Biology

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    A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions
    (Springer Nature, 2017-05-02) Conte, Matthew A.; Gammerdinger, William J.; Bartie, Kerry L.; Penman, David J.; Kocher, Thomas D.
    Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species. A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing. Dozens of candidate de novo assemblies were generated and an optimal assembly (contig NG50 of 3.3Mbp) was selected using principal component analysis of likelihood scores calculated from several paired-end sequencing libraries. Comparison of the new assembly to the previous O. niloticus genome assembly reveals that recently duplicated portions of the genome are now well represented. The overall number of genes in the new assembly increased by 27.3%, including a 67% increase in pseudogenes. The new tilapia genome assembly correctly represents two recent vasa gene duplication events that have been verified with BAC sequencing. At total of 146Mbp of additional transposable element sequence are now assembled, a large proportion of which are recent insertions. Large centromeric satellite repeats are assembled and annotated in cichlid fish for the first time. Finally, the new assembly identifies the long-range structure of both a ~9Mbp XY sex determination region on LG1 in O. niloticus, and a ~50Mbp WZ sex determination region on LG3 in the related species O. aureus. This study highlights the use of long read sequencing to correctly assemble recent duplications and to characterize repeat-filled regions of the genome. The study serves as an example of the need for high quality genome assemblies and provides a framework for identifying sex determining genes in tilapia and related fish species.
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    Molecular evolutionary studies on Trypanosoma cruzi, the agent of Chagas disease
    (2013) Flores Lopez, Carlos Alberto; Machado, Carlos A; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The use of DNA sequences to address diverse evolutionary questions has increased steadily with the growing availability of genome sequence data. In this study, I make use of DNA sequence data to describe several evolutionary aspects of the protozoan parasite responsible for Chagas disease, Trypanosoma cruzi. Chagas is estimated to infect 7.7 million people and cause the deaths of approximately ten thousand people every year in Latin America. Just like many other parasitic diseases, Chagas does not have a vaccine or an effective drug treatment. In this body of work, I specifically: (1) describe the evolutionary history of the major strains of the parasite through the use of phylogenetic analyses of 32 loci and demonstrate that the parasite's original classification into two major evolutionary lineages does not reflect the evolutionary history of the parasite, (2) demonstrate that there is strong evidence for just one major recent hybridization event during the history of T. cruzi divergence and not two as previously suggested, (3) show that all major extant T. cruzi lineages diverged recently (less than 3 million years ago), well before the arrival of humans in the Americas, (4) describe a new T. cruzi lineage that appears to have diverged in North America ("TcNA"), (5) show that a significantly larger fraction of protein-coding genes have experienced positive selection in T. cruzi than in Leishmania spp., a pattern likely due to the greater versatility of T. cruzi in its host range, cell tropism and cell invasion mechanisms, and (6) illustrate a recent major expansion of a few surface protein families in T. cruzi that seem to be linked to the evolution of the parasite's ability to invade multiple cell tissues and multiple host species. These results demonstrate the applicability and power of molecular evolutionary analyses for understanding parasitic diseases.