The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Seagrasses colonized the sea(1) on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet(2). Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes(3), genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae(4) and that is important for ion homoeostasis, nutrient uptake and O-2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming(5,6), to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants(7)

The genome of the seagrass <i>Zostera marina</i> reveals angiosperm adaptation to the sea

Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants

SUFFIX TREE, MINWISE HASHING AND STREAMING ALGORITHMS FOR BIG DATA ANALYSIS IN BIOINFORMATICS

In this dissertation, we worked on several algorithmic problems in bioinformatics using mainly three approaches: (a) a streaming model, (b) sux-tree based indexing, and (c) minwise-hashing (minhash) and locality-sensitive hashing (LSH). The streaming models are useful for large data problems where a good approximation needs to be achieved with limited space usage. We developed an approximation algorithm (Kmer-Estimate) using the streaming approach to obtain a better estimation of the frequency of k-mer counts. A k-mer, a subsequence of length k, plays an important role in many bioinformatics analyses such as genome distance estimation. We also developed new methods that use sux tree, a trie data structure, for alignment-free, non-pairwise algorithms for a conserved non-coding sequence (CNS) identification problem. We provided two different algorithms: STAG-CNS to identify exact-matched CNSs and DiCE to identify CNSs with mismatches. Using our algorithms, CNSs among various grass species were identified. A different approach was employed for identification of longer CNSs ( 100 bp, mostly found in animals). In our new method (MinCNE), the minhash approach was used to estimate the Jaccard similarity. Using also LSH, k-mers extracted from genomic sequences were clustered and CNSs were identified. Another new algorithm (MinIsoClust) that also uses minhash and LSH techniques was developed for an isoform clustering problem. Isoforms are generated from the same gene but by alternative splicing. As the isoform sequences share some exons but in different combinations, regular sequencing clustering methods do not work well. Our algorithm generates clusters for isoform sequences based on their shared minhash signatures. Finally, we discuss de novo transcriptome assembly algorithms and how to improve the assembly accuracy using ensemble approaches. First, we did a comprehensive performance analysis on different transcriptome assemblers using simulated benchmark datasets. Then, we developed a new ensemble approach (Minsemble) for the de novo transcriptome assembly problem that integrates isoform-clustering using minhash technique to identify potentially correct transcripts from various de novo transcriptome assemblers. Minsemble identified more correctly assembled transcripts as well as genes compared to other de novo and ensemble methods. Adviser: Jitender S. Deogu

On impact and volcanism across the Cretaceous-Paleogene boundary

The cause of the end-Cretaceous mass extinction is vigorously debated, owing to the occurrence of a very large bolide impact and flood basalt volcanism near the boundary. Disentangling their relative importance is complicated by uncertainty regarding kill mechanisms and the relative timing of volcanogenic outgassing, impact, and extinction. We used carbon cycle modeling and paleotemperature records to constrain the timing of volcanogenic outgassing. We found support for major outgassing beginning and ending distinctly before the impact, with only the impact coinciding with mass extinction and biologically amplified carbon cycle change. Our models show that these extinction-related carbon cycle changes would have allowed the ocean to absorb massive amounts of carbon dioxide, thus limiting the global warming otherwise expected from postextinction volcanism

Reconstructing the southern Greenland Ice Sheet and deep ocean circulation during the Plio-Pleistocene intensification of Northern Hemisphere glaciation

The Greenland Ice Sheet (GrIS) is thought to have reached modern-like extents during cold stages for the first time during the Plio-Pleistocene intensification of Northern Hemisphere glaciation (iNHG, ~3.6–2.4 million years ago, Ma). However, questions remain regarding the spatial maturation of the southern GrIS during this time – a region thought to be particularly sensitive to changes in climate – including its extent during the mid-Piacenzian warm period (mPWP; 3.264–3.025 Ma), considered an analogue to near-future climate with atmospheric CO2 levels >400 ppmv and temperatures elevated by ~2–3 °C relative to today. Difficulties in obtaining long continuous sediment core records back to the late Pliocene in the subpolar North Atlantic, as well as chronological uncertainty in existing records, have previously hampered efforts to address these unknowns. In this thesis, I present high-resolution records of ice-rafted debris concentration and provenance, environmental magnetics and elemental X-ray fluorescence (XRF) spanning ~3.2–2.2 Ma from North Atlantic Integrated Ocean Drilling Program Site U1307 on Eirik Drift, just offshore southern Greenland. The study benefits from a newly-resolved high-fidelity relative paleointensity-based age model, the first of its kind for high-latitude sediments deposited during this interval, which enables variability in the records to be accurately and precisely dated. This multi-proxy approach enables constraints to be placed on the spatio-temporal evolution of iceberg-calving margins on southern Greenland, as well as contemporaneous changes in surface water productivity and delivery of glaciofluvial silt via the deep Western Boundary Undercurrent (WBUC) to Eirik Drift during iNHG. Provenance analysis of ice-rafted debris pinpoints the evolution of important modern-day southern Greenland iceberg-calving sources, revealing that a modern-like GrIS with extensive southern iceberg-calving margins had developed by ~2.4 Ma. Elevated glaciofluvial erosion throughout the mPWP traced by XRF and magnetics refutes predictions for complete GrIS deglaciation during this time, and sedimentation rates and environmental magnetics provide the first direct evidence that the strength of the WBUC changed contemporaneously with increasing southern GrIS extents between 2.9 and 2.7 Ma

An adaptive admission control and load balancing algorithm for a QoS-aware Web system

The main objective of this thesis focuses on the design of an adaptive algorithm for admission control and content-aware load balancing for Web traffic. In order to set the context of this work, several reviews are included to introduce the reader in the background concepts of Web load balancing, admission control and the Internet traffic characteristics that may affect the good performance of a Web site. The admission control and load balancing algorithm described in this thesis manages the distribution of traffic to a Web cluster based on QoS requirements. The goal of the proposed scheduling algorithm is to avoid situations in which the system provides a lower performance than desired due to servers' congestion. This is achieved through the implementation of forecasting calculations. Obviously, the increase of the computational cost of the algorithm results in some overhead. This is the reason for designing an adaptive time slot scheduling that sets the execution times of the algorithm depending on the burstiness that is arriving to the system. Therefore, the predictive scheduling algorithm proposed includes an adaptive overhead control. Once defined the scheduling of the algorithm, we design the admission control module based on throughput predictions. The results obtained by several throughput predictors are compared and one of them is selected to be included in our algorithm. The utilisation level that the Web servers will have in the near future is also forecasted and reserved for each service depending on the Service Level Agreement (SLA). Our load balancing strategy is based on a classical policy. Hence, a comparison of several classical load balancing policies is also included in order to know which of them better fits our algorithm. A simulation model has been designed to obtain the results presented in this thesis