negative regulator of it. So far there is little information on how high-level regulators are connected to floral phenotype. A model is presented of how sex-determining genes could lead to different floral morphologies via MADS-box floral developmental genes.

Genome of the tropical plant Marchantia inflexa: implications for sex chromosome evolution and dehydration tolerance

We present a draft genome assembly for the tropical liverwort, Marchantia inflexa, which adds to a growing body of genomic resources for bryophytes and provides an important perspective on the evolution and diversification of land plants. We specifically address questions related to sex chromosome evolution, sexual dimorphisms, and the genomic underpinnings of dehydration tolerance. This assembly leveraged the recently published genome of related liverwort, M. polymorpha, to improve scaffolding and annotation, aid in the identification of sex-linked sequences, and quantify patterns of sequence differentiation within Marchantia. We find that genes on sex chromosomes are under greater diversifying selection than autosomal and organellar genes. Interestingly, this is driven primarily by divergence of male-specific genes, while divergence of other sex-linked genes is similar to autosomal genes. Through analysis of sex-specific read coverage, we identify and validate genetic sex markers for M. inflexa, which will enable diagnosis of sex for non-reproductive individuals. To investigate dehydration tolerance, we capitalized on a difference between genetic lines, which allowed us to identify multiple dehydration associated genes two of which were sex-linked, suggesting that dehydration tolerance may be impacted by sex-specific genes.

The genetic dimension of pest pressure in the tropical rainforest

Wet tropical forests are among the most diverse ecosystems on Earth and can host several hundreds of tree species per hectare. To maintain such diversity, the community must contain large numbers of relatively rare species rather than be dominated by a few very common trees, as is often the case in temperate forests. Explaining the mechanisms preventing dominance by common species has been a major task of tropical forest ecology. One of the most promising mechanisms is negative density dependence (NDD) of tree abundance driven by pests, including fungal diseases ('pest pressure'). NDD entails that the chance of survival of a sapling increases with the distance from a mature tree of the same species, thus preventing species from becoming locally dominant. Curiously, the strength of NDD is negatively correlated with abundance, meaning that tree species that are more common generally show weaker NDD (Comita et al. ). Interactions between plants and soil pathogens have been shown to play an important role in NDD (Klironomos ), and rare species are apparently more strongly affected (Mangan et al. ). However, the genetic mechanisms underlying this phenomenon have remained obscure. In this issue of Molecular Ecology, Marden et al. () suggest that reduced diversity of the genes involved in pathogen recognition (Resistance genes or R genes) could explain why NDD is stronger in locally rare species.

Hybridization between pollination syndromes as an ecological and evolutionary resource

In plants, pollination syndromes (the correlated presence of many features of relevance to pollination mode, for instance pollination by a particular animal clade) are a striking feature of plant biodiversity, providing great floral phenotypic diversity (Fenster et al. ). Adaptation to a particular animal pollinator provides an explanation for why recently diverged plants can have such extreme differentiation in floral form. One might expect such elaborate adaptations to provide a high degree of pollinator specificity and hence reproductive isolation, but there are many cases where substantial gene flow exists between extreme floral morphs (see Table 1), and the resulting hybrids may be highly fertile. This gene flow provides tremendous opportunities to study the genetics and biology of the pollination syndromes by providing intermediate forms and segregating genotypes. If it is true that pollination syndromes result from adaptation under strong selection, we will expect such flowers to be crucibles of natural selection. If strong selection for particular floral phenotypes can be shown, then this, when coupled with hybridization, will give us one of the most valuable of all experimental systems for evolutionary research: gene flow and selection in balance. In this issue of Molecular Ecology, the paper of Milano et al. () delivers this. It shows that in populations of the Ipomopsis aggregata complex, gene flow between pollination morphs is high and selection to stabilize those morphs is also high: a probable case of gene flow-selection balance.

DNA Methylation and the Evolution of Developmental Complexity in Plants

All land plants so far examined use DNA methylation to silence transposons (TEs). DNA methylation therefore appears to have been co-opted in evolution from an original function in TE management to a developmental function (gene regulation) in both phenotypic plasticity and in normal development. The significance of DNA methylation to the evolution of developmental complexity in plants lies in its role in the management of developmental pathways. As such it is more important in fine tuning the presence, absence, and placement of organs rather than having a central role in the evolution of new organs. Nevertheless, its importance should not be underestimated as it contributes considerably to the range of phenotypic expression and complexity available to plants: the subject of the emerging field of epi-evodevo. Furthermore, changes in DNA methylation can function as a "soft" mutation that may be important in the early stages of major evolutionary novelty.

Temporal, but not spatial, changes in expression patterns of petal identity genes are associated with loss of papillate conical cells and the shift to bird pollination in Macaronesian Lotus (Leguminosae)

In the generally bee-pollinated genus Lotus a group of four species have evolved bird-pollinated flowers. The floral changes in these species include altered petal orientation, shape and texture. In Lotus these characters are associated with dorsiventral petal identity, suggesting that shifts in the expression of dorsal identity genes may be involved in the evolution of bird pollination. Of particular interest is Lotus japonicus CYCLOIDEA 2 (LjCYC2), known to determine the presence of papillate conical cells on the dorsal petal in L. japonicus. Bird-pollinated species are unusual in not having papillate conical cells on the dorsal petal. Using RT-PCR at various stages of flower development, we determined the timing of expression in all petal types for the three putative petal identity genes (CYC-like genes) in different species with contrasting floral morphology and pollination syndromes. In bird-pollinated species the dorsal identity gene, LjCYC2, is not expressed at the floral stage when papillate conical cells are normally differentiating in bee-pollinated species. In contrast, in bee-pollinated species, LjCYC2 is expressed during conical cell development. Changes in the timing of expression of the above two genes are associated with modifications in petal growth and lateralisation of the dorsal and ventral petals in the bird-pollinated species. This study indicates that changes in the timing, rather than spatial distribution, of expression likely contribute to the modifications of petal micromorphology and petal size during the transition from bee to bird pollination in Macaronesian Lotus species.

Sexual epigenetics: gender-specific methylation of a gene in the sex determining region of Populus balsamifera

Methylation has frequently been implicated in gender determination in plants. The recent discovery of the sex determining region (SDR) of balsam poplar, Populus balsamifera, pinpointed 13 genes with differentiated X and Y copies. We tested these genes for differential methylation using whole methylome sequencing of xylem tissue of multiple individuals grown under field conditions in two common gardens. The only SDR gene to show a marked pattern of gender-specific methylation is PbRR9, a member of the two component response regulator (type-A) gene family, involved in cytokinin signalling. It is an ortholog of Arabidopsis genes ARR16 and ARR17. The strongest patterns of differential methylation (mostly male-biased) are found in the putative promoter and the first intron. The 4th intron is strongly methylated in both sexes and the 5th intron is unmethylated in both sexes. Using a statistical learning algorithm we find that it is possible accurately to assign trees to gender using genome-wide methylation patterns alone. The strongest predictor is the region coincident with PbRR9, showing that this gene stands out against all genes in the genome in having the strongest sex-specific methylation pattern. We propose the hypothesis that PbRR9 has a direct, epigenetically mediated, role in poplar sex determination.

Salix transect of Europe: structured genetic variation and isolation-by-distance in the nettle psyllid, Trioza urticae (Psylloidea, Hemiptera), from Greece to Arctic Norway

BACKGROUND

The common nettle (Urtica dioica L.) is co-associated with willows (Salix spp.) in riparian habitats across Europe. We sampled the widespread nettle psyllid, Trioza urticae (Linné, 1758), from Urtica in willow habitats on a megatransect of Europe from the Aegean to the Arctic Ocean. The aim of this study was to use an unusually widespread insect to assess the influence of geographic distances and natural geographic barriers on patterns of genetic variation and haplotype distribution.

NEW INFORMATION

Phylogeographic analysis using DNA sequences of two mtDNA regions, COI and cytB, shows that T. urticae specimens are organized into four regional groups (southern, central, northern and arctic). These groups are supported by both phylogenetic analysis (four geographically-based clades) and network analysis (four major haplotype groups). The boundary between southern and central groups corresponds to the Carpathian Mountains and the boundary between the central and northern groups corresponds to the Gulf of Finland. Overall these groups form a latitudinal cline in genetic diversity, which decreases with increasing latitude.

Salix transect of Europe: patterns in the most abundant chrysomelid beetle (Coleoptera: Chrysomelidae) herbivores of willow from Greece to Arctic Norway

BACKGROUND

Chrysomelid beetles associated with willow (Salix spp.) were surveyed at 41 sites across Europe, from Greece (lat. 38.8 °N) to arctic Norway (lat. 69.7 °N).

NEW INFORMATION

In all, 34 willow-associated chrysomelid species were encountered, of which eight were very abundant. The abundant species were: Crepidodera aurata Marsham, 1802 at 27 sites, Phratora vitellinae (Linnaeus, 1758) at 21 sites, Galerucella lineola (Fabricius, 1781) at 19 sites, Crepidodera fulvicornis (Fabricius, 1792) at 19 sites, Plagiodera versicolora (Laicharting, 1781) at 11 sites, Crepidodera plutus (Latreille, 1804) at nine sites, Chrysomela vigintipunctata Scopoli, 1763 at nine sites and Gonioctena pallida (Linnaeus, 1758) at eight sites. The mean number of willow associated chrysomelid morphospecies at each site was 4.2. Around 20% of the total variance in chrysomelid distribution could be accounted for by latitude, but this is mainly due to distinctive occurrence patterns at the northern and southern parts of the transect. There was a paucity of chrysomelids at Greek sites and a distinctively northern faunal composition at sites north of Poland. Considerable site-to-site variation in colour was noted, except in G. lineola, which was chromatically invariant.

Salix transect of Europe: variation in ploidy and genome size in willow-associated common nettle, Urtica dioica L. sens. lat., from Greece to arctic Norway

Background

The common stinging nettle, Urticadioica L. sensu lato, is an invertebrate "superhost", its clonal patches maintaining large populations of insects and molluscs. It is extremely widespread in Europe and highly variable, and two ploidy levels (diploid and tetraploid) are known. However, geographical patterns in cytotype variation require further study.

New information

We assembled a collection of nettles in conjunction with a transect of Europe from the Aegean to Arctic Norway (primarily conducted to examine the diversity of Salix and Salix-associated insects). Using flow cytometry to measure genome size, our sample of 29 plants reveals 5 diploids and 24 tetraploids. Two diploids were found in SE Europe (Bulgaria and Romania) and three diploids in S. Finland. More detailed cytotype surveys in these regions are suggested. The tetraploid genome size (2C value) varied between accessions from 2.36 to 2.59 pg. The diploids varied from 1.31 to 1.35 pg per 2C nucleus, equivalent to a haploid genome size of c. 650 Mbp. Within the tetraploids, we find that the most northerly samples (from N. Finland and arctic Norway) have a generally higher genome size. This is possibly indicative of a distinct population in this region.

Salix transect of Europe: latitudinal patterns in willow diversity from Greece to arctic Norway

Background

Willows (Salix spp.) are ecosystem "foundation species" that are hosts to large numbers of associated insects. Determining their patterns of distribution across Europe is therefore of interest for understanding the spatial distribution of associated fauna. The aim of this study was to record species composition at multiple sites on a long latitudinal gradient (megatransect) across Europe as a baseline for the future detailed analysis of insect fauna at these sites. In this way we used willow stands as comparable mesocosms in which to study floristic and faunistic changes with latitude across Europe.

New information

To determine spatial patterning of  an ecologically important group on a latitudinal gradient across Europe, we sampled willows at the stand level in 42 sites, approximately 100 km apart, from the Aegean (38.8°N) to the Arctic Ocean (70.6°N), but at a similar longitude (21.2 to 26.1°E). The sites were predominantly lowland (elevations 1 to 556 metres amsl, median = 95 m) and wet (associated with rivers, lakes, drainage ditches or wet meadows). The median number of willow taxa (species and hybrids) per stand was four, and varied from one to nine. There is a progressive increase in willow diversity from south to north with the median number of taxa per stand in southern Europe being three, and in northern Europe six. A total of 20 willow species were recorded, along with 12 hybrids. The most widespread willow in the transect was Salixalba L. (occurring in 20 sites out of 42) followed by S.triandra L. (15 sites), S.caprea L., S.phylicifolia L. (14 sites) and S.myrsinifolia Salisb., Salix×fragilis L. (13 sites). Voucher specimens from this study are deposited in the herbaria of the Natural History Museum (BM) and the Royal Botanic Gardens Kew (K). These samples provide a "snapshot" of willow diversity along a latitudinal gradient and an indication of the geographically changing taxonomic diversity that is presented to willow-feeding herbivores across Europe. It is anticipated that further papers will examine the insect fauna collected from these sites as part of this study.

Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

Background

Some clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus.

Results

The Trifolium plastomes fell into two groups: those of Trifolium boissieri, T. strictum and T. glanduliferum (representing subgenus Chronosemium and subg. Trifolium section Paramesus) were tractable, assembled readily and were not unusual in the general context of Fabeae plastomes. The other Trifolium species (“core Trifolium”) proved refractory to assembly mainly because of numerous short duplications. These species form a single clade, which we call the “refractory clade” (comprising subg, Trifolium sections Lupinaster, Trifolium, Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the refractory clade are the presence of numerous short duplications and 7-15% longer genomes than the tractable species. Molecular dating estimates that the origin of the most recent common ancestor (MRCA) of the refractory clade is approximately 13.1 million years ago (MYA). This is considerably younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA) and Trifolium subg. Trifolium (16.1 MYA).

Conclusions

We conclude that the unusual repetitive plastome type previously characterized in Trifolium subterraneum had a single origin within Trifolium and is characteristic of most (but not all) species of subgenus Trifolium. It appears that an ancestral plastome within Trifolium underwent an evolutionary change resulting in plastomes that either actively promoted, were permissive to, or were unable to control, duplications within the genome. The precise mechanism of this important change in the mode and tempo of plastome evolution deserves further investigation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0228-6) contains supplementary material, which is available to authorized users.

DNA barcodes successfully identified Macaronesian Lotus (Leguminosae) species within early diverged lineages of Cape Verde and mainland Africa

Plant DNA barcoding currently relies on the application of a two-locus combination, matK + rbcL. Despite the universality of these two gene regions across plants, it is suspected that this combination might not have sufficient variation to discriminate closely related species. In this study, we tested the performance of this two-locus plant barcode along with the additional plastid regions trnH-psbA, rpoC1 and rpoB and the nuclear region internal transcribed spacer (nrITS) in a group of 38 species of Lotus from the Macaronesian region. The group has radiated into the five archipelagos within this region from mid-Miocene to early Pleistocene, and thus provides both early divergent and recent radiations that pose a particularly difficult challenge for barcoding. The group also has 10 species considered under different levels of conservation concern. We found different levels of species discrimination depending on the age of the lineages. We obtained 100 % of the species identification from mainland Africa and Cape Verde when all six regions were combined. These lineages radiated >4.5 Mya; however, in the most recent radiations from the end of the Pliocene to the mid-Pleistocene (3.5-1.5 Mya), only 30 % of the species were identified. Of the regions examined, the intergenic region trnH-psbA was the most variable and had the greatest discriminatory power (18 %) of the plastid regions when analysed alone. The nrITS region was the best region when analysed alone with a discriminatory power of 26 % of the species. Overall, we identified 52 % of the species and 30 % of the endangered or threatened species within this group when all six regions were combined. Our results are consistent with those of other studies that indicate that additional approaches to barcoding will be needed in recently evolved groups, such as the inclusion of faster evolving regions from the nuclear genome.

Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species

Background

Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species.

Results

(i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome.

Conclusions

(i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a “fingerprint” to identify and characterize cacao accessions.

Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

PREMISE OF STUDY

To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA-barcoding using next-generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions of the traditional DNA-barcoding loci in the plastid and ribosomal DNA, we call our approach ultra-barcoding (UBC).

METHODS

We used high-throughput next-generation sequencing to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an individual of the related species T. grandiflorum, as well as an additional publicly available whole plastid genome of T. cacao.

KEY RESULTS

All individuals of T. cacao examined were uniquely distinguished, and evidence of reticulation and gene flow was observed. Sequence variation was observed in some of the canonical barcoding regions between species, but other regions of the chloroplast were more variable both within species and between species, as were ribosomal spacers. Furthermore, no single region provides the level of data available using the complete plastid genome and rDNA.

CONCLUSIONS

Our data demonstrate that UBC is a viable, increasingly cost-effective approach for reliably distinguishing varieties and even individual genotypes of T. cacao. This approach shows great promise for applications where very closely related or interbreeding taxa must be distinguished.

Botany without borders: barcoding in focus

This recent meeting, held on the campus of the University of British Columbia, attracted 1200 delegates and a vast array of talks, but was notable for a remarkable showing of talks and posters on DNA barcoding in plants, spread through many sessions. The Canadian Centre for DNA Barcoding defines barcoding as 'species identification and discovery through the analysis of short, standardized gene regions known as DNA barcodes'. This approach is somewhat controversial in animals (Rubinoff et al., 2006), although it has been shown to be useful and reliable in many metazoan taxa (Meyer & Paulay 2005; Hajibabaei et al., 2007), in which the mitochondrial cytochrome oxidase I (COI) gene is used. However, in land plants, COI evolves far too slowly to be useful, and there is no obvious single universal alternative (Fazekas et al., 2008).Genes that work well in one taxon may perform poorly in other taxa. Additionally, some perfectly good plant species,reproductively isolated and morphologically and ecologically distinct, are too young to show much sequence divergence at most loci. Nevertheless, as we saw at this conference, progress has been made towards identifying genes that serve many of the functions of DNA barcodes, at least in some plant taxa.

Bird-pollinated flowers in an evolutionary and molecular context

Evolutionary shifts to bird pollination (ornithophily) have occurred independently in many lineages of flowering plants. This shift affects many floral features, particularly those responsible for the attraction of birds, deterrence of illegitimate flower visitors (particularly bees), protection from vigorous foraging by birds, and accurate placement of pollen on bird's bodies. Red coloration appears to play a major role in both bee-deterrence and bird-attraction. Other mechanisms of bird-attraction include the production of abundant dilute nectar and the provision of secondary perches (for non-hovering birds). As a result of selection for similar phenotypic traits in unrelated bird-pollinated species, a floral syndrome of ornithophily can be recognized, and this review surveys the component floral traits. The strong convergent evolution evident in bird-pollinated flowers raises a question about the nature of the genetic mechanisms underlying such transitions and whether the same gene systems are involved in most cases. As yet there is too little information to answer this question. However, some promising model systems have been developed that include closely related bee and bird-pollinated flowers, such as Ipomoea, Mimulus, and Lotus. Recent studies of floral developmental genetics have identified numerous genes important in the development of the floral phenotype, which are also potential candidates for involvement in shifts between bee-pollination and bird pollination. As more whole-genome information becomes available, progress should be rapid.

Phenotype ontologies: the bridge between genomics and evolution

Understanding the developmental and genetic underpinnings of particular evolutionary changes has been hindered by inadequate databases of evolutionary anatomy and by the lack of a computational approach to identify underlying candidate genes and regulators. By contrast, model organism studies have been enhanced by ontologies shared among genomic databases. Here, we suggest that evolutionary and genomics databases can be developed to exchange and use information through shared phenotype and anatomy ontologies. This would facilitate computing on evolutionary questions pertaining to the genetic basis of evolutionary change, the genetic and developmental bases of correlated characters and independent evolution, biomedical parallels to evolutionary change, and the ecological and paleontological correlates of particular types of change in genes, gene networks and developmental pathways.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Legume comparative genomics: progress in phylogenetics and phylogenomics

The legumes are the focus of numerous rapidly expanding genomic projects, all of which involve members of one part of the Leguminosae, the subfamily Papilionoideae. This subfamily is monophyletic, and recent studies concur on a series of clades within it that are well supported and have received informal names. These include the Cladrastis clade, the genistoids (including Lupinus), the mirbelioids, the dalbergioids (including Arachis), the millettioids (including Glycine and Phaseolus), and the hologalegina (galegoid) legumes, which comprise the robinioids (including Lotus) and the inverted repeat loss (IRL) clade (including Medicago and Pisum). The canavanine-accumulating legumes appear to fall into a single clade, consistent with the idea that the production of this toxic amino acid evolved only once. Recent advances in analytical techniques for dating phylogenies support an 'early explosion hypothesis', suggesting that much of the morphological diversity of the legume family evolved rapidly around 50-60 million years ago. Within the papilionoids, the divergence between Glycine and Medicago is estimated to have taken place around 54 million years ago. There is strong evidence for a palaeoduplication event that affected both Glycine (a millettioid) and Medicago (from the IRL clade). As more genomic data are forthcoming for Arachis, it will be possible to test whether this event extends to the dalbergioids.

Molecular phylogeny of Incarvillea (Bignoniaceae) based on ITS and trnL-F sequences

Incarvillea is a herbaceous and temperate member of Bignoniaceae, previously divided into four subgenera, Niedzwedzkia, Amphicome, Incarvillea, and Pteroscleris. Niedzwedzkia and Amphicome have in the past been treated as independent genera. Different relationships have been proposed for the four subgenera. Here, maximum parsimony analysis using ITS and trnL-F sequences resulted in similar trees and showed that the genus is monophyletic. Analysis of the combined data resulted in a single tree with five major clades highly supported and well resolved. The relationships of the five major clades are (subgenus Niedzwedzkia (Incarvillea olgae (subgenus Amphicome (subgenus Incarvillea, subgenus Pteroscleris)))). All four subgenera are well supported for monophyly, with the exception of subgenus Incarvillea, represented here by I. sinensis and I. olgae. Incarvillea olgae is not closely related to I. sinensis, a conclusion supported by morphology. The two basal monotypic subgenera are found in Central Asia. The most species-rich subgenus, Pteroscleris, has 10 species in the Himalaya-Hengduan Mountains and may have dispersed early from central Asia to eastern Asia. Short branch lengths on the molecular trees within Pteroscleris suggest a recent and rapid radiation of this rosette-forming subgenus, perhaps connected with the uplift of the Himalaya-Hengduan massif.

The role of KNOX genes in the evolution of morphological novelty in Streptocarpus

The genus Streptocarpus comprises species with diverse body plans. Caulescent species produce leaves from a conventional shoot apical meristem (SAM), whereas acaulescent species lack a conventional SAM and produce only a single leaf (the unifoliate form) or clusters of leaves from the base of more mature leaves (the rosulate form). These distinct morphologies reflect fundamental differences in the role of the SAM and the process of leaf specification. A subfamily of KNOTTED-like homeobox (KNOX) genes are known to be important in regulating meristem function and leaf development in model species with conventional morphologies. To test the involvement of KNOX genes in Streptocarpus evolution, two parologous KNOX genes (SSTM1 and SSTM2) were isolated from species with different growth forms. Their phylogenetic analysis suggested a gene duplication before the subgeneric split of Streptocarpus and resolved species relationships, supporting multiple evolutionary origins of the rosulate and unifoliate morphologies. In S. saxorum, a caulescent species with a conventional SAM, KNOX proteins were expressed in the SAM and transiently downregulated in incipient leaf primordia. The ability of acaulescent species to initiate leaves from existing leaves was found to correlate with SSTM1 expression and KNOX protein accumulation in leaves and to reflect genetic differences at two loci. Neither locus corresponded to SSTM1, suggesting that cis-acting differences in SSTM1 regulation were not responsible for evolution of the rosulate and unifoliate forms. However, the involvement of KNOX proteins in leaf formation in rosulate species suggests that they have played an indirect role in the development of morphological diversity in Streptocarpus.

Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences

Phylogenetic relationships of eight species of Saintpaulia H. Wendl., 19 species of Streptocarpus Lindl. (representing all major growth forms within the genus), and two outgroups (Haberlea rhodopensis Friv., Chirita spadiciformis W. T. Wang) were examined using comparative nucleotide sequences from the two internal transcribed spacers (ITS) of nuclear ribosomal DNA. The length of the ITS 1 region ranged from 228 to 249 base pairs (bp) and the ITS 2 region from 196 to 245 bp. Pairwise sequence divergence across both spacers for ingroup and outgroup species ranged from 0 to 29%. Streptocarpus is not monophyletic, and Saintpaulia is nested within Streptocarpus subgenus Streptocarpella. Streptocarpus subgenus Streptocarpus is monophyletic. The ITS sequence data demonstrate that the unifoliate Streptocarpus species form a clade, and are also characterized by a unique 47-bp deletion in ITS 2. The results strongly support the monophyly of (1) Saintpaulia, and (2) Saintpaulia plus the African members of the subgenus Streptocarpella of Streptocarpus. The data suggest the evolution of Saintpaulia from Streptocarpus subgenus Streptocarpella. The differences in flower and vegetative characters are probably due to ecological adaptation leading to a relatively rapid radiation of Saintpaulia.