Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution

Acknowledgements: This work was supported by the Biotechnology and Biological Sciences Research Council grant BBS/E/D/10002070 and the Frimedbio program of the Research Council of Norway (grant number 241016). MKG received studentship funding from a University of Aberdeen Elphinstone scholarship with additional support from the Government of Karnataka. We thank Dr Sebastian Beggel, Dr Bernhard C. Stoeckle, Jens-Eike Täuber and Ms Haiyu Ding at the Aquatic Systems Biology Unit, Technical University of Munich for their support in sampling huchen. We thank Dr Torfinn Nome for supporting bioinformatic analyses. We thank Madhusudhan Gundappa (Twitter: @fish_lines) for providing species illustrations in Figure 1. We also thanks Dr Gareth Gillard (Norwegian University of Life Sciences) for support with the RNA-Seq data. The Earlham Institute performed library preparation and sequencing used in the huchen genome assembly.Peer reviewedPublisher PD

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

publishedVersio

Investigating evolution of gene regulation with crossspecies comparative transcriptomics

An essential ability of all lifeforms is to regulate the activity of its genes. This ability is what allows multicellular organisms to generate hundreds of completely different cells despite having the same genome. It is also this ability that allows organisms to adjust dynamically to external conditions, including how plants in temperate climates adjusts their metabolism in preparation for the coming winter as we study in paper 1 and 2 of this thesis. Quantification of gene expression by RNA sequencing or microarrays is a common method for investigating gene regulation. However, comparing gene expression across species to study evolution of gene regulation presents many challenges. In the first paper, we investigated the evolution of cold adaption in grass by comparing the transcriptomic response to cold in five diverse species of temperate grasses (Pooideae). Two of these species, Barley and Brachypodium distachyon, are well characterized and their cold-response has been studied before. The three other species, which are less studied, belong to early diverging Pooideae tribes. By comparing the cold-response from both early and later diverging species it was possible to investigate to what extent the cold-response has been conserved since their common ancestor, or if it evolved gradually within the Pooideae. Although we observed a significant common response in all species, there were extensive differences. These differences did not follow the phylogeny, as we would expect if there was a gradual evolution. These results indicate that any conserved cold-response either involved very few genes or that the cold-response evolved independently in each lineage. In the second paper, instead of looking at the entire transcriptome, we look specifically at orthologs of a handful of well-known cold-tolerance genes. By inspecting their phylogeny, we see that gene duplication have played an important role both early and later in the evolution of some of the cold-tolerance genes. This includes the CBF gene family, which is known to contain master regulators of cold-response. By investigating the protein sequences we also find that some of the functional protein motifs was missing in the early diverging species, suggesting a gradual and lineage specific evolution of cold-tolerance functions. One of the challenges when comparing gene regulation across species is to acquire directly comparable samples. While we designed the experiment in paper 1 so that the samples should be as similar as possible across species, most experiments found in public databases are not suitable for direct comparison. In the third paper we investigate the use of co-expression to indirectly compare the expression similarities of orthologs. This approach makes it possible to use samples that are not directly comparable. The current methods for co-expression based comparison are not so well studied and we find that we can develop an improved method. Applying our new method to public gene expression data from five plant species, we investigate the link between gene duplication and expression divergence

Investigating evolution of gene regulation with crossspecies comparative transcriptomics

An essential ability of all lifeforms is to regulate the activity of its genes. This ability is what allows multicellular organisms to generate hundreds of completely different cells despite having the same genome. It is also this ability that allows organisms to adjust dynamically to external conditions, including how plants in temperate climates adjusts their metabolism in preparation for the coming winter as we study in paper 1 and 2 of this thesis. Quantification of gene expression by RNA sequencing or microarrays is a common method for investigating gene regulation. However, comparing gene expression across species to study evolution of gene regulation presents many challenges. In the first paper, we investigated the evolution of cold adaption in grass by comparing the transcriptomic response to cold in five diverse species of temperate grasses (Pooideae). Two of these species, Barley and Brachypodium distachyon, are well characterized and their cold-response has been studied before. The three other species, which are less studied, belong to early diverging Pooideae tribes. By comparing the cold-response from both early and later diverging species it was possible to investigate to what extent the cold-response has been conserved since their common ancestor, or if it evolved gradually within the Pooideae. Although we observed a significant common response in all species, there were extensive differences. These differences did not follow the phylogeny, as we would expect if there was a gradual evolution. These results indicate that any conserved cold-response either involved very few genes or that the cold-response evolved independently in each lineage. In the second paper, instead of looking at the entire transcriptome, we look specifically at orthologs of a handful of well-known cold-tolerance genes. By inspecting their phylogeny, we see that gene duplication have played an important role both early and later in the evolution of some of the cold-tolerance genes. This includes the CBF gene family, which is known to contain master regulators of cold-response. By investigating the protein sequences we also find that some of the functional protein motifs was missing in the early diverging species, suggesting a gradual and lineage specific evolution of cold-tolerance functions. One of the challenges when comparing gene regulation across species is to acquire directly comparable samples. While we designed the experiment in paper 1 so that the samples should be as similar as possible across species, most experiments found in public databases are not suitable for direct comparison. In the third paper we investigate the use of co-expression to indirectly compare the expression similarities of orthologs. This approach makes it possible to use samples that are not directly comparable. The current methods for co-expression based comparison are not so well studied and we find that we can develop an improved method. Applying our new method to public gene expression data from five plant species, we investigate the link between gene duplication and expression divergence

Implementing Ultrasound Beamforming on the GPU using CUDA

This thesis discusses the implementation of ultrasound beamforming on the GPU using CUDA. Fractional delay filters and the need for it when implementing beamforming is discussed. An introduction to CUDA programming is given as well as a study of the workings of the NVIDIA Tesla GPU(or G80). A number of suggestions for implementing beamforming on a GPU is presented as well as an actual implementation and an evaluation of it's performance

Analysis of homeolog specific transcription in hexaploid wheat

Bread wheat (Triticum aestivum, BBAADD) is one of the most important food-crops world-wide. The genome of bread wheat is allohexaploid, meaning that it contains three related diploid genomes (termed A, B and D). This implies that most wheat genes exist in three similar copies (i.e. homeologs), which together with the fact that the genome mainly consists of repeats from transposable elements, makes the wheat genome very hard to sequence and assemble. Currently there is an effort by the International Wheat Genome Sequencing Consortium (IWGSC) to generate a wheat genome reference sequence. An enabling factor is the use of flow cytometry to isolate the individual chromosome arms which then can be sequenced and assembled separately. The final reference sequence is still a long way from being finished, however a short-read shot-gun sequence assembly of each chromosome arm, referred to as chromosome survey sequencing (CSS) assembly, has been made available from the IWGSC. Using the CSS assembly as reference for analyses of RNA-sequencing (RNA-seq) data enables us, for the first time, to distinguish and quantify the transcription level of the homeologous genes. In this study I use RNA-seq data sampled from the starchy endosperm, aleurone layer, and transfer cells of the developing wheat endosperm to analyze the homeolog-specific aspects of the hexaploid transcriptome. I found that three quarters of the genes have an expression bias towards either one of the sub-genomes, but that no sub-genome is favored on a general level. The pattern of homeolog bias shows no correlation with functional gene-groups, but 28% of the genes show developmentally controlled homeolog-specific regulation when comparing the sampled tissues. There is also evidence supporting that the D-genome has a different distribution of expression levels than A and B. This could be explained by the polyploidization history, or indicate the presence of hybridization in a D-genome ancestor. Greater understanding of the mechanisms that govern homeolog-specific gene regulation can have an impact on the way breeding of allopolyploids is performed. This study illustrates the importance of homeolog specific reference sequences, and the potential hexaploid wheat has as a model to study mechanism of gene-regulation in allopolyploids

Implementing Ultrasound Beamforming on the GPU using CUDA

This thesis discusses the implementation of ultrasound beamforming on the GPU using CUDA. Fractional delay filters and the need for it when implementing beamforming is discussed. An introduction to CUDA programming is given as well as a study of the workings of the NVIDIA Tesla GPU(or G80). A number of suggestions for implementing beamforming on a GPU is presented as well as an actual implementation and an evaluation of it's performance