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Single Cell Sequencing Facilitates Genome-Enabled Biology in Uncultured Fungi and Resolves Deep Branches on the Fungal Tree of Life.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Single Cell Sequencing Facilitates Genome-Enabled Biology in Uncultured Fungi and Resolves Deep Branches on the Fungal Tree of Life./
作者:	Amses, Kevin Riley.
面頁冊數:	1 online resource (165 pages)
附註:	Source: Dissertations Abstracts International, Volume: 83-05, Section: B.
Contained By:	Dissertations Abstracts International83-05B.
標題:	Bioinformatics. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28845206click for full text (PQDT)
ISBN:	9798471101548

Single Cell Sequencing Facilitates Genome-Enabled Biology in Uncultured Fungi and Resolves Deep Branches on the Fungal Tree of Life.
Amses, Kevin Riley.

Single Cell Sequencing Facilitates Genome-Enabled Biology in Uncultured Fungi and Resolves Deep Branches on the Fungal Tree of Life. - 1 online resource (165 pages)

Source: Dissertations Abstracts International, Volume: 83-05, Section: B.

Thesis (Ph.D.)--University of Michigan, 2021.

Includes bibliographical references

Microbial life on Earth is the most diverse life on Earth. The magnitude of microbial diversity is obscured by their small statures, relatively short list of defining morphological characteristics, and general recalcitrance to being separated from nature and brought into the laboratory. Most microbes cannot be grown under axenic conditions (i.e., uncultured), a simple reality that impedes their discovery in complex natural systems and downstream studies to understand their biology. A point no less important in the age of genome-enabled biological research, the uncultured status of most microbes precludes sequencing of their genomes via conventional high-throughput sequencing, which requires ample input material. Single cell sequencing offers a viable workaround to this central obstacle by enabling the amplification of genomic DNA from individual cells up to amounts more than sufficient for sequencing. That said, this workaround introduces biases to sequence composition and exacerbates contamination, both of which present unique challenges to downstream genome-scale analyses. Fungi constitute a diverse lineage of heterotrophic eukaryotes that sometimes blur the line between microbial and macroscopic life. Our understanding of fungi is wildly incomplete and biased toward fungi that produce macroscopic forms or those that can be grown under axenic conditions. Even in the age of genome-enabled biological research, most fungi that are microscopic, uncultured, or especially both remain poorly understood. In this dissertation, I use single cell sequencing, sometimes combined with conventional genome sequencing, to address this gap by conducting genome-enabled biological research in uncultured or under-sampled sectors of the fungal tree of life. In Chapter 2, I design and deploy a novel computational approach to filtering the biased and often contaminated sequence data associated with single cell sequencing. I demonstrate its ability to outperform available filtering approaches using genuine and mock datasets. In Chapter 3, I use single cell sequencing of predatory fungi to discover novel endohyphal bacteria colonizing fungi in a phylum where this type of symbiosis was entirely unknown. Genome-scale phylogenetic analyses implicate recent interphylum host switches for bacteria thought to transmit predominantly vertically. The novel bacterial endosymbionts discovered have similar genomes to other endohyphal bacteria but have, in some cases, acquired and retained horizontally transferred genes from animals. In Chapter 4, I use genome-scale data to infer a robustly supported phylogeny of zoosporic fungi. Mapping of genetic traits and ploidy inferred from sequence data suggests that fungal evolution has been driven by gradual loss and that most early diverging lineages have diploid-dominant life cycles. In Chapter 5, I use genome-scale data to resolve a disagreement between classical taxonomy and molecular phylogenetics revolving around the phylogenetic placement of the enigmatic, arthropod-mummifying fungal genus Neozygites. Through the development of novel computational methods, genome-scale phylogenetics, and a comparative approach, this dissertation demonstrates the utility of single cell sequencing in closing vast gaps in our understanding of fungi.

Electronic reproduction.
Ann Arbor, Mich. :
ProQuest,
2023

Mode of access: World Wide Web

ISBN: 9798471101548Subjects--Topical Terms:

553671
Bioinformatics.
Subjects--Index Terms:

Single cell genomicsIndex Terms--Genre/Form:

542853
Electronic books.

Single Cell Sequencing Facilitates Genome-Enabled Biology in Uncultured Fungi and Resolves Deep Branches on the Fungal Tree of Life.
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