Assembly, annotation and analysis of chloroplast genomes

Xiao Zhong

doi:10.26182/5f333d9ac2bee

Assembly, annotation and analysis of chloroplast genomes

Xiao Zhong

School of Molecular Sciences

Research output: Thesis › Doctoral Thesis

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Abstract

Chloroplast genome data is useful for phylogenetic analyses, for species identification and for tracing evolutionary adaptations. Current sequencing technology enables us to obtain complete plastome on a large scale. The aim of this study was to develop robust computational plastome assembly and annotation tools and databases. In particular, a novel annotation algorithm was developed to address challenges in plastome annotation. The annotation software Chloe (https://chloe.plantenergy.edu.au) was used to re-annotate the ~4000 available plastomes of land plants in GenBank, and annotate the newly assembled plastomes. These newly developed tools and databases are valuable resources for future studies in chloroplast genomics.

Original language	English
Qualification	Doctor of Philosophy
Awarding Institution	The University of Western Australia
Supervisors/Advisors	Small, Ian, Supervisor Tonti-Filippini, Julian, Supervisor Vacher, Michael, Supervisor
Award date	15 Jul 2020
DOIs	https://doi.org/10.26182/5f333d9ac2bee
Publication status	Unpublished - 2020

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10.26182/5f333d9ac2bee

THESIS - DOCTOR OF PHILOSOPHY - ZHONG, Xiao - 2020
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Cite this

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title = "Assembly, annotation and analysis of chloroplast genomes",

abstract = "Chloroplast genome data is useful for phylogenetic analyses, for species identification and for tracing evolutionary adaptations. Current sequencing technology enables us to obtain complete plastome on a large scale. The aim of this study was to develop robust computational plastome assembly and annotation tools and databases. In particular, a novel annotation algorithm was developed to address challenges in plastome annotation. The annotation software Chloe (https://chloe.plantenergy.edu.au) was used to re-annotate the ~4000 available plastomes of land plants in GenBank, and annotate the newly assembled plastomes. These newly developed tools and databases are valuable resources for future studies in chloroplast genomics.",

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AB - Chloroplast genome data is useful for phylogenetic analyses, for species identification and for tracing evolutionary adaptations. Current sequencing technology enables us to obtain complete plastome on a large scale. The aim of this study was to develop robust computational plastome assembly and annotation tools and databases. In particular, a novel annotation algorithm was developed to address challenges in plastome annotation. The annotation software Chloe (https://chloe.plantenergy.edu.au) was used to re-annotate the ~4000 available plastomes of land plants in GenBank, and annotate the newly assembled plastomes. These newly developed tools and databases are valuable resources for future studies in chloroplast genomics.

KW - Chloroplast genome

KW - Plastome assembly

KW - Plastome annotation

KW - Chloe software

KW - Re-annotated RefSeq

KW - Ptilotus plastid DNA

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DO - 10.26182/5f333d9ac2bee

M3 - Doctoral Thesis

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Assembly, annotation and analysis of chloroplast genomes

Abstract

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