Detection of rare paternal chloroplast inheritance in controlled crosses of the endangered sunflower Helianthus verticillatus

Genetic diversities in wild and cultivated populations of the two closely-related medical plants species, Tripterygium Wilfordii and T. Hypoglaucum (Celastraceae)

BACKGROUND

The sustainable supply of medicinal plants is important, and cultivating and domesticating them has been suggested as an optimal strategy. However, this can lead to a loss of genetic diversity. Tripterygium wilfordii Hook. f. is a medicinal plant commonly used in traditional Chinese medicine, but its wild populations are dwindling due to excessive harvesting. To protect the species and meet the increasing demand, it is urgent to cultivate it on a large scale. However, distinguishing between T. wilfordii and T. hypoglaucum, two similar species with different medicinal properties, is challenging. Therefore, it is crucial to understand the genetic diversity and population structure of these species for their sustainable utilization.

RESULTS

In this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. Our results indicated that the two species maintain a high level of genetic divergence, indicating possible genetic bases for the different contents of bioactive compounds of the two species. T. wilfordii showed lower genetic diversity and less subdivided population structures of both markers than T. hypoglaucum. The potential factors in shaping these interesting differences might be differentiated pollen-to-seed migration rates, interbreeding, and history of population divergence. Analyses of cpDNA and microsatellite loci supported that the two species are genetically distinct entities. In addition, a significant reduction of genetic diversity was observed for cultivated populations of the two species, which mainly resulted from the small initial population size and propagated vegetative practice during their cultivation.

CONCLUSION

Our findings indicate significant genetic divergence between T. wilfordii and T. hypoglaucum. The genetic diversity and population structure analyses provide important insights into the sustainable cultivation and utilization of these medicinal plants. Accurate identification and conservation efforts are necessary for both species to ensure the safety and effectiveness of crude drug use. Our study also highlighted the importance of combined analyses of different DNA markers in addressing population genetics of medicinal plants because of the contrasts of inheritance and rates of gene flow. Large-scale cultivation programs should consider preserving genetic diversity to enhance the long-term sustainability of T. wilfordii and T. hypoglaucum. Our study proposed that some populations showed higher genetic diversity and distinctness, which can be considered with priority for conservation and as the sources for future breeding and genetic improvement.

Characterization of chloroplast genome and phylogenetic analysis of the Elaeagnus hybrid variety E. 'viridis' (Elaeagnaceae)

Elaeagnus 'viridis', an artificial hybrid of E. macrophylla (♂) Thunb. (1784) × E. pungens (♀) Thunb. (1784), is known for its economic and ecological value. In this study, we sequenced and assembled the whole chloroplast (cp) genome of E. 'viridis'. The results showed that its cp genome was 152,284 bp long, showing a typical quadripartite structure and containing a large single-copy region (LSC, 82,299 bp), a small single-copy region (SSC, 18,239 bp), and a pair of inverted repeats (IRs, 51,746 bp). The cp genome contains 132 genes, including 86 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 66 common PCGs revealed that E. 'viridis' is most closely related to its maternal parent E. pungens. The chloroplast genomic information reported in this study will shed some useful light for further genetic studies in the genus Elaeagnus.

Polyploid Nicotiana section Suaveolentes originated by hybridization of two ancestral Nicotiana clades

Introduction

Nicotiana section Suaveolentes is an almost all-Australian clade of allopolyploid tobacco species that emerged through hybridization between diploid relatives of the genus. In this study, we aimed to assess the phylogenetic relationship of the Suaveolentes section with several Nicotiana diploid species based on both plastidial and nuclear genes.

Methods

The Nicotiana plastome-based phylogenetic analysis representing 47 newly re-built plastid genomes suggested that an ancestor of N. section Noctiflorae is the most likely maternal donor of the Suaveolentes clade. Nevertheless, we found clear evidence of plastid recombination with an ancestor from the Sylvestres clade. We analyzed 411 maximum likelihood-based phylogenetic trees from a set of conserved nuclear diploid single copy gene families following an approach that assessed the genomic origin of each homeolog.

Results

We found that Nicotiana section Suaveolentes is monophyletic with contributions from the sections Alatae, Sylvestres, Petunioides and Noctiflorae. The dating of the divergence between these sections indicates that the Suaveolentes hybridization predates the split between Alatae/Sylvestres, and Noctiflorae/Petunioides.

Discussion

We propose that Nicotiana section Suaveolentes arose from the hybridization of two ancestral species from which the Noctiflorae/Petunioides and Alatae/Sylvestres sections are derived, with Noctiflorae the maternal parent. This study is a good example in which the use of genome wide data provided additional evidence about the origin of a complex polyploid clade.

Origin and evolutionary history of Populus (Salicaceae): Further insights based on time divergence and biogeographic analysis

INTRODUCTION

Populus (Salicaceae) species harbour rich biodiversity and are widely distributed throughout the Northern Hemisphere. However, the origin and biogeography of Populus remain poorly understood.

METHODS

We infer the divergence times and the historical biogeography of the genus Populus through phylogenetic analysis of 34 chloroplast fragments based on a large sample.

RESULTS AND DISCUSSION

Eurasia is the likely location of the early divergences of Salicaceae after the Cretaceous-Paleogene (K-Pg) mass extinction, followed by recurrent spread to the remainder of the Old World and the New World beginning in the Eocene; the extant Populus species began to diversity during the early Oligocene (approximately 27.24 Ma), climate changes during the Oligocene may have facilitated the diversification of modern poplar species; three separate lineages of Populus from Eurasia colonized North America in the Cenozoic via the Bering Land Bridges (BLB); We hypothesize that the present day disjunction in Populus can be explained by two scenarios: (i) Populus likely originated in Eurasia and subsequently colonized other regions, including North America; and (ii) the fact that the ancestor of the genus Populus that was once widely distributed in the Northern Hemisphere and eventually wiped out due to the higher extinction rates in North America, similar to the African Rand flora. We hypothesize that disparities in extinction across the evolutionary history of Populus in different regions shape the modern biogeography of Populus. Further studies with dense sampling and more evidence are required to test these hypotheses. Our research underscores the significance of combining phylogenetic analyses with biogeographic interpretations to enhance our knowledge of the origin, divergence, and distribution of biodiversity in temperate plant floras.

Pan-mitogenomics reveals the genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification

Although interactions between the cytoplasmic and nuclear genomes occurred during diversification of many plants, the evolutionary conflicts due to cytonuclear interactions are poorly understood in crop breeding. Here, we constructed a pan-mitogenome and identified chimeric open reading frames (ORFs) generated by extensive structural variations (SVs). Meanwhile, short reads from 184 accessions of citrus species were combined to construct three variation maps for the nuclear, mitochondrial, and chloroplast genomes. The population genomic data showed discordant topologies between the cytoplasmic and nuclear genomes because of differences in mutation rates and levels of heteroplasmy from paternal leakage. An analysis of species-specific SVs indicated that mitochondrial heteroplasmy was common and that chloroplast heteroplasmy was undetectable. Interestingly, we found a prominent divergence in the mitogenomes and the highest genetic load in the, which may provide the basis for cytoplasmic male sterility (CMS) and thus influence the reshuffling of the cytoplasmic and nuclear genomes during hybridization. Using cytoplasmic replacement experiments, we identified a type of species-specific CMS in mandarin related to two chimeric mitochondrial genes. Our analyses indicate that cytoplasmic genomes from mandarin have rarely been maintained in hybrids and that paternal leakage produced very low levels of mitochondrial heteroplasmy in mandarin. A genome-wide association study (GWAS) provided evidence for three nuclear genes that encode pentatricopeptide repeat (PPR) proteins contributing to the cytonuclear interactions in the Citrus genus. Our study demonstrates the occurrence of evolutionary conflicts between cytoplasmic and nuclear genomes in citrus and has important implications for genetics and breeding.

First report of leaf anthracnose on the Whorled Sunflower, Helianthus verticillatus, caused by Colletotrichum fioriniae in the United States

Whorled sunflower, Helianthus verticillatus Small, is an endangered (U.S. Fish and Wildlife Service 2014) perennial sunflower species indigenous to the southern United States (Matthews et al. 2002; Ellis et al. 2008). Helianthus verticillatus has a showy yellow floral display in the Fall that attracts a diversity of insect visitors (Strange et al. 2020). Its hardiness in the landscape and late-season blooming makes it a potential ornamental (Trigiano et al. 2021). In June 2021, anthracnose-like lesions were observed on mature leaves collected from potted H. verticillatus plants grown in the nursery compound at the University of Tennessee, Knoxville, TN, USA. Irregularly shaped leaf spots with 1‒2 mm tan centers were observed on mature leaves, which later expanded to 3‒5 mm, and became dark brown- to- black surrounded by chlorotic halos (Fig.1). Lesions from three infected leaves were excised from a single potted plant, trimmed to 1.5-cm squares with green borders, and surface-sterilized (Trigiano et al. 2018). Tissues were placed onto potato dextrose agar (PDA), amended with 100 mg/ml of each streptomycin sulfate and chlorotetracycline, and incubated at 21 °C in the dark until axenic cultures were obtained. Initially, appressed white- to- pale gray mycelia were formed that turned light pinkish-orange with age (Fig. 2A). Conidia (Fig. 2B-C) were single-celled, hyaline, and cylindrical- to- fusiform with acute ends, and were similar to Colletotrichum fioriniae (Damm et al. 2012). Conidia measured 8.9 ± 1.3 μm long and 3.3 ± 0.6 μm wide (N=40). Genomic DNA was isolated with a Phire Direct Plant PCR kit (Thermo FisherScientific, Waltham, MA). The partial beta-tubulin (TUB2) gene, chitin synthase 1 (CHS-1) gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, and the internal transcribed spacer (ITS) region of ribosomal DNA were amplified with primers T1/BT2B, CHS-354R/CHS-79F, GDF1/GDR1, and ITS1/ITS4, respectively and sequenced (Damm et al. 2012). The resulting sequences were submitted to GenBank (TUB2, ON036471; CHS-1, ON036472; GAPDH, ON036470; and ITS, ON008206). Consensus sequences had 100% identity with C. fioriniae type culture CBS 128517 accessions JQ949943 (TUB2), JQ948953 (CHS-1), JQ948622 (GAPDH), and MH865005 (ITS rDNA). Because H. verticillatus is endangered, and the scarcity of available plant material, Koch's postulates were performed using a detached leaf assay (Boggess et al. 2022). Six healthy leaves were surface-sterilized using the previously described protocol, longitudinally bisected, and placed on 1.5% water agar in three 15 × 100 mm petri dishes. Three half leaves were inoculated with sterile, 5 mm-diameter PDA plugs (controls). The remaining three leaves were inoculated with 5 mm-diameter PDA plugs of C. fioriniae and incubated as described previously. After ten days, necrotic lesions developed on leaves inoculated with C. fioriniae and were similar to the initially observed lesions on plants. Lesions did not develop on control leaves. Colletotrichum fioriniae was re-isolated from lesions using the previously described protocol. The disease does not appear to cause mortality of H. verticillatus and does not require control measures but does reduce the aesthetic value of the plant. To the best of our knowledge, this is the first report of C. fioriniae infecting H. verticillatus in the United States.

Disentangling Complex Inheritance Patterns of Plant Organellar Genomes: An Example From Carrot

Plant mitochondria and plastids display an array of inheritance patterns and varying levels of heteroplasmy, where individuals harbor more than 1 version of a mitochondrial or plastid genome. Organelle inheritance in plants has the potential to be quite complex and can vary with plant growth, development, and reproduction. Few studies have sought to investigate these complicated patterns of within-individual variation and inheritance using experimental crosses in plants. We carried out crosses in carrot, Daucus carota L. (Apiaceae), which has previously been shown to exhibit organellar heteroplasmy. We used mitochondrial and plastid markers to begin to disentangle the patterns of organellar inheritance and the fate of heteroplasmic variation, with special focus on cases where the mother displayed heteroplasmy. We also investigated heteroplasmy across the plant, assaying leaf samples at different development stages and ages. Mitochondrial and plastid paternal leakage was rare and offspring received remarkably similar heteroplasmic mixtures to their heteroplasmic mothers, indicating that heteroplasmy is maintained over the course of maternal inheritance. When offspring did differ from their mother, they were likely to exhibit a loss of the genetic variation that was present in their mother. Finally, we found that mitochondrial variation did not vary significantly over plant development, indicating that substantial vegetative sorting did not occur. Our study is one of the first to quantitatively investigate inheritance patterns and heteroplasmy in plants using controlled crosses, and we look forward to future studies making use of whole genome information to study the complex evolutionary dynamics of plant organellar genomes.

Propagation Methods for the Conservation and Preservation of the Endangered Whorled Sunflower (Helianthus verticillatus)

Helianthus verticillatus Small, the whorled sunflower, is a perennial species only found at a few sites in the southeastern United States and was declared federally (USA) endangered in 2014. The species spreads locally via rhizomes and can produce copious seeds when sexually compatible genotypes are present. Vegetative propagation of the species via cuttings and the optimum conditions for seed germination have not been determined. To investigate asexual propagation via cuttings, stem sections were harvested in late May, June, and July in Knoxville, Tennessee (USA) and trimmed to a minimum of two nodes. The base of the cuttings was treated with either auxin or water, and grown in a Promix BX potting medium with intermittent mist and 50% shade for one month. Seeds were harvested from a population of multiple genotypes in Maryville, Tennessee and used to determine viability and the range of temperatures suitable for germination. A clonal population was developed and used for three years to assess sexual compatibility at three locations in Knoxville, Tennessee. Ninety-five percent of the cuttings from May rooted in two-to-three weeks and formed more than 20 adventitious roots per cutting with auxin and 18 with water treatments. The ability of cuttings to root decreased in June to about 20%, and none rooted in July with either water or auxin pretreatments. Pre-germination tetrazolium tests indicated that about 91% of seeds (achenes) were viable. Subsequent germination tests revealed high germination at varying temperatures (96 to 99% of seeds (achenes) germinated at 22/11, 27/15, and 29/19 °C), whereas germination was significantly inhibited by 33/24 °C. Fifty percent of the seeds germinated at 22/11 °C in 7.5 days, whereas only 2.0 to 2.5 days were required for 50% germination at 27/15, 29/19, and 33/24 °C. Seeds were not produced at any of the clonal planting locations during the three years. Vegetative propagation via rooted cuttings was successful in the mid-spring, seed germination was possible over a wide range of temperatures, and self-incompatibility was evident in this species. The results of this study will permit fast and efficient propagation of multiple and selected genotypes for conservation, commerce, and breeding of elite cultivars with disease resistance or other desirable attributes.

Clade-Specific Plastid Inheritance Patterns Including Frequent Biparental Inheritance in Passiflora Interspecific Crosses

Plastid inheritance in angiosperms is presumed to be largely maternal, with the potential to inherit plastids biparentally estimated for about 20% of species. In Passiflora, maternal, paternal and biparental inheritance has been reported; however, these studies were limited in the number of crosses and progeny examined. To improve the understanding of plastid transmission in Passiflora, the progeny of 45 interspecific crosses were analyzed in the three subgenera: Passiflora, Decaloba and Astrophea. Plastid types were assessed following restriction digestion of PCR amplified plastid DNA in hybrid embryos, cotyledons and leaves at different developmental stages. Clade-specific patterns of inheritance were detected such that hybrid progeny from subgenera Passiflora and Astrophea predominantly inherited paternal plastids with occasional incidences of maternal inheritance, whereas subgenus Decaloba showed predominantly maternal and biparental inheritance. Biparental plastid inheritance was also detected in some hybrids from subgenus Passiflora. Heteroplasmy due to biparental inheritance was restricted to hybrid cotyledons and first leaves with a single parental plastid type detectable in mature plants. This indicates that in Passiflora, plastid retention at later stages of plant development may not reflect the plastid inheritance patterns in embryos. Passiflora exhibits diverse patterns of plastid inheritance, providing an excellent system to investigate underlying mechanisms in angiosperms.

Landscape Genetics of Plants: Challenges and Opportunities

Dispersal is one of the most important but least understood processes in plant ecology and evolutionary biology. Dispersal of seeds maintains and establishes populations, and pollen and seed dispersal are responsible for gene flow within and among populations. Traditional views of dispersal and gene flow assume models that are governed solely by geographic distance and do not account for variation in dispersal vector behavior in response to heterogenous landscapes. Landscape genetics integrates population genetics with Geographic Information Systems (GIS) to evaluate the effects of landscape features on gene flow patterns (effective dispersal). Surprisingly, relatively few landscape genetic studies have been conducted on plants. Plants present advantages because their populations are stationary, allowing more reliable estimates of the effects of landscape features on effective dispersal rates. On the other hand, plant dispersal is intrinsically complex because it depends on the habitat preferences of the plant and its pollen and seed dispersal vectors. We discuss strategies to assess the separate contributions of pollen and seed movement to effective dispersal and to delineate the effects of plant habitat quality from those of landscape features that affect vector behavior. Preliminary analyses of seed dispersal for three species indicate that isolation by landscape resistance is a better predictor of the rates and patterns of dispersal than geographic distance. Rates of effective dispersal are lower in areas of high plant habitat quality, which may be due to the effects of the shape of the dispersal kernel or to movement behaviors of biotic vectors. Landscape genetic studies in plants have the potential to provide novel insights into the process of gene flow among populations and to improve our understanding of the behavior of biotic and abiotic dispersal vectors in response to heterogeneous landscapes.

Genetic Diversity and Conservation Status of Helianthus verticillatus, an Endangered Sunflower of the Southern United States

Evaluating species diversity and patterns of population genetic variation is an essential aspect of conservation biology to determine appropriate management strategies and preserve the biodiversity of native plants. Habitat fragmentation and potential habitat loss are often an outcome of a reduction in naturally occurring wildfires and controlled prescribed burning, as seen in Helianthus verticillatus (whorled sunflower). This endangered, wild relative of the common sunflower, Helianthus annuus, is endemic to four locations in Alabama, Georgia, and Tennessee, United States. Despite its endangered status, there is no recovery plan for H. verticillatus, and knowledge related to its basic plant biology and importance in ecosystem services is mostly unknown. In this study, we utilized 14 microsatellite loci to investigate fine-scale population structure and genetic diversity of H. verticillatus individuals found on two sampling sites within the Georgia population. Our results indicated moderate genetic diversity and the presence of two distinct genetic clusters. Analyses of molecular variance indicated that the majority of variance was individually based, thus confirming high genetic differentiation and limited gene flow between H. verticillatus collection sites. The evidence of a population bottleneck in these sites suggests a recent reduction in population size that could be explained by habitat loss and population fragmentation. Also, high levels of linkage disequilibrium were detected, putatively suggesting clonal reproduction among these individuals. Our study provides a better understanding of fine-scale genetic diversity and spatial distribution of H. verticillatus populations in Georgia. Our results can underpin an original recovery plan for H. verticillatus that could be utilized for the conservation of this endangered species and to promote its persistence in the wild.

Rare maternal and biparental transmission of the cucumber mitochondrial DNA reveals sorting of polymorphisms among progenies

We used a mitochondrial (mt) mutant of cucumber to document rare maternal transmission of mt polymorphisms and demonstrate that polymorphisms can become more prevalent and sort to progenies to increase mt DNA diversity. The mitochondrial (mt) DNAs of most angiosperms show maternal inheritance, although relatively rare biparental or paternal transmission has been documented. The mt DNAs of plants in the genus Cucumis (family Cucurbitaceae) are paternally transmitted in intra- and interspecific crosses. MSC16 is an inbred line of cucumber (Cucumis sativus) with a mitochondrially associated mosaic (MSC) phenotype. MSC16 was crossed as the male parent to wild-type cultivar Calypso, and hybrid progenies were evaluated for the wild-type phenotype in order to screen for rare maternal or biparental transmission of the mt DNA. We then used standard and droplet digital (dd) PCR to study the transmission of polymorphic mt markers across three generations. We observed evidence for occasional maternal and biparental transmission of the mt DNA in cucumber. The transmission of specific regions of the maternal mt DNA could be as high as 17.8%, although the amounts of these maternal regions were often much lower relative to paternally transmitted regions. Different combinations of maternal and paternal mt polymorphisms were detected in progenies across generations, indicating that relatively rare maternal regions can be transmitted to progenies and become predominant to increase mt DNA diversity over generations.

Plastid genomes reveal recurrent formation of allopolyploid Fragaria

PREMISE OF THE STUDY

Recurrent formation of polyploid taxa is a common observation in many plant groups. Haploid, cytoplasmic genomes like the plastid genome can be used to overcome the problem of homeologous genes and recombination in polyploid taxa. Fragaria (Rosaceae) contains several octo- and decaploid species. We use plastome sequences to infer the plastid ancestry of these taxa with special focus on the decaploid Fragaria cascadensis.

METHODS

We used genome skimming of 96 polyploid Fragaria samples on a single Illumina HiSeq 3000 lane to obtain whole plastome sequences. These sequences were used for phylogenetic reconstructions and dating analyses. Ploidy of all samples was inferred with flow cytometry, and plastid inheritance was examined in a controlled cross of F. cascadensis.

KEY RESULTS

The plastid genome phylogeny shows that only the octoploid F. chiloensis is monophyletic, all other polyploid taxa were supported to be para- or polyphyletic. The decaploid Fragaria cascadensis has biparental plastid inheritance and four different plastid donors. Diversification of the F. cascadensis clades occurred in the last 230,000 years. The southern part of its distribution range harbors considerably higher genetic diversity, suggestive of a potential refugium.

CONCLUSIONS

Fragaria cascadensis had at least four independent origins from parents with different plastomes. In contrast, para- and polyphyletic taxa of the octoploid Fragaria species are best explained by incomplete lineage sorting and/or hybridization. Biogeographic patterns in F. cascadensis are probably a result of range shift during the last glacial maximum.

An efficient pipeline to generate data for studies in plastid population genomics and phylogeography

PREMISE OF THE STUDY

Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole-genome sequencing is expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among single-nucleotide polymorphisms (SNPs) are lost in pooled samples, and treating SNP allele frequencies as independent markers provides biased estimates of genetic structure.

METHODS

We developed sampling methodologies and an application, CallHap, that uses a least-squares algorithm to evaluate the fit between observed and predicted SNP allele frequencies from pooled samples based on haplotype network phylogeny structure, thus enabling pooling for chloroplast sequencing for large-scale studies of chloroplast genomic variation. This method was tested using artificially constructed test networks and pools, and pooled samples of Lasthenia californica (California goldfields) from southern Oregon, USA.

RESULTS

CallHap reliably recovered network topologies and haplotype frequencies from pooled samples.

DISCUSSION

The CallHap pipeline allows for the efficient use of resources for estimation of genetic structure for studies using nonrecombining haplotypes such as intraspecific variation in chloroplast, mitochondrial, bacterial, or viral DNA.

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)

Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of ∼35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.

Natural history of the narrow endemics Ipomoea cavalcantei and I. marabaensis from Amazon Canga savannahs

Amazon comprises a vast variety of ecosystems, including savannah-like Canga barrens that evolved on iron-lateritic rock plateaus of the Carajás Mountain range. Individual Cangas are enclosed by the rain forest, indicating insular isolation that enables speciation and plant community differentiation. To establish a framework for the research on natural history and conservation management of endemic Canga species, seven chloroplast DNA loci and an ITS2 nuclear DNA locus were used to study natural molecular variation of the red flowered Ipomoea cavalcantei and the lilac flowered I. marabaensis. Partitioning of the nuclear and chloroplast gene alleles strongly suggested that the species share the most recent common ancestor, pointing a new independent event of the red flower origin in the genus. Chloroplast gene allele analysis showed strong genetic differentiation between Canga populations, implying a limited role of seed dispersal in exchange of individuals between Cangas. Closed haplotype network topology indicated a requirement for the paternal inheritance in generation of cytoplasmic genetic variation. Tenfold higher nucleotide diversity in the nuclear ITS2 sequences distinguished I. cavalcantei from I. marabaensis, implying a different pace of evolutionary changes. Thus, Canga ecosystems offer powerful venues for the study of speciation, multitrait adaptation and the origins of genetic variation.

Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.

Lake sedimentary DNA accurately records 20th Century introductions of exotic conifers in Scotland

Sedimentary DNA (sedDNA) has recently emerged as a new proxy for reconstructing past vegetation, but its taphonomy, source area and representation biases need better assessment. We investigated how sedDNA in recent sediments of two small Scottish lakes reflects a major vegetation change, using well-documented 20^th Century plantations of exotic conifers as an experimental system. We used next-generation sequencing to barcode sedDNA retrieved from subrecent lake sediments. For comparison, pollen was analysed from the same samples. The sedDNA record contains 73 taxa (mainly genus or species), all but one of which are present in the study area. Pollen and sedDNA shared 35% of taxa, which partly reflects a difference in source area. More aquatic taxa were recorded in sedDNA, whereas taxa assumed to be of regional rather than local origin were recorded only as pollen. The chronology of the sediments and planting records are well aligned, and sedDNA of exotic conifers appears in high quantities with the establishment of plantations around the lakes. SedDNA recorded other changes in local vegetation that accompanied afforestation. There were no signs of DNA leaching in the sediments or DNA originating from pollen.

Patterns of Gene Flow between Crop and Wild Carrot, Daucus carota (Apiaceae) in the United States

Studies of gene flow between crops and their wild relatives have implications for both management practices for cultivation and understanding the risk of transgene escape. These types of studies may also yield insight into population dynamics and the evolutionary consequences of gene flow for wild relatives of crop species. Moreover, the comparison of genetic markers with different modes of inheritance, or transmission, such as those of the nuclear and chloroplast genomes, can inform the relative risk of transgene escape via pollen versus seed. Here we investigate patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in two regions of the United States. We employed 15 nuclear simple sequence repeat (SSR) markers and one polymorphic chloroplast marker. Further, we utilized both conventional population genetic metrics along with Shannon diversity indices as the latter have been proposed to be more sensitive to allele frequency changes and differentiation. We found that populations in both regions that were proximal to crop fields showed lower levels of differentiation to the crops than populations that were located farther away. We also found that Shannon measures were more sensitive to differences in both genetic diversity and differentiation in our study. Finally, we found indirect evidence of paternal transmission of chloroplast DNA and accompanying lower than expected levels of chloroplast genetic structure amongst populations as might be expected if chloroplast DNA genes flow through both seed and pollen. Our findings of substantial gene flow for both nuclear and chloroplast markers demonstrate the efficiency of both pollen and seed to transfer genetic information amongst populations of carrot.

Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species

PREMISE OF THE STUDY

Molecular phylogenies derived from all three plant genomes can provide insight into the evolutionary history of plant groups influenced by reticulation. We sought to reconstruct mitochondrial exome, chloroplast, and nuclear genome phylogenies for octoploid Fragaria and their diploid ancestors and to document patterns of incongruence between and within the cytoplasmic genomes and interpret these in the context of evolutionary origin of the octoploid strawberries.

METHODS

Using a genome-skimming approach, we assembled chloroplast genomes and mitochondrial exomes, and we used the POLiMAPS method to assemble nuclear sequence for octoploid species and constructed phylogenies from all three genomes. We assessed incongruence between and within cytoplasmic genomes using topology-based phylogenetic incongruence tests.

KEY RESULTS

The incongruent cytoplasmic genome phylogeny with respect to the placement of octoploids suggests potential breakage in linkage disequilibrium of cytoplasmic genomes during allopolyploid origin of the octoploids. Furthermore, a single mitochondrial chimeric gene with a putative role in cytoplasmic male sterility yields a phylogeny that is inconsistent with the rest of the mitochondrial genome but consistent with the chloroplast phylogeny, suggesting intracellular gene transfer between heteroplasmic mitochondria, possibly driven by selection to overcome the effects of mito-nuclear incompatibility in octoploid origins.

CONCLUSIONS

This work expands on the current understanding of evolutionary history of the octoploid ancestors of cultivated strawberry. It demonstrates phylogenetic incongruence between cytoplasmic genomes in octoploids with respect to diploid ancestors, indicating breakage in linkage disequilibrium of cytoplasmic genomes. We discuss potential organism-level processes that may have contributed to the observed incongruence in Fragaria.

Why are most organelle genomes transmitted maternally?

Why the DNA-containing organelles, chloroplasts, and mitochondria, are inherited maternally is a long standing and unsolved question. However, recent years have seen a paradigm shift, in that the absoluteness of uniparental inheritance is increasingly questioned. Here, we review the field and propose a unifying model for organelle inheritance. We argue that the predominance of the maternal mode is a result of higher mutational load in the paternal gamete. Uniparental inheritance evolved from relaxed organelle inheritance patterns because it avoids the spread of selfish cytoplasmic elements. However, on evolutionary timescales, uniparentally inherited organelles are susceptible to mutational meltdown (Muller's ratchet). To prevent this, fall-back to relaxed inheritance patterns occurs, allowing low levels of sexual organelle recombination. Since sexual organelle recombination is insufficient to mitigate the effects of selfish cytoplasmic elements, various mechanisms for uniparental inheritance then evolve again independently. Organelle inheritance must therefore be seen as an evolutionary unstable trait, with a strong general bias to the uniparental, maternal, mode.

Maternal inheritance of mitochondrial genomes and complex inheritance of chloroplast genomes in Actinidia Lind.: evidences from interspecific crosses

The inheritance pattern of chloroplast and mitochondria is a critical determinant in studying plant phylogenetics, biogeography and hybridization. To better understand chloroplast and mitochondrial inheritance patterns in Actinidia (traditionally called kiwifruit), we performed 11 artificial interspecific crosses and studied the ploidy levels, morphology, and sequence polymorphisms of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) of parents and progenies. Sequence analysis showed that the mtDNA haplotypes of F1 hybrids entirely matched those of the female parents, indicating strictly maternal inheritance of Actinidia mtDNA. However, the cpDNA haplotypes of F1 hybrids, which were predominantly derived from the male parent (9 crosses), could also originate from the mother (1 cross) or both parents (1 cross), demonstrating paternal, maternal, and biparental inheritance of Actinidia cpDNA. The inheritance patterns of the cpDNA in Actinidia hybrids differed according to the species and genotypes chosen to be the parents, rather than the ploidy levels of the parent selected. The multiple inheritance modes of Actinidia cpDNA contradicted the strictly paternal inheritance patterns observed in previous studies, and provided new insights into the use of cpDNA markers in studies of phylogenetics, biogeography and introgression in Actinidia and other angiosperms.

Exceptional inheritance of plastids via pollen in Nicotiana sylvestris with no detectable paternal mitochondrial DNA in the progeny

Plastids and mitochondria, the DNA-containing cytoplasmic organelles, are maternally inherited in the majority of angiosperm species. Even in plants with strict maternal inheritance, exceptional paternal transmission of plastids has been observed. Our objective was to detect rare leakage of plastids via pollen in Nicotiana sylvestris and to determine if pollen transmission of plastids results in co-transmission of paternal mitochondria. As father plants, we used N. sylvestris plants with transgenic, selectable plastids and wild-type mitochondria. As mother plants, we used N. sylvestris plants with Nicotiana undulata cytoplasm, including the CMS-92 mitochondria that cause cytoplasmic male sterility (CMS) by homeotic transformation of the stamens. We report here exceptional paternal plastid DNA in approximately 0.002% of N. sylvestris seedlings. However, we did not detect paternal mitochondrial DNA in any of the six plastid-transmission lines, suggesting independent transmission of the cytoplasmic organelles via pollen. When we used fertile N. sylvestris as mothers, we obtained eight fertile plastid transmission lines, which did not transmit their plastids via pollen at higher frequencies than their fathers. We discuss the implications for transgene containment and plant evolutionary histories inferred from cytoplasmic phylogenies.

Molecular evidence for maternal inheritance of the chloroplast genome in tea, Camellia sinensis (L.) O. Kuntze

BACKGROUND

Tea is the most consumed beverage worldwide after water. Yet very little is known about the genetics of tea in comparison with other crop species. Here we have taken advantage of the polymorphic nature of microsatellite DNA to investigate the mode of chloroplast inheritance in tea, Camellia sinensis (L.) O. Kuntze. This is important for the correct interpretation of phylogeny and introgression data as well as assessing the suitability of chloroplast transformation as a means for transgene containment in tea.

RESULTS

The study was based on six Japanese tea cultivars, namely Aj2, CK23, Hatsumomiji, Nka05, Yamanoibuki and Kanayamidori used to generate four informative families. The parental pairs in the crosses differed at a single chlroroplast locus with respect to an imperfect microsatellite repeat of 16 nucleotide bases. In agreement with earlier cytological studies, all 61 progeny displayed a cpDNA profile that was consistent with the maternal inheritance of chloroplasts in tea.

CONCLUSIONS

The data generated here provide the first molecular evidence of the plastid inheritance in tea. However, we suggest that additional families and polymorphic markers be screened for increasing the confidence in the observed maternal inheritance of chloroplasts in this important crop species.

Contrasting patterns of pollen and seed flow influence the spatial genetic structure of sweet vernal grass (Anthoxanthum odoratum) populations

The spatial genetic structure of plant populations is determined by a combination of gene flow, genetic drift, and natural selection. Gene flow in most plants can result from either seed or pollen dispersal, but detailed investigations of pollen and seed flow among populations that have diverged following local adaptation are lacking. In this study, we compared pollen and seed flow among 10 populations of sweet vernal grass (Anthoxanthum odoratum) on the Park Grass Experiment. Overall, estimates of genetic differentiation that were based on chloroplast DNA (cpDNA) and, which therefore resulted primarily from seed flow, were lower (average F(ST) = 0.058) than previously published estimates that were based on nuclear DNA (average F(ST) = 0.095). Unlike nuclear DNA, cpDNA showed no pattern of isolation by adaptation; cpDNA differentiation was, however, inversely correlated with the number of additions (nutrients and lime) that each plot had received. We suggest that natural selection is restricting pollen flow among plots, whereas nutrient additions are increasing seed flow and genetic diversity by facilitating the successful germination and growth of immigrant seeds. This study highlights the importance of considering all potential gene flow mechanisms when investigating determinants of spatial genetic structure, and cautions against the widespread assumption that pollen flow is more important than seed flow for population connectivity in wind-pollinated species.

Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines

BACKGROUND

Parthenium argentatum (guayule) is an industrial crop that produces latex, which was recently commercialized as a source of latex rubber safe for people with Type I latex allergy. The complete plastid genome of P. argentatum was sequenced. The sequence provides important information useful for genetic engineering strategies. Comparison to the sequences of plastid genomes from three other members of the Asteraceae, Lactuca sativa, Guitozia abyssinica and Helianthus annuus revealed details of the evolution of the four genomes. Chloroplast-specific DNA barcodes were developed for identification of Parthenium species and lines.

RESULTS

The complete plastid genome of P. argentatum is 152,803 bp. Based on the overall comparison of individual protein coding genes with those in L. sativa, G. abyssinica and H. annuus, we demonstrate that the P. argentatum chloroplast genome sequence is most closely related to that of H. annuus. Similar to chloroplast genomes in G. abyssinica, L. sativa and H. annuus, the plastid genome of P. argentatum has a large 23 kb inversion with a smaller 3.4 kb inversion, within the large inversion. Using the matK and psbA-trnH spacer chloroplast DNA barcodes, three of the four Parthenium species tested, P. tomentosum, P. hysterophorus and P. schottii, can be differentiated from P. argentatum. In addition, we identified lines within P. argentatum.

CONCLUSION

The genome sequence of the P. argentatum chloroplast will enrich the sequence resources of plastid genomes in commercial crops. The availability of the complete plastid genome sequence may facilitate transformation efficiency by using the precise sequence of endogenous flanking sequences and regulatory elements in chloroplast transformation vectors. The DNA barcoding study forms the foundation for genetic identification of commercially significant lines of P. argentatum that are important for producing latex.