Comparative plastomics of Amaryllidaceae: inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq.

Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution.

The complete plastome of the South African species, Amaryllis belladonna L. (Amaryllidaceae).

The complete plastome sequence of Amaryllis belladonna L. is assembled and annotated. This is the type species of Amaryllis and therefore the type of the family Amaryllidaceae and as such, is important to document the phylogenetic position of the family. The plastome sequence has a length of 158,145 bp, with the large single copy (LSC) regions comprising 85,963 bp, the small single copy (SSC) 18634 bp and two identical inverted repeats (IR) regions each of 26,774 bp. Phylogenetic analysis fully resolved Amaryllis in a clade with Crinum L. in the Amaryllidoideae, as expected, with the Allioideae as a sister group. Agapanthus (Agapanthoideae) is a sister to the other two subfamilies in the Amaryllidaceae. The phylogenetic tree produced corresponds to previous topologies based on plastome molecular markers including matK, ndhF and rbcL. This is the first paper reporting the whole plastome comparison of the type genera of all three subfamilies in the Amaryllidaceae.

When do apples stop growing, and why does it matter?

Apples in the commercial food chain are harvested up to two weeks before maturity. We explore apple fruit development through the growing season to establish the point at which physical features differentiating those cultivars become evident. This is relevant both for the understanding of the growing process and to ensure that any identification and classification tools can be used both on ripened-on-tree and stored fruit. Current literature presents some contradictory findings on apple growth, we studied 12 apple cultivars in the Brogdale National Fruit Collection, UK over two seasons to establish patterns of growth. Fruit were sampled at regular time points throughout the growing season and four morphometrics (maximum length, maximum diameter, weight, and centroid size) were collected. These were regressed against growing degree days in order to appropriately describe the growth pattern observed. All four morphometrics were adequately described using log-log linear regressions, with adjusted R2 estimates ranging from 78.3% (maximum length) to 86.7% (weight). For all four morphometrics, a 10% increase in growing degree days was associated with a 1% increase in the morphometric. Our findings refine previous work presenting rapid early growth followed by a plateau in later stages of development and contrast with published expo-linear models. We established that apples harvested for commercial storage purposes, two weeks prior to maturity, showed only a modest decrease in size compared with ripened-on-tree fruit, demonstrating that size morphometric approaches are appropriate for classification of apple fruit at point of harvest.

Apples before the fall: Does shape stability coincide with maturity?

Fruit shape is the result of the interaction between genetic, epigenetic, environmental factors and stochastic processes. As a core biological descriptor both for taxonomy and horticulture, the point at which shape stability is reached becomes paramount in apple cultivar identification, and authentication in commerce. Twelve apple cultivars were sampled at regular intervals from anthesis to harvest over two growing seasons. Linear and geometric morphometrics were analysed to establish if and when shape stabilised and whether fruit asymmetry influenced this. Shape stability was detected in seven cultivars, four asymmetric and three symmetric. The remaining five did not stabilise. Shape stability, as defined here, is cultivar-dependent, and when it occurs, it is late in the growing season. Geometric morphometrics detected stability more readily than linear, especially in symmetric cultivars. Key shape features are important in apple marketing, giving the distinctness and apparent uniformity between cultivars expected at point of sale.

The complete plastome of Hyacinthoides non-scripta (L.) Chouard ex Rothm. (Asparagaceae).

The whole plastome sequence of Hyacinthoides non-scripta, was assembled and annotated in this study. This is the first complete plastid genome for the genus Hyacinthoides. The plastome is 155,035 bp long and consists of a large single-copy (LSC) region spanning 83,947 bp, a small single-copy (SSC) region spanning 18,496 bp, and two inverted repeat (IR) regions, each of which is 26,296 bp in length. There are 132 genes annotated in the plastome, of which the protein-coding gene infA has pseudogenized.

Nomenclatural changes in Coleus and Plectranthus (Lamiaceae): a tale of more than two genera.

A synopsis of the genera Coleus Lour, Equilabium A.J.Paton, Mwany. & Culham and Plectranthus L'Hér. (Lamiaceae, Tribe Ocimeae, Subtribe Plecranthinae) is presented. Generic delimitation follows a recently published molecular phylogeny which identified Coleus as the sister of the remaining genera of Subtribe Plectranthinae; Plectranthus as sister to Tetradenia Benth. and Thorncroftia N.E.Br., and a separate phylogenetically distinct genus Equilabium comprising species previously placed in Plectranthus. In this treatment, 294 species of Coleus, 42 of Equilabium, and 72 of Plectranthus are recognized. All but one of the combinations in Equilabium are new as only the genus and type species have been previously published. Two-hundred and twelve names are changed to combinations in Coleus from Plectranthus, Pycnostachys Hook. and Anisochilus Benth.

Enhancing identification accuracy for powdery mildews using previously underexploited DNA loci.

The internal transcribed spacer (ITS) DNA marker is routinely used for fungal identification but gives a clear result for only three out of four powdery mildew samples. A search for new markers indicates that some genes offer enhanced identification in comparison with ITS. Others fail due to amplification and sequencing difficulties and lack of informative variability. Powdery mildews (Ascomycota, Erysiphales) are biotrophic, fungal plant pathogens that commonly occur worldwide on a wide range of host plants. They are unsightly and greatly reduce the vigor of their hosts and have major impacts on crop and other cultivated plants. Species within this order are straightforward to spot, but difficult to identify. A citizen science scheme was run in 2013-2016 in the UK to gather a wide array of samples on which identification methods could be developed. Current techniques for identification and phylogenetic reconstruction show scope for improvement. In this paper, we review genes used in other fungal groups for discrimination at species level. Working protocols for amplification and sequencing of seven genes (actin, ß-tubulin, calmodulin,Chs, elongation factor 1-α [EF1-α], Mcm7, and Tsr1) are developed with varying success; Mcm7 proves to be the most useful at differentiation between closely related, phylogenetically young powdery mildew species for phylogenetic reconstruction when used separately and in tandem with ITS. We therefore propose this as the most appropriate candidate gene to be used commonly in powdery mildew diagnostics alongside the ITS; furthermore, this could be transferred to similarly troublesome fungal clades.

The complete plastome of Daphne laureola L. (Thymelaeaceae).

The complete plastome sequence for the type species of Daphne, Daphne laureola, was assembled and annotated in this study. The total length of the D. laureola plastome is 171,613 bp and comprises the large single copy (LSC) spanning 85,316 bp, the small single copy (SSC) spanning 2855 bp, and two inverted repeat (IR) regions each of 41,721 bp length. The SSC contains only two genes: ndhF and rpl32. This sequence extends the list of Thymelaeaceae plastomes to be used in future systematic studies of the family and is the first European species to be sampled.

Can you make morphometrics work when you know the right answer? Pick and mix approaches for apple identification.

Morphological classification of living things has challenged science for several centuries and has led to a wide range of objective morphometric approaches in data gathering and analysis. In this paper we explore those methods using apple cultivars, a model biological system in which discrete groups are pre-defined but in which there is a high level of overall morphological similarity. The effectiveness of morphometric techniques in discovering the groups is evaluated using statistical learning tools. No one technique proved optimal in classification on every occasion, linear morphometric techniques slightly out-performing geometric (72.6% accuracy on test set versus 66.7%). The combined use of these techniques with post-hoc knowledge of their individual successes with particular cultivars achieves a notably higher classification accuracy (77.8%). From this we conclude that even with pre-determined discrete categories, a range of approaches is needed where those categories are intrinsically similar to each other, and we raise the question of whether in studies where potentially continuous natural variation is being categorised the level of match between categories is routinely set too high.

The complete chloroplast genome of Narcissus poeticus L. (Amaryllidaceae: Amaryllidoideae).

The first complete chloroplast genome sequence for Narcissus is assembled and annotated in this study. The total length of the N. poeticus chloroplast genome is 160,099 bp and comprises the large single copy (LSC) spanning 86,445 bp, the small single copy (SSC) spanning 16,434 bp, and two inverted repeat regions each of 28,610 bp length. The truncated copy of ycf1 before the junction between IRB and SSC was 1277-2428 bp longer than in other included Asparagales samples. A potential pseudogene, cemA, was also identified. This is the first reported plastome for Amaryllidaceae subfamily Amaryllidoideae.

Microsatellite markers for hoop-petticoat daffodils (Narcissus sect. Bulbocodii; Amaryllidaceae).

PREMISE OF THE STUDY: Microsatellite markers were developed using hoop-petticoat daffodils (Narcissus sect. Bulbocodii; Amaryllidaceae) to aid in the taxonomic revision of the section, and to further evaluate their broad applicability for daffodil cultivar identification. METHODS AND RESULTS: Three hundred fifty-one primer pairs were developed using a commercial service. Nineteen polymorphic and repeatable markers were developed by screening 67 of these primer pairs. Of these, 11 chosen markers were used to screen 317 samples; the number of alleles per locus ranged from four to 21, and the observed heterozygosity ranged from 0.101 to 0.297. There were null genotypes in some samples for six of the markers. All the microsatellites were transferable to other Narcissus sections. CONCLUSIONS: The results indicate that these new markers have sufficient potential variation to be used for taxonomic revision of the genus and to distinguish many commercial daffodil cultivars.

A decadal view of biodiversity informatics: challenges and priorities.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

How global is the global biodiversity information facility?

There is a concerted global effort to digitize biodiversity occurrence data from herbarium and museum collections that together offer an unparalleled archive of life on Earth over the past few centuries. The Global Biodiversity Information Facility provides the largest single gateway to these data. Since 2004 it has provided a single point of access to specimen data from databases of biological surveys and collections. Biologists now have rapid access to more than 120 million observations, for use in many biological analyses. We investigate the quality and coverage of data digitally available, from the perspective of a biologist seeking distribution data for spatial analysis on a global scale. We present an example of automatic verification of geographic data using distributions from the International Legume Database and Information Service to test empirically, issues of geographic coverage and accuracy. There are over 1/2 million records covering 31% of all Legume species, and 84% of these records pass geographic validation. These data are not yet a global biodiversity resource for all species, or all countries. A user will encounter many biases and gaps in these data which should be understood before data are used or analyzed. The data are notably deficient in many of the world's biodiversity hotspots. The deficiencies in data coverage can be resolved by an increased application of resources to digitize and publish data throughout these most diverse regions. But in the push to provide ever more data online, we should not forget that consistent data quality is of paramount importance if the data are to be useful in capturing a meaningful picture of life on Earth.

A phyloclimatic study of Cyclamen.

BACKGROUND: The impact of global climate change on plant distribution, speciation and extinction is of current concern. Examining species climatic preferences via bioclimatic niche modelling is a key tool to study this impact. There is an established link between bioclimatic niche models and phylogenetic diversification. A next step is to examine future distribution predictions from a phylogenetic perspective. We present such a study using Cyclamen (Myrsinaceae), a group which demonstrates morphological and phenological adaptations to its seasonal Mediterranean-type climate. How will the predicted climate change affect future distribution of this popular genus of garden plants? RESULTS: We demonstrate phylogenetic structure for some climatic characteristics, and show that most Cyclamen have distinct climatic niches, with the exception of several wide-ranging, geographically expansive, species. We reconstruct climate preferences for hypothetical ancestral Cyclamen. The ancestral Cyclamen lineage has a preference for the seasonal Mediterranean climate characteristic of dry summers and wet winters. Future bioclimatic niches, based on BIOCLIM and Maxent models, are examined with reference to a future climate scenario for the 2050s. Over the next 50 years we predict a northward shift in the area of climatic suitability, with many areas of current distribution becoming climatically unsuitable. The area of climatic suitability for every Cyclamen species is predicted to decrease. For many species, there may be no areas with a suitable climate regardless of dispersal ability, these species are considered to be at high risk of extinction. This risk is examined from a phylogenetic perspective. CONCLUSION: Examining bioclimatic niches from a phylogenetic perspective permits novel interpretations of these models. In particular, reconstruction of ancestral niches can provide testable hypothesis about the historical development of lineages. In the future we can expect a northwards shift in climatic suitability for the genus Cyclamen. If this proves to be the case then dispersal is the best chance of survival, which seems highly unlikely for ant-dispersed Cyclamen. Human-assisted establishment of Cyclamen species well outside their native ranges offers hope and could provide the only means of dispersal to potentially suitable future environments. Even without human intervention the phylogenetic perspective demonstrates that major lineages could survive climate change even if many species are lost.

Development of a PCR-based assay for rapid and reliable identification of pathogenic Fusaria.

Identification of Fusarium species has always been difficult due to confusing phenotypic classification systems. We have developed a fluorescent-based polymerase chain reaction assay that allows for rapid and reliable identification of five toxigenic and pathogenic Fusarium species. The species includes Fusarium avenaceum, F. culmorum, F. equiseti, F. oxysporum and F. sambucinum. The method is based on the PCR amplification of species-specific DNA fragments using fluorescent oligonucleotide primers, which were designed based on sequence divergence within the internal transcribed spacer region of nuclear ribosomal DNA. Besides providing an accurate, reliable, and quick diagnosis of these Fusaria, another advantage with this method is that it reduces the potential for exposure to carcinogenic chemicals as it substitutes the use of fluorescent dyes in place of ethidium bromide. Apart from its multidisciplinary importance and usefulness, it also obviates the need for gel electrophoresis.

Restriction analysis of PCR amplified nrDNA regions revealed intraspecific variation within populations of Fusarium culmorum.

Seventy-five isolates of Fusarium culmorum with diverse geographical origin and host were analyzed using restriction digestion of polymerase chain reaction amplified nuclear ribosomal DNA intergenic spacer (IGS) and 28S gene regions. The 28S gene was conserved and has produced identical restriction patterns, however, the IGS region was substantially variable. The isolates were divided into 29 unique IGS haplotypes. There was limited resolution between clustering of isolates and their origin and/or host. The variability was distributed largely equally at both macro- and micro-geographical scale. The phylogeographic distribution pattern suggests a seed-borne dispersal of F. culmorum.

Cylindrocladium buxicola, a new species affecting Buxus spp., and its phylogenetic status.

A leaf and twig blight disease of Buxus spp. was found to be associated with a new species of Cylindrocladium. The novel species status was confirmed using morphological characters, sequencing of the ribosomal 5.8S RNA gene and the flanking internal transcribed spacers (ITS), the ß-tubulin gene, and the high mobility group (HMG) of the MAT2 mating type gene. Cylindrocladium buxicola is proposed as a new name. Fifteen isolates from the UK and one isolate from New Zealand were paired in all combinations but no fertile perithecia were obtained suggesting that C. buxicola is heterothallic and all isolates belonged to one mating type. AFLP analysis showed that the isolates collected in the UK and New Zealand are genetically homogenous. Phylogenetic analyses indicated that this species falls within a new lineage.