Recent warming across the North Atlantic region may be contributing to an expansion in barley cultivation

Although grass dominates most agricultural systems in the North Atlantic region (NAR), spring barley is the most important cereal and is used for animal feed and food and drink products. Recent changes in climate have resulted in warmer conditions across the NAR which have major implications for crop production. In this paper, we investigate the thermal requirement of spring barley in the region and use the results to examine the effects of recent trends in temperature and rainfall on barley cultivation, based on 11 regional meteorological sites. At these sites, between 1975 and 2015, we found significant warming trends for several months of the cropping season and significant trends for increases in the cropping season degree days (CSDD). In recent years, this has resulted in an increased proportion of years when the estimated minimum thermal requirement for barley has been met at sites above about 60°N. However, annual variations in CSDD are large and years still occur at these sites where this is insufficient. While warming could potentially allow an earlier start and later end to the cropping season, it is likely that high rainfall at maritime sites, and low rainfall at continental sites, will limit the ability of growers to benefit from this. Warming is considered to have been one of the main factors contributing to the large expansion of the area of barley cultivated in Iceland since the 1990s.publishedVersio

Investigations into plant genome evolution using massive parallel sequencing

The advancements of various massively parallel sequencing (MPS) methods in the last five years have enabled researchers to tackle biological problems that until recently seemed intractable. One of the most widely used MPS methods comes from Illumina®, which combines short and accurate sequencing reads with high throughput. Data generated using Illumina sequencing is used in every chapter of this thesis to characterize patterns of genome evolution using phylogenetic approaches in various plant genera. The thesis is focused on three main aspects of plant genome evolution: transposable elements (chapter 2), polyploidy (chapters 3 and 4) and plastid genomes (chapters 5 and 6). In every chapter phylogenetic hypotheses are generated from sequences assembled from Illumina reads, which I use to frame my research questions. In chapter 2 I investigated intra- and interspecific patterns of transposable element (TE) abundance in Theobroma cacao and related species. I found that reference based mapping of short sequencing reads works well to characterize TEs within the same species but is not reliable for interspecific comparison. In chapter 3 I used Illumina sequenced transcriptomes of 11 flax species, to investigate the presence of paleopolyploidy event within the genus. I discovered a previously unknown paleopolyploidy event, occurring 23 – 42 million years ago. In chapter 4 I used low coverage Illumina whole genome sequencing to test a hypothesis regarding the allopolyploid origin of a North-American Lathyrus species, L. venosus. I conclude that L. venosus is not of hybrid origin, since no incongruencies were detected between nuclear and plastid phylogenies. In chapter 5 I pinpointed the evolutionary origin of highly repetitive plastid genomes that are known to exist within the clover genus (Trifolium). I discovered that the repetitive plastomes are restricted to a single clade within Trifolium, which I estimated to be 12.4 – 13.8 million years old. In chapter 6 I investigated the pattern of gene rearrangements in the IRLC clade of legumes. While plastomes are highly rearranged in this group, I characterized certain highly conserved gene blocks that have not been rearranged internally, and argue that these blocks may represent the fundamental gene regulatory organization of the plastid.Science, Faculty ofBotany, Department ofGraduat

Trifolium_plastid_coding

A concatenated matrix of 59 protein coding plastid genes. Only coding regions were used, introns and intergenic regions were excluded in the alignment, due to plastome rearrangements (see manuscript of further description). The alignment was generated using Mafft v7.053b using -auto flag and trimmed using TrimAl with the -automated1 flag. This process was pipelined using Plast2Phy (https://github.com/saemi/plast2phy)

Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

Background: Some clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus. Results: The Trifolium plastomes fell into two groups: those of Trifolium boissieri, T. strictum and T. glanduliferum (representing subgenus Chronosemium and subg. Trifolium section Paramesus) were tractable, assembled readily and were not unusual in the general context of Fabeae plastomes. The other Trifolium species (“core Trifolium”) proved refractory to assembly mainly because of numerous short duplications. These species form a single clade, which we call the “refractory clade” (comprising subg, Trifolium sections Lupinaster, Trifolium, Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the refractory clade are the presence of numerous short duplications and 7-15% longer genomes than the tractable species. Molecular dating estimates that the origin of the most recent common ancestor (MRCA) of the refractory clade is approximately 13.1 million years ago (MYA). This is considerably younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA) and Trifolium subg. Trifolium (16.1 MYA). Conclusions: We conclude that the unusual repetitive plastome type previously characterized in Trifolium subterraneum had a single origin within Trifolium and is characteristic of most (but not all) species of subgenus Trifolium. It appears that an ancestral plastome within Trifolium underwent an evolutionary change resulting in plastomes that either actively promoted, were permissive to, or were unable to control, duplications within the genome. The precise mechanism of this important change in the mode and tempo of plastome evolution deserves further investigation.Botany, Department ofZoology, Department ofScience, Faculty ofReviewedFacult

Trifolium_plastid_coding_ML

ML tree generated using GARLI (the config file is the ReadMe file). The model used GTR+G, based on a jModelTest search and an AIC test. 10 starts were prefromed and a 100 bootstrap replicates. Medicago truncatula is the outrgroup

Transposon fingerprinting using low coverage whole genome shotgun sequencing in Cacao (Theobroma cacao L.) and related species

Background. Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species. Results (i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome. Conclusions (i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a “fingerprint” to identify and characterize cacao accessions.Botany, Department ofNon UBCScience, Faculty ofReviewedFacult