Evolution at the tips: Asclepias phylogenomics and new perspectives on leaf surfaces

Contrasting patterns of genetic and phenotypic divergence of two sympatric congeners, Phragmites australis and P. hirsuta, in heterogeneous habitats

Habitat heterogeneity leads to genome-wide differentiation and morphological and ecological differentiation, which will progress along the speciation continuum, eventually leading to speciation. Phragmites hirsuta and Phragmites australis are sympatric congeners that coexist in saline-alkaline meadow soil (SAS) and sandy soil (SS) habitats of the Songnen Meadow. The results provided genetic evidence for two separate species of reeds. Genetic diversity and spatial genetic structure supported the specialist-generalist variation hypothesis (SGVH) in these two sympatric reed species, suggesting that P. australis is a generalist and P. hirsuta is a habitat specialist. When we compared these different species with respect to phenotypic and genetic variation patterns in different habitats, we found that the phenotypic differentiation of P. australis between the two habitats was higher than that of P. hirsuta. Multiple subtle differences in morphology, genetic background, and habitat use collectively contribute to ecological success for similar congeners. This study provided evidence of the two reed congeners, which should contribute to their success in harsh environments.

Role of plant relatedness in plant-soil feedback dynamics of sympatric Asclepias species

Plants affect associated biotic and abiotic edaphic factors, with reciprocal feedbacks from soil characteristics affecting plants. These two-way interactions between plants and soils are collectively known as plant-soil feedbacks (PSFs). The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of PSFs, although the strength and direction of feedbacks among sympatric congeners are not well-understood. We examined plant-soil feedback responses of Asclepias syriaca, a common clonal milkweed species, with several sympatric congeners across a gradient of increasing phylogenetic distances (A. tuberosa, A. viridis, A. sullivantii, and A. verticillata, respectively). Plant-soil feedbacks were measured through productivity and colonization by arbuscular mycorrhizal (AM) fungi. Asclepias syriaca produced less biomass in soils conditioned by the most phylogenetically distant species (A. verticillata), relative to conspecific-conditioned soils. Similarly, arbuscular mycorrhizal (AM) fungal colonization of A. syriaca roots was reduced when grown in soils conditioned by A. verticillata, compared with colonization in plants grown in soil conditioned by any of the other three Asclepias species, indicating mycorrhizal associations are a potential mechanism of observed positive PSFs. This display of differences between the most phylogenetically distant, but not close or intermediate, paring(s) suggests a potential phylogenetic threshold, although other exogenous factors cannot be ruled out. Overall, these results highlight the potential role of phylogenetic distance in influencing positive PSFs through mutualists. The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of plant-soil feedbacks (PSFs), although the strength and direction of feedbacks among sympatric congeners are not well-understood. Congeneric, sympatric milkweeds typically generated positive PSFs in terms of productivity and AM fungal colonization, suggesting the low likelihood of coexistence among tested pairs, with a strength of feedback increasing as the phylogenetic distance increases.

The complete plastome of Cynanchum rostellatum (Apocynaceae), an indigenous plant in Korea

The climbing plant Cynanchum rostellatum (Turcz.) Liede & Khanum is widely distributed throughout Korea and Northeast Asia as a member of the Apocynaceae family. Although this plant has a high value in medicinal and industrial purposes, genetic research on this plant is insufficient. This study announces the complete plastid genome (plastome) sequence of C. rostellatum with 663× mean coverage, which was assembled using 763 Mbp short-read data generated by the Illumina HiSeq X platform. The C. rostellatum plastome was 158,018 bp in length and displayed the typical quadripartite structure composed of the large single-copy (LSC) region (89,058 bp), the small single-copy (SSC) region (18,718 bp), and a pair of inverted repeat (IR) regions (25,116 bp). A total of 129 genes have been annotated, including 84 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis indicated the genus Cynanchum including 12 Cynanchum plastome sequences, was monophyletic and was located within the sub-family Asclepiadoideae. Two C. rostellatum plastomes, including the plastome assembled in this study, formed a subclade and were sister to the C. thesioides plastome, whereas the other C. rostellatum, which was previously reported one, was located within the clade of C. wilfordii and C. bungei.

Evolution of shade tolerance is associated with attenuation of shade avoidance and reduced phenotypic plasticity in North American milkweeds

PREMISE

Mismatches between light conditions and light-capture strategy can reduce plant performance and prevent colonization of novel habitats. Although light-capture strategies tend to be highly conserved among closely related species, evolutionary transitions from shaded to unshaded habitats (and vice versa) occur in numerous plant lineages.

METHODS

We combined phylogenetic approaches with field and greenhouse experiments to investigate evolutionary constraints on light-capture strategy in North American milkweeds (genus Asclepias) and to determine whether colonization of shaded habitats in this heliophilic clade is associated with reduced plasticity and attenuation of the shade avoidance response.

RESULTS

Colonization of shaded habitats has occurred at least 10 times in this genus, including at least once in each major North American clade. Evolutionary transitions between habitats exhibit strong directional bias, with shifts from full-sun to shaded habitats occurring at least three times as often as the opposite transition. In field and greenhouse experiments, sun species responded to shade by increasing internode length, height, and specific leaf area, consistent with the shade avoidance response; paired shade species exhibited reduced plasticity overall, and only one trait (specific leaf area) responded to experimental shade.

CONCLUSIONS

Our results suggest that milkweeds colonized shaded environments multiple times using a light-capture strategy distinct from the ancestral (putatively shade avoidant) strategy, including a general attenuation of plasticity in response to variable light conditions. This pattern bolsters the notion that shade avoidance and tolerance represent divergent evolutionary strategies for maximizing performance under qualitatively different types of shade.

Genome size and identification of repetitive DNA sequences using low coverage sequencing in Hancornia speciosa Gomes (Apocynaceae: Gentianales)

Repetitive DNA is an important component of eukaryotic genomes, accounting for more than 90% of the genome size of some species, including mobile elements and satellite DNA sequences. The aim of study was to characterize the genome of Hancornia speciosa Gomes using C-value genome size estimate and repetitive DNA sequences analysis. The genome size estimate was obtained by flow cytometry and the repetitive DNA sequences were accessed using graph-based clustering. Evolutionary relationships among species of Apocynaceae was obtained using reads of Catharanthus roseus L., Rhayza stricta Decne, and Asclepias syriaca L. from the NCBI and analyzed by graph-based clustering. The genome size estimates in two botanical varieties showed 2C-values ranging from 0.88 to 1.08 pg, indicating small genome size. Clusters representing repeats making up at least 0.01% of the genome revealed the proportion of repetitive DNA ranging from 19.87% (H. speciosa) to 51.674% (A. syriaca), of which the mobile elements were more abundant. Satellite DNA sequences were not found in H. speciosa and R. stricta, while at least one satellite was detected in C. roseus and A. syriaca, suggesting that the LTR retrotransposon Ty3/Gypsy/Chromovirus may have replaced the satellite DNA in H. speciosa and R. stricta.

Light/heat effects on RNA editing in chloroplast NADH-plastoquinone oxidoreductase subunit 2 (ndhB) gene of Calotropis (Calotropis procera)

Background

RNA editing is common in terrestrial plants, especially in mitochondria and chloroplast. In the photosynthesis process, NAD dehydrogenase plays a very important role. Subunit 2 of NADH-dehydrogenase is one of the major subunits in NAD dehydrogenase complex. Using desert plant Calotropis (Calotropis procera), this study focuses on the RNA editing activity of ndhB based on light time.

Results

NdhB (NADH-dehydrogenase subunit 2) gene accession no. MK144329 was isolated from Calotropis procera genomic data (PRJNA292713). Additionally, using RNA-seq data, the cDNA of the ndhB gene of C. procera was isolated at three daylight periods, i.e., dawn (accession no. MK165161), at midday (accession no. MK165160), and pre-dusk (accession no. MK165159). Seven RNA editing sites have been found in several different positions (nucleotide no. C467, C586, C611, C737, C746, C830, and C1481) within the ndhB coding region. The rate of these alterations was deferentially edited across the three daylight periods. RNA editing rate of ndhB gene was highest at dawn, (87.5, 79.6, 78.5, 76, 68.6, 39.3, and 96.9%, respectively), less in midday (74.8, 54.1, 62.6, 47.4, 45.5, 47.4, and 93.4%, respectively), and less at pre-dusk (67, 52.6, 56.9, 40.1, 40.7, 33.2, and 90%, respectively), also all these sites were validated by qRT-PCR.

Conclusion

The differential editing of chloroplast ndhB gene across light periods may be led to a somehow relations between the RNA editing and control of photosynthesis.

Agrobacterium tumefaciens-Mediated Transformation of Three Milkweed Species (Asclepias hallii, A. syriaca, and A. tuberosa: Apocynaceae)

Milkweeds have ecological significance for insect herbivores that rely on them as hosts for either part of or the entirety of their life cycles. Interesting interactions, some of which are not completely understood, have evolved over time. To develop these species as models to elucidate the interplay with insect herbivores, we established Agrobacterium tumefaciens-mediated transformation approaches for Asclepias hallii (Hall's milkweed), A. syriaca (common milkweed), and A. tuberosa (butterflyweed). The method is based on infection of stem internodal explants, which were more amenable to transformation than leaf explants. We found that addition of freshly prepared dithiothreitol was critical to prevent browning of stem explants. Depending on the species, the time from infection to the regeneration of transgenic lines ranges from 2 to 4 months. Transformation efficiency for A. hallii was 9%, whereas efficiencies for A. syriaca and A. tuberosa were 6% and 13%, respectively. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Agrobacterium tumefaciens-mediated transformation of Asclepias internodal stem explants Basic Protocol 2: Preparation of Agrobacterium glycerol stocks containing gene constructs.

Phenolic Profile, Antioxidant and Anti-Proliferative Activities of Methanolic Extracts from Asclepias linaria Cav. Leaves

Asclepias linaria Cav. (Apocynaceae) is a shrubby plant endemic of Mexico which has been used in traditional medicine. However, the bioactive potential of this plant remains unexplored. In this study, the phenolic composition, antioxidant, and cytotoxic activities of A. linaria leaves were determined. In order to estimate the phenolic composition of the leaves, the total phenolic, flavonoid, and condensed tannins contents were determined. Furthermore, the antioxidant activity was measured by the scavenging activity of the 2,2-diphenyl-1-picrylhydrazyl (DPPH^•) and 2,2′-azino-bis[3-ethylbenzothiazoline-6-sulphonic acid] (ABTS^•+) radicals and the total antioxidant capacity. The phenolic compounds identified in the A. linaria leaves by ultra-performance liquid chromatography coupled to mass spectrometry (UPLC-MS) include phenolic acids, such as p-coumaric and ferulic acid, as well as flavonoids, such as rutin and quercetin. The leaves’ extracts of A. linaria showed a high scavenging activity of DPPH^• and ABTS^•+ radicals (IC₅₀ 0.12 ± 0.001 and 0.51 ± 0.003 µg/mL, respectively), high total antioxidant capacity values (99.77 ± 4.32 mg of ascorbic acid equivalents/g of dry tissue), and had a cytotoxic effect against K562 and HL60 hematologic neoplasia cells lines, but no toxicity towards the normal mononuclear cell line was observed. These results highlight the potential of A. linaria and could be considered as a possible alternative source of anticancer compounds.

A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae

Milkweeds (Asclepias) are used in wide-ranging studies including floral development, pollination biology, plant-insect interactions and co-evolution, secondary metabolite chemistry, and rapid diversification. We present a transcriptome and draft nuclear genome assembly of the common milkweed, Asclepias syriaca. This reconstruction of the nuclear genome is augmented by linkage group information, adding to existing chloroplast and mitochondrial genomic resources for this member of the Apocynaceae subfamily Asclepiadoideae. The genome was sequenced to 80.4× depth and the draft assembly contains 54,266 scaffolds ≥1 kbp, with N50 = 3,415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome. A total of 14,474 protein-coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated. A large proportion of gene space is represented in the assembly, with 96.7% of Asclepias transcripts, 88.4% of transcripts from the related genus Calotropis, and 90.6% of proteins from Coffea mapping to the assembly. Scaffolds covering 75 Mbp of the Asclepias assembly formed 11 linkage groups. Comparisons of these groups with pseudochromosomes in Coffea found that six chromosomes show consistent stability in gene content, while one may have a long history of fragmentation and rearrangement. The progesterone 5β-reductase gene family, a key component of cardenolide production, is likely reduced in Asclepias relative to other Apocynaceae. The genome and transcriptome of common milkweed provide a rich resource for future studies of the ecology and evolution of a charismatic plant family.

Trade-offs constrain the evolution of an inducible defense within but not between plant species

Inducible defense is a common form of phenotypic plasticity, and inducibility (change in defense after herbivore attack) has long been predicted to trade off with constitutive (or baseline) defense to manage resource allocation. Although such trade-offs likely constrain evolution within species, the extent to which they influence divergence among species is unresolved. We studied cardenolide toxins among genetic families in eight North American Asclepias species, spanning the full range of defense in the genus. Using common environment experiments and chemical assays, we report a consistent trade-off (negative genetic correlation) between concentrations of constitutive cardenolides and their inducibility within each species. However, no trade-off was found in a phylogenetic analysis across species. To investigate factors driving differences in defense allocation among species we used latitude as a proxy for growing season and herbivore pressure and found that divergence into lower latitudes resulted in evolution of higher cardenolides overall. Next we used an enzymatic assay of the cellular target of cardenolides (sodium-potassium ATPase) and confirm that higher cardenolides resulted in stronger toxicity to a sensitive species, but not to specialized monarch butterflies. Thus, plant speciation into biogeographic regions with alternative resources or pest pressure resulted in the macroevolution of cardenolide defense, especially against unspecialized herbivores. Nonetheless, trade-offs persist in the extent to which this defense is allocated constitutively or is inducible among genotypes within each species.

NGS-Indel Coder: A pipeline to code indel characters in phylogenomic data with an example of its application in milkweeds (Asclepias)

Targeted genome sequencing approaches allow characterization of evolutionary relationships using a considerable number of nuclear genes and informative characters. However, most phylogenomic analyses only utilize single nucleotide polymorphisms (SNPs). Studies at the species level, especially in groups that have recently radiated, often recover low amounts of phylogenetically informative variation in coding regions, and require non-coding sequences, which are richer in indels, to resolve gene trees. Here, NGS-Indel Coder, a pipeline to detect and omit false positive indels inferred from assemblies of short read sequence data, was developed to resolve the relationships among and within major clades of the American milkweeds (Asclepias), which are the result of a rapid and recent evolutionary radiation, and whose phylogeny has been difficult to resolve. This pipeline was applied to a Hyb-Seq data set of 768 loci including targeted exons and flanking intron regions from 33 milkweed species. Robust species tree inference was improved by excluding small alignment partitions (<100 bp) that increased gene tree ambiguity and incongruence. To further investigate the robustness of indel coding, data sets that included small and large indels were explored, and species trees derived from concatenated loci versus coalescent methods based on gene trees were compared. The phylogeny of Asclepias obtained using nuclear data was well resolved, and phylogenetic information from indels improved resolution of specific nodes. The Temperate North American, Mexican Highland, and Incarnatae clades were well supported as monophyletic. Asclepias coulteri, which has been considered part of the Sonoran Desert clade based on plastome analyses, was placed as sister to all the other milkweed species studied here, rather than as a member of that clade. Two groups within the Temperate North American and Mexican clades were not resolved, and the inferred relationships strongly conflicted when comparing results based on data sets that did or did not include indel characters. This new pipeline represents a step forward in making maximal use of the information content in phylogenomic data sets.

The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection

The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata, a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae-Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.