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    Assembly of Two CCDD Rice Genomes, Oryza grandiglumis and Oryza latifolia, and the Study of Their Evolutionary Changes

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    Aseel Alsantely thesis.pdf
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    5.453Mb
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    Description:
    Aseel Alsantely Thesis
    Embargo End Date:
    2022-01-06
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    Type
    Thesis
    Authors
    Alsantely, Aseel O. cc
    Advisors
    Wing, Rod Anthony cc
    Committee members
    Gojobori, Takashi cc
    Zuccolo, Andrea
    Program
    Bioscience
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Date
    2021-01
    Embargo End Date
    2022-01-06
    Permanent link to this record
    http://hdl.handle.net/10754/666825
    
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    Show full item record
    Access Restrictions
    At the time of archiving, the student author of this thesis opted to temporarily restrict access to it. The full text of this thesis will become available to the public after the expiration of the embargo on 2022-01-06.
    Abstract
    Every day more than half of the world consumes rice as a primary dietary resource. Thus, rice is one of the most important food crops in the world. Rice and its wild relatives are part of the genus Oryza. Studying the genome structure, function, and evolution of Oryza species in a comparative genomics framework is a useful approach to provide a wealth of knowledge that can significantly improve valuable agronomic traits. The Oryza genus includes 27 species, with 11 different genome types as identified by genetic and cytogenetic analyses. Six genome types, including that of domesticated rice - O. sativa and O. glaberrima, are diploid, and the remaining 5 are tetraploids. Three of the tetraploid species contain the CCDD genome types (O. grandiglumis, O. latifolia, and O. alta), which arose less than 2 million years ago. Polyploidization is one of the major contributors to evolutionary divergence and can thereby lead to adaptation to new environmental niches. An important first step in the characterization of the polyploid Oryza species is the generation of a high-quality reference genome sequence. Unfortunately, up until recently, the generation of such an important and fundamental resource from polyploid species has been challenging, primarily due to their genome complexity and repetitive sequence content. In this project, I assembled two high-quality genomes assemblies for O. grandiglumis and O. latifolia using PacBio long-read sequencing technology and an assembly pipeline that employed 3 genome assemblers (i.e., Canu/2.0, Mecat2, and Flye/2.5) and multiple rounds of sequence polishing with 5 both Arrow and Pilon/1.23. After the primary assembly, sequence contigs were arranged into pseudomolecules, and homeologous chromosomes were assigned to their respective genome types (i.e., CC or DD). Finally, the assemblies were extensively edited manually to close as many gaps as possible. Both assemblies were then analyzed for transposable element and structural variant content between species and homoeologous chromosomes. This enabled us to study the evolutionary divergence of those two genomes, and to explore the possibility of neo-domesticating either species in future research for my PhD dissertation.
    Citation
    Alsantely, A. O. (2021). Assembly of Two CCDD Rice Genomes, Oryza grandiglumis and Oryza latifolia, and the Study of Their Evolutionary Changes. KAUST Research Repository. https://doi.org/10.25781/KAUST-5S45B
    DOI
    10.25781/KAUST-5S45B
    ae974a485f413a2113503eed53cd6c53
    10.25781/KAUST-5S45B
    Scopus Count
    Collections
    Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Theses

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