دورية أكاديمية
Complete Sequence Construction of the Highly Repetitive Ribosomal RNA Gene Repeats in Eukaryotes Using Whole Genome Sequence Data.
| العنوان: | Complete Sequence Construction of the Highly Repetitive Ribosomal RNA Gene Repeats in Eukaryotes Using Whole Genome Sequence Data. |
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| المؤلفون: | Agrawal S; Institute of Natural and Mathematical Sciences, Massey University, Private Bag 102-904, Auckland, 0632, New Zealand. saumya.agrawal@gmail.com.; School of Biological Sciences, University of Auckland, Auckland, New Zealand. saumya.agrawal@gmail.com., Ganley AR; Institute of Natural and Mathematical Sciences, Massey University, Private Bag 102-904, Auckland, 0632, New Zealand. A.R.Ganley@massey.ac.nz.; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand. A.R.Ganley@massey.ac.nz. |
| المصدر: | Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2016; Vol. 1455, pp. 161-81. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: Totowa, NJ : Humana Press Original Publication: Clifton, N.J. : Humana Press, |
| مواضيع طبية MeSH: | Genes, rRNA* , Genomics*/methods , Repetitive Sequences, Nucleic Acid* , Whole Genome Sequencing*, Computational Biology/*methods , Eukaryota/*genetics, Evolution, Molecular ; Phylogeny ; Sequence Analysis, DNA ; Software ; Tandem Repeat Sequences ; Web Browser |
| مستخلص: | The ribosomal RNA genes (rDNA) encode the major rRNA species of the ribosome, and thus are essential across life. These genes are highly repetitive in most eukaryotes, forming blocks of tandem repeats that form the core of nucleoli. The primary role of the rDNA in encoding rRNA has been long understood, but more recently the rDNA has been implicated in a number of other important biological phenomena, including genome stability, cell cycle, and epigenetic silencing. Noncoding elements, primarily located in the intergenic spacer region, appear to mediate many of these phenomena. Although sequence information is available for the genomes of many organisms, in almost all cases rDNA repeat sequences are lacking, primarily due to problems in assembling these intriguing regions during whole genome assemblies. Here, we present a method to obtain complete rDNA repeat unit sequences from whole genome assemblies. Limitations of next generation sequencing (NGS) data make them unsuitable for assembling complete rDNA unit sequences; therefore, the method we present relies on the use of Sanger whole genome sequence data. Our method makes use of the Arachne assembler, which can assemble highly repetitive regions such as the rDNA in a memory-efficient way. We provide a detailed step-by-step protocol for generating rDNA sequences from whole genome Sanger sequence data using Arachne, for refining complete rDNA unit sequences, and for validating the sequences obtained. In principle, our method will work for any species where the rDNA is organized into tandem repeats. This will help researchers working on species without a complete rDNA sequence, those working on evolutionary aspects of the rDNA, and those interested in conducting phylogenetic footprinting studies with the rDNA. |
| فهرسة مساهمة: | Keywords: Arachne; Repeats; Ribosomal RNA; Sanger; Whole genome assembly; Whole genome sequencing; rDNA |
| تواريخ الأحداث: | Date Created: 20160901 Date Completed: 20180112 Latest Revision: 20180404 |
| رمز التحديث: | 20240628 |
| DOI: | 10.1007/978-1-4939-3792-9_13 |
| PMID: | 27576718 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1940-6029 |
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| DOI: | 10.1007/978-1-4939-3792-9_13 |