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Background and Aims New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. Methods We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. Key Results Using sliding-window population genetic analyses we find that differentiation is concentrated within 'islands' of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. Conclusions We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth's climate rapidly changes. [ABSTRACT FROM AUTHOR]

Typha angustifolia L., known as narrowleaf cattail, is widely distributed in Eurasia but has been introduced to North America. Typha angustifolia is a semi-aquatic, wetland obligate plant that is widely distributed in Eurasia and North America. It is ecologically important for nutrient cycling in wetlands where it occurs and is used in phytoremediation and traditional medicine. In order to construct a high-quality genome for Typha angustifolia and investigate genes in response to high nitrogen stress, we carried out complete genome sequencing and high-nitrogen-stress experiments. We generated a chromosomal-level genome of T. angustifolia, which had 15 pseudochromosomes, a size of 207 Mb, and a contig N50 length of 13.57 Mb. Genome duplication analyses detected no recent whole-genome duplication (WGD) event for T. angustifolia. An analysis of gene family expansion and contraction showed that T. angustifolia gained 1,310 genes and lost 1,426 genes. High-nitrogen-stress experiments showed that a high nitrogen level had a significant inhibitory effect on root growth and differential gene expression analyses using 24 samples found 128 differentially expressed genes (DEGs) between the nitrogen-treated and control groups. DEGs in the roots and leaves were enriched in alanines, aspartate, and glutamate metabolism, nitrogen metabolism, photosynthesis, phenylpropanoid biosynthesis, plant-pathogen interaction, and mitogen-activated protein kinase pathways, among others. This study provides genomic data for a medicinal and ecologically important herb and lays a theoretical foundation for plant-assisted water pollution remediation. [ABSTRACT FROM AUTHOR]

North America has experienced a massive increase in cropland use since 1800, accompanied more recently by the intensification of agricultural practices. Through genome analysis of present-day and historical samples spanning environments over the past two centuries, we studied the effect of these changes in farming on the extent and tempo of evolution across the native range of the common waterhemp (Amaranthus tuberculatus), a now pervasive agricultural weed. Modern agriculture has imposed strengths of selection rarely observed in the wild, with notable shifts in allele frequency trajectories since agricultural intensification in the 1960s. An evolutionary response to this extreme selection was facilitated by a concurrent human-mediated range shift. By reshaping genome-wide diversity across the landscape, agriculture has driven the success of this weed in the 21st century. [ABSTRACT FROM AUTHOR]

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudochromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n=9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research. [ABSTRACT FROM AUTHOR]

Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments. Vallejo-Marín et al. combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. They found that M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range, and hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. [ABSTRACT FROM AUTHOR]

Erigeron annuus (L.) Pers. (annual, daisy or tall fleabane) is an annual herb native to North America but has been introduced and naturalized worldwide. In this study, its complete chloroplast (cp) genome was assembled from Illumina sequencing reads. The cp genome is 153,177 bp long with an A + T-biased base composition. It encodes a panel of 113 genes, including 80 protein-coding, 29 tRNA, and four rRNA genes. Nineteen genes are completely or partially duplicated, while 17 genes possess one or two introns. Phylogenetic analysis suggested E. annuus is mostly closely related to Erigeron canadensis L. and that the two genera Conyza and Erigeron are not mutually monophyletic. [ABSTRACT FROM AUTHOR]

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia. We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti. [ABSTRACT FROM AUTHOR]

Abstract: Accumulating evidence supports the feasibility of creating biotic soil environments that promote root health using selected plant genotypes. Five years of field experimentation conducted in the semiarid grasslands of North America revealed genotypic variation in the influence of chickpea on the composition of the soil microbial community and on the establishment of the subsequent crop. A 2-year experiment documented the effects of four chickpea cultivars on the arable soil microbiome using cultural methods, the cloning and sequencing of soil-extracted DNA, and fatty acid methyl ester profiling. Cultivar CDC Frontier was characterized by low bacterial biomass, whereas Amit and CDC Anna selected similarly structured bacterial communities but contrasting soil fungal communities. Amit and CDC Anna became colonized by arbuscular mycorrhizal (AM) fungi to the same extent, but the arable soil planted with CDC Anna hosted the highest level of culturable fungal diversity, whereas the soil planted with Amit hosted the lowest. The highest diversity of culturable fungi and the richness of AM fungal ribotypes (11) were also associated with CDC Anna. Amit was preferentially associated with the antagonist species Penicillium canescens. Higher durum wheat stand density was found after CDC Anna than after Amit, indicating that microbial diversity is an important feature of productive soils. The influence of chickpea genotype on the arable soil microbiome and on the establishment of the subsequent durum wheat crop was related to the soil water reserve at depths of 30–120 cm and was eliminated when the chickpea crops experienced drought. Genetic variation in the influence of chickpea on the soil microbiome suggests the possibility of selecting genotypes to engineer beneficial soil biotic environments. Inadequate levels of soil water could limit the success of this strategy, however, in rainfed cropping systems of the semiarid grasslands of North America. [Copyright &y& Elsevier]

Genome-wide association studies (GWAS) can be a useful approach to detect quantitative trait loci (QTL) controlling complex traits in crop plants. Oat (Avena sativa L.) ß-glucan is a soluble dietary fiber and has been shown to have positive health benefits. We report a GWAS involving 446 elite oat breeding lines from North America genotyped with 1005 diversity arrays technology (DArT) markers and with phenotypic data from both historical and balanced 2-yr data. Association analyses accounting for pair-wise relationships and population structure were conducted using single-marker tests and least absolute shrinkage and selection operator (LASSO). Single-marker tests yielded six and 15 significant markers for the historical and balanced data sets, respectively. The LASSO method selected 24 and 37 markers as the most important in explaining ß-glucan concentration for the historical and balanced data sets, respectively. Comparisons of genetic location showed that 15 of the markers in our study were found on the same linkage groups as QTL identified in previous studies. Four of the markers colocalized to within 4 cM of three previously detected QTL, suggesting concordance between QTL detected in our study and previous studies. Two of the significant markers were also adjacent to a ß-glucan candidate gene in the rice (Oryza sativa L.) genome. Our findings suggest that GWAS can be used for QTL detection for the purpose of gene discovery and for marker-assisted selection to improve ß-glucan concentration in elite oat. [ABSTRACT FROM AUTHOR]

Many Epichloë endophytes found in cool-season grasses are interspecific hybrids possessing much or all of the genomes of two or three progenitors. Here we characterize Epichloë canadensis sp. nov., a hybrid species inhabiting the grass species Elymus canadensis native to North America. Three distinct morphotypes were identified that were separated into two groups by molecular phylogenetic analysis. Sequence analysis of the translation elongation factor 1-α (tefA) and β-tubulin (tubB) genes revealed two copies in all isolates examined. Phylogenetic analyses indicated that allele 1 of each gene was derived from Epichloë amarillans and allele 2 from Epichloë elymi. This is the first documentation of an interspecific hybrid endophyte derived from parents of strictly North American origins. Alkaloid gene profiling using primers specific to genes in the peramine, loline, indole-diterpene and ergot alkaloid pathways may indicate chemotypic variation in the ergot alkaloid and loline pathways between the assigned morphotypes. All isolates have the gene enabling the production of peramine but lack genes in the indole-diterpene biosynthesis pathway. Morphology and phylogenetic evidence support the designation of isolates from El. canadensis as a new interspecific hybrid species. [ABSTRACT FROM AUTHOR]

Wild potato ( Solanum L. sect. Petota Dumort.) species contain diploids (2 n = 2 x = 24) to hexaploids (2 n = 6 x = 72). J.G. Hawkes classified all hexaploid Mexican species in series Demissa Bukasov and, according to a classic five-genome hypothesis of M. Matsubayashi in 1991, all members of series Demissa are allopolyploids. We investigated the genome composition of members of Hawkes's series Demissa with genomic in situ hybridization (GISH), using labeled DNA of their putative progenitors having diploid AA, BB, or PP genome species or with DNA of tetraploid species having AABB or AAAaAa genomes. GISH analyses support S. hougasii Correll as an allopolyploid with one AA component genome and another BB component genome. Our results also indicate that the third genome of S. hougasii is more closely related to P or a P genome-related species. Solanum demissum Lindl., in contrast, has all three chromosome sets related to the basic A genome, similar to the GISH results of polyploid species of series Acaulia Juz. Our results support a more recent taxonomic division of the Mexican hexaploid species into two groups: the allopolyploid Iopetala group containing S. hougasii, and an autopolyploid Acaulia group containing S. demissum with South American species S. acaule Bitter and S. albicans (Ochoa) Ochoa. [ABSTRACT FROM AUTHOR]

Penstemon is the largest genus in North America with more than 270 reported species. However, little is known about its genome size. This information may be useful in developing hybrids for landscape use and for gaining insight into its current taxonomy. Using flow cytometry, we estimated the genome size of approximately 40% of the genus (115 accessions from 105 different species). Genome sizes for both reported and probable diploids range from P. dissectus 2C = 0.94 pg (1C = 462 Mbp) to P. pachyphyllus var. mucronatus 2C = 1.88 pg (1C = 919 Mbp), and the polyploids range from P. attenuatus var. attenuatus 2C = 2.35 pg (1C = 1148 Mbp) to P. digitalis 2C = 6.45 pg (1C = 3152 Mbp). Chromosome counts were done for ten previously published and four previously unreported Penstemon species (P. dissectus, P. navajoa, P. caespitosus var. desertipicti, and P. ramaleyi). These counts were compiled with all previously published chromosome data and compared with the flow cytometry results. Ploidy within this study ranged from diploid to dodecaploid. These data were compared and contrasted with the current taxonomy of Penstemon and previously published internal transcribed spacer and chloroplast DNA phylogenetic work. Based on genome size and previous studies, reassigning P. montanus to the subgenus Penstemon and P. personatus to the subgenus Dasanthera, would better reflect the phylogeny of the genus. Furthermore, our data concur with previous studies suggesting that the subgenus Habroanthus be included in the subgenus Penstemon. The DNA content of subgenus Penstemon exhibits high plasticity and spans a sixfold increase from the smallest to the largest genome (P. linarioides subsp. sileri and P. digitalis, respectively). Our study found flow cytometry to be useful in species identification and verification. Le genre Penstemon est le plus grand en Amérique du Nord avec plus de 270 espèces connues. Cependant, on en connaît peu sur la taille des génomes au sein de ce genre. Cette information pourrait s'avérer utile pour le développement d'hybrides à des fins ornementales et pour fournir un éclairage sur la taxonomie. En faisant appel à la cytométrie en flux, les auteurs ont évalué la taille du génome chez environ 40 % des espèces de ce genre (115 accessions appartenant à 105 espèces). La taille du génome chez les espèces diploïdes confirmées ou probables varie entre chez le P. dissectus 2C = 0,94 pg (1C = 462 Mb [mégabases]) et le P. pachyphyllus var. mucronatus 2C = 1,88 pg (1C = 919 Mb). Chez les espèces polyploïdes, cette gamme varie du P. attenuatus var. attenuatus 2C = 2,35 pg (1C = 1,148 Mb) au P. digitalis 2C = 6,45 pg (1C = 3,152 Mb). Des décomptes chromosomiques ont été réalisés pour dix espèces déjà décrites et pour quatre espèces inédites de Penstemon (P. dissectus, P. navajoa, P. caespitosus var. desertipicti et P. ramaleyi). Ces décomptes ont été compilés avec toutes les données chromosomiques disponibles et comparés aux résultats de l'analyse de cytométrie en flux. Dans ce travail, les niveaux de ploïdie observés ont varié entre la diploïdie et la dodécaploïdie. Ces données ont été comparées et contrastées avec la taxonomie actuelle des Penstemon ainsi qu'avec les données phylogénétiques basées sur les ITS et l'ADNcp. Sur la base de la taille des génomes et des travaux antérieurs, il serait justifié de placer le P. montanus au sein du sous-genre Penstemon et le P. personatus au sein du sous-genre Dasanthera afin de mieux refléter la phylogénie au sein de ce genre. De plus, les données obtenues au cours de ce travail concordent avec les études antérieures voulant qu'on inclue le sous-genre Habroanthus au sein du sous-genre Penstemon. Le contenu en ADN au sein du sous-genre Penstemon affiche une grande plasticité, le plus petit génome (P. linarioides subsp. sileri) étant six fois plus petit que le plus grand (P. digitalis). Cette étude a montré que la cytométrie en flux est utile pour l'identification et la validation des espèces. [ABSTRACT FROM AUTHOR]

The article presents a study which establishes the first bacterial artificial chromosomes (BAC) library for switchgrass, a grass native to North America which is being developed into a biomass fuel crop. The switchgrass BAC library was constructed by partial digestion of nuclear DNA and comparative analysis of two genomic regions with orthologs of the rice OsBRI1 was conducted. The switchgrass BAC library and comparative analysis presents a glimpse into the structure of switchgrass genome.

Background: Elymus (Poaceae) is a large genus of polyploid species in the wheat tribe Triticeae. It is polyphyletic, exhibiting many distinct allopolyploid genome combinations, and its history might be further complicated by introgression and lineage sorting. We focus on a subset of Elymus species with a tetraploid genome complement derived from Pseudoroegneria (genome St) and Hordeum (H). We confirm the species' allopolyploidy, identify possible genome donors, and pinpoint instances of apparent introgression or incomplete lineage sorting. Methodology/Principal Findings: We sequenced portions of three unlinked nuclear genes-phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I-from 27 individuals, representing 14 Eurasian and North American StStHH Elymus species. Elymus sequences were combined with existing data from monogenomic representatives of the tribe, and gene trees were estimated separately for each data set using maximum likelihood. Trees were examined for evidence of allopolyploidy and additional reticulate patterns. All trees confirm the StStHH genome configuration of the Elymus species. They suggest that the StStHH group originated in North America, and do not support separate North American and European origins. Our results point to North American Pseudoroegneria and Hordeum species as potential genome donors to Elymus. Diploid P. spicata is a prospective St-genome donor, though conflict among trees involving P. spicata and the Eurasian P. strigosa suggests either introgression of GBSSI sequences from P. strigosa into North American Elymus and Pseudoroegneria, or incomplete lineage sorting of ancestral GBSSI polymorphism. Diploid H. californicum and/or allotetraploid H. jubatum are possible H-genome donors; direct involvement of an allotetraploid Hordeum species would simultaneously introduce two distinct H genomes to Elymus, consistent with some of the relationships among H-genome sequences in Hordeum and Elymus. Conclusions/Significance: Comparisons among molecular phylogenetic trees confirm allopolyploidy, identify potential genome donors, and highlight cases of apparent introgression or incomplete lineage sorting. The complicated history of this group emphasizes an inherent problem with interpreting conflicts among bifurcating trees-identifying introgression and determining its direction depend on which tree is chosen as a starting point of comparison. In spite of difficulties with interpretation, differences among gene trees allow us to identify reticulate species and develop hypotheses about underlying evolutionary processes. [ABSTRACT FROM AUTHOR]

Characterization of the determinants of economically important phenotypes showing complex inheritance should lead to the more effective use of genetic resources. This study was conducted to determine the number, genome location and effects of QTLs determining malting quality in the two North American barley quality standards. Using a doubled-haploid population of 140 lines from the cross of Harrington×Morex, malting quality phenotype data sets from eight environments, and a 107-marker linkage map, QTL analyses were performed using simple interval mapping and simplified composite interval mapping procedures. Seventeen QTLs were associated with seven grain and malting quality traits (percentage of plump kernels, test weight, grain protein percentage, soluble/total protein ratio, α-amylase activity, diastatic power and malt-extract percentage). QTLs for multiple traits were coincident. The loci controlling inflorescence type [vrs1 on chromosome 2(2H) and int-c on chromosome 4(4H)] were coincident with QTLs affecting all traits except malt-extract percentage. The largest effect QTLs, for the percentage of plump kernels, test weight protein percentage, S/T ratio and diastatic power, were coincident with the vrs1 locus. QTL analyses were conducted separately for each sub-population (six-rowed and two-rowed). Eleven new QTLs were detected in the subpopulations. There were significant interactions between the vrs1 and int-c loci for grain-protein percentage and S/T protein ratio. Results suggest that this mating of two different germplasm groups caused a disruption of the balance of traits. Information on the number, position and effects of QTLs determining components of malting quality may be useful for maintaining specific allele configurations that determine target quality profiles. [ABSTRACT FROM AUTHOR]

The authors discuss the study by G. T. Slavov and colleagues on application of whole genome sequencing (WGS) in the genomic selection in forest tree. The authors state that the study reveals geographic differentiation in black cottonwood, Populus trichocarpa in multiple spatial scales in western North America through the use of Infineum single nucleotide polymorphism (SNP) detection assays. Moreover, the study demonstrates the essential role of WGS in general and applied science.