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NLR-Finder: An Easy and Efficient Annotation Tool for the NLR Superfamily in Plant Genomes

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dc.contributor.advisor최도일-
dc.contributor.author박지은-
dc.date.accessioned2017-07-14T06:17:21Z-
dc.date.available2017-07-14T06:17:21Z-
dc.date.issued2017-02-
dc.identifier.other000000141930-
dc.identifier.urihttps://hdl.handle.net/10371/125453-
dc.description학위논문 (석사)-- 서울대학교 대학원 : 협동과정농생명유전체학전공, 2017. 2. 최도일.-
dc.description.abstractGene annotation is an essential process to identify gene structures and define biological functions. It is an important step for subsequent analyses including gene cloning and identification of genes for agricultural traits. However, current gene annotation misrepresents the whole gene repertoire due to biased gene model construction. Nucleotide-binding and leucine-rich repeat (NLR) superfamily is one of the poorly annotated gene families in plants. The NLR family tends to be clustered in genomes by segmental and tandem duplications, which makes the gene annotation challenging. The NLR-Finder was developed for unbiased genome-wide identification of the NLR superfamily in assembled plant genomes. The NLR-Finder firstly detects candidate NLR gene regions by extending 30 kb to both sides of all the identified NB-ARC domain regions. Secondly, evidence-based NLR genes are predicted by aligning published proteins and transcriptome sequences to the candidate gene regions. Thirdly, additional NLR genes are extracted using an ab initio prediction approach. Lastly, final NLR gene models are generated by integration of the evidence- and ab initio-based NLR genes. The re-annotation was performed using the NLR-Finder on 17 different plant genomes. On average, public annotation tools identified about 310 genes, whereas the NLR-Finder annotated about 497 genes. In Gossypium hirsutum and Vigna radiata, the number of re-annotated genes tripled compared to that of publicly available data. The re-annotated genes were successfully validated by comparing with high-quality annotations of Arabidopsis thaliana, Brachypodium distachyon, and Solanum lycopersicum. This study demonstrated that the NLR-Finder provides an easy-to-use and efficient method to annotate the NLR superfamily in plant genomes.-
dc.description.tableofcontentsINTRODUCTION 1

LITERATURE REVIEWS 3
Gene annotation 3
Annotation errors 4
Nucleotide-binding and leucine-rich repeat (NLR) genes 5

MATERIALS AND METHODS 8
Plant genomes, protein data, and transcriptome collection 8
Workflow of the NLR-Finder 10

RESULTS 16
Transcriptome raw data preprocessing and reference assembly 16
Re-annotation of NLR genes with the NLR-Finder 16
Validation of the NLR-Finder using high-quality plant genomes 22

DISCUSSION 30

REFERENCES 33

ABSTRACT IN KOREAN 37
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dc.formatapplication/pdf-
dc.format.extent1162944 bytes-
dc.format.mediumapplication/pdf-
dc.language.isoko-
dc.publisher서울대학교 대학원-
dc.subjectannotation-
dc.subjectnucleotide-binding and leucine-rich repeat (NLR) genes-
dc.subjectdisease resistance genes-
dc.subjectbioinformatics tool-
dc.subject.ddc576-
dc.titleNLR-Finder: An Easy and Efficient Annotation Tool for the NLR Superfamily in Plant Genomes-
dc.typeThesis-
dc.description.degreeMaster-
dc.citation.pages37-
dc.contributor.affiliation농업생명과학대학 협동과정농생명유전체학전공-
dc.date.awarded2017-02-
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College of Agriculture and Life Sciences (농업생명과학대학)Program in Agricultural Genomics (협동과정-농생명유전체학전공)Theses (Master's Degree_협동과정-농생명유전체학전공)
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