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Interspecific hybridization events have played a major role in plant speciation, yet the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production. We estimated genetic distances between C. arabica and all species that are known to be closely related to C. arabica using genotyping‐by‐sequencing (GBS) data. In addition, we reconstructed a time‐calibrated multilabeled phylogenetic tree of 24 species to estimate the age of the C. arabica hybridization event. Ancestral states of self‐compatibility were also inferred to shed new light on the evolution of self‐compatibility in Coffea. Coffea canephora and C. eugenioides were confirmed as the putative progenitor species of C. arabica. These species most likely hybridized between 1.08 million and 543 000 years ago, coinciding with periods of environmental upheaval, which may have induced range shifts of the progenitor species that facilitated the emergence of C. arabica. [ABSTRACT FROM AUTHOR]

More severe seasonal stresses resulting from climate change affect the survival of perennial plant species. The growth–survival trade‐off exemplified in dormant species is a key issue to understand adaptation. As the validity of this trade‐off has yet to be tested in non‐dormant species, it was assessed by exploring the intraspecific variability of strategies to face drought and frost within perennial ryegrass.Three common gardens compared 385 European perennial ryegrass populations along a latitudinal environmental gradient over 3‐years. Persistence, productivity and physiological traits were recorded under contrasting seasonal environments.Decoupling plant responses, that is, growth under favourable summers/winters and plant survival under harsh summers/winters, showed a general trade‐off between growth potential and dehydration survival. Three groups of perennial ryegrass populations were identified according to their contrasting strategies: (a) year‐round productive but stress sensitive populations from wet areas; (b) drought‐tolerant populations with low summer growth potential from drought‐prone areas and (c) frost‐tolerant populations with low winter growth potential from frost‐prone areas. Overall, the populations surviving drought best were more resource conservative, whereas populations of the other groups were more resource acquisitive. However, such overall functional patterns were less meaningful than seasonal variations of resource acquisition potentials. The predicted potential biogeographical distribution of these groups suggests shifts of areas of suitability under climate change over the next decades in Europe. Dehydration escape and dehydration tolerance through reduction of growth potential in summer may become the strategies best adapted to an increasingly large area of Europe.The large intraspecific variability of phenological adaptations within perennial ryegrass reveals that the seasonal modulation of growth potential is crucial to plant adaptation under severe chronic abiotic stresses. The global plant economics spectrum cannot account for contrasting seasonal trade‐offs, which points out the importance of integrating phenological traits as key components of plant strategies. The identification of the trade‐off between growth potential and frost or drought stress survival in this non‐dormant species provides key knowledge to understand the future regional distribution of this major species for grassland ecosystem services. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

Agricultural grasslands are often cultivated as mixtures of grasses and legumes, and an extensive body of literature is available regarding interspecific interactions, and how these relate to yield and agronomic performance. However, knowledge of the impact of intraspecific diversity on grassland functioning is scarce. We investigated these effects during a 4-year field trial established with perennial ryegrass (Lolium perenne) and red clover (Trifolium pratense). We simulated different levels of intraspecific functional diversity by sowing single cultivars or by combining cultivars with contrasting growth habits, in monospecific or bispecific settings (i.e. perennial ryegrass whether or not in combination with red clover). Replicate field plots were established for seven seed compositions. We determined yield parameters and monitored differences in genetic diversity in the ryegrass component among seed compositions, and temporal changes in the genetic composition and genetic diversity at the within plot level. The composition of cultivars of both species affected the yield and species abundance. In general, the presence of clover had a positive effect on the yield. The cultivar composition of the ryegrass component had a significant effect on the yield, both in monoculture, and in combination with clover. For the genetic analyses, we validated empirically that genotyping-by-sequencing of pooled samples (pool-GBS) is a suitable method for accurate measurement of population allele frequencies, and obtained a dataset of 22,324 SNPs with complete data. We present a method to investigate the temporal dynamics of cultivars in seed mixtures grown under field conditions, and show how cultivar abundances vary during subsequent years. We screened the SNP panel for outlier loci, putatively under selection during the cultivation period, but none were detected. [ABSTRACT FROM AUTHOR]

Despite current advances in next-generation sequencing data analysis procedures, de novo assembly of a reference sequence required for SNP discovery and expression analysis is still a major challenge in genetically uncharacterized, highly heterozygous species. High levels of polymorphism inherent to outbreeding crop species hamper De Bruijn Graph-based de novo assembly algorithms, causing transcript fragmentation and the redundant assembly of allelic contigs. If multiple genotypes are sequenced to study genetic diversity, primary de novo assembly is best performed per genotype to limit the level of polymorphism and avoid transcript fragmentation. Here, we propose an Orthology Guided Assembly procedure that first uses sequence similarity (t BLASTn) to proteins of a model species to select allelic and fragmented contigs from all genotypes and then performs CAP3 clustering on a gene-by-gene basis. Thus, we simultaneously annotate putative orthologues for each protein of the model species, resolve allelic redundancy and fragmentation and create a de novo transcript sequence representing the consensus of all alleles present in the sequenced genotypes. We demonstrate the procedure using RNA-seq data from 14 genotypes of Lolium perenne to generate a reference transcriptome for gene discovery and translational research, to reveal the transcriptome-wide distribution and density of SNPs in an outbreeding crop and to illustrate the effect of polymorphisms on the assembly procedure. The results presented here illustrate that constructing a non-redundant reference sequence is essential for comparative genomics, orthology-based annotation and candidate gene selection but also for read mapping and subsequent polymorphism discovery and/or read count-based gene expression analysis. [ABSTRACT FROM AUTHOR]

Columnea latent viroid (CLVd) is one of the most serious tomato diseases. In general, viroids have high mutation rates. This generates a population of variants (so-called quasi-species) that co-exist in their host and exhibit a huge level of genetic diversity. To study the population of CLVd in individual host plants, we used amplicon sequencing using specific CLVd primers linked with a sample-specific index sequence to amplify libraries. An infectious clone of a CLVd isolate Chaipayon-1 was inoculated on different solanaceous host plants. Six replicates of the amplicon sequencing results showed very high reproducibility. On average, we obtained 133,449 CLVd reads per PCR-replicate and 79 to 561 viroid sequence variants, depending on the plant species. We identified 19 major variants (>1.0% mean relative abundance) in which a total of 16 single-nucleotide polymorphisms (SNPs) and two single nucleotide insertions were observed. All major variants contained a combination of 4 to 6 SNPs. Secondary structure prediction clustered all major variants into a tomato/bolo maka group with four loops (I, II, IV and V), and a chili pepper group with four loops (I, III, IV and V) at the terminal right domain, compared to the CLVd Chaipayon-1 which consists of five loops (I, II, III, IV and V). [ABSTRACT FROM AUTHOR]