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Genomic powerhouse: de novo assembly and phylogenetic analyses of Anolis mitochondrial genomes
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Comșa, Lim Caden. Genomic powerhouse: de novo assembly and phylogenetic analyses of Anolis mitochondrial genomes. Retrieved from https://doi.org/doi:10.7282/t3-nnvc-3r67

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TitleGenomic powerhouse: de novo assembly and phylogenetic analyses of Anolis mitochondrial genomes
NameComșa, Lim Caden (author); Geneva, Anthony (chair); Savage, Amy (member); Grigoriev, Andrey (member); Rutgers University; Graduate School - Camden
Date Created2023
Other Date2022-10 (degree)
SubjectGenetics, Zoology, Evolution & development, Anoles, Anolis, Bayesian phylogenetics, Evolutionary tree, Mitochondrial genomics, MrBayes
Extent52 pages : illustrations
DescriptionAnoles, lizards belonging to the genus Anolis, are a model clade for the fields of evolutionary biology, ecology, and their intersection. However, despite extensive study of the genus, very little genomic data are available for the over 425 species in the genus. We set out to improve availability of genomic data among Anolis species by assembling mitochondrial (mito-)genomes of several anole species, as well as to test for the conservation of mitochondrial structure and genetic elements. We created a pipeline to process short-read sequencing files and generate mito-genome assemblies. We implemented the pipeline on whole genome sequencing (WGS) reads from our own datasets, as well as on WGS and Target Capture sequencing (TC) data publicly available on the Short Reads Archive (SRA) website from the National Center for Biotechnology Information (NCBI). We successfully de novo assembled and annotated 18 complete mito-genomes using our pipeline, including one genome from off-target reads pulled from a TC dataset. We found that the structure of the mito-genomes was conserved across all analyzed species. Protein coding and ribosomal RNA genes from the mito-genomes were extracted and used to perform single-gene or concatenated and partitioned phylogenetic simulations via MrBayes. Our phylogenetic analyses showed strong support for the monophyly of Anolis and for several relationships between the eight subgenera of anoles that have remained unresolved based on previous phylogenetic analysis of smaller sequence datasets. We show that mito-genomic data such as these are relatively easy to generate and can improve scientific understanding of Anolis by opening up new avenues for hypothesis-driven research, such as investigating potential differences in mitochondrial evolutionary rates between different Anolis lineages.
NoteM.S.
NoteIncludes bibliographical references
Genretheses
Persistent URLhttps://doi.org/doi:10.7282/t3-nnvc-3r67
LanguageEnglish
CollectionCamden Graduate School Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.
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