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Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing.
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- معلومة اضافية
- المصدر:
Publisher: Oxford University Press Country of Publication: England NLM ID: 101566598 Publication Model: Print Cited Medium: Internet ISSN: 2160-1836 (Electronic) Linking ISSN: 21601836 NLM ISO Abbreviation: G3 (Bethesda) Subsets: MEDLINE
- بيانات النشر:
Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Bethesda, MD : Genetics Society of America, 2011-
- الموضوع:
- نبذة مختصرة :
Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes.
Competing Interests: Conflicts of interest The authors declare no conflict of interest.
(© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
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- Grant Information:
RGPIN-2017-03807 Libyan Ministry of Higher Education and Scientific Research
- Contributed Indexing:
Keywords: Daphnia pulex; concerted evolution; copy number variation; intragenomic rDNA polymorphism; polymorphic nucleotide sites; ribosomal RNA gene
- الرقم المعرف:
0 (DNA, Ribosomal)
- الموضوع:
Date Created: 20240521 Date Completed: 20240708 Latest Revision: 20240710
- الموضوع:
20240710
- الرقم المعرف:
PMC11228840
- الرقم المعرف:
10.1093/g3journal/jkae105
- الرقم المعرف:
38771699
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