Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing.

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

Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Bethesda, MD : Genetics Society of America, 2011-

Daphnia*/genetics ; DNA Copy Number Variations* ; DNA, Ribosomal*/genetics ; Polymorphism, Single Nucleotide* ; Whole Genome Sequencing*/methods; Animals ; Haplotypes ; Genetic Variation ; Linkage Disequilibrium ; Genome ; Genetics, Population ; Daphnia pulex

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.)

Mol Biol Evol. 2005 May;22(5):1309-19. (PMID: 15746016)
Q Rev Biol. 1995 Sep;70(3):297-320. (PMID: 7568673)
Carcinogenesis. 2019 Aug 22;40(8):975-978. (PMID: 30859204)
Mol Biol Evol. 1988 Jul;5(4):393-414. (PMID: 3136295)
Genetics. 1995 Dec;141(4):1327-37. (PMID: 8601477)
Genome Res. 2013 Oct;23(10):1749-62. (PMID: 23800452)
Genome Res. 2009 Apr;19(4):626-35. (PMID: 19141593)
Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168)
Nat Commun. 2014 Sep 11;5:4850. (PMID: 25209200)
Dev Cell. 2019 Mar 25;48(6):811-826.e6. (PMID: 30799226)
Philos Trans R Soc Lond B Biol Sci. 1996 Mar 29;351(1337):349-60. (PMID: 8730787)
Sci China Life Sci. 2019 Feb;62(2):203-214. (PMID: 30671886)
Yeast. 2009 Feb;26(2):125-38. (PMID: 19235779)
Nature. 2000 Jun 22;405(6789):907-13. (PMID: 10879524)
Chromosoma. 2000 Jun;109(3):161-72. (PMID: 10929194)
Proc Natl Acad Sci U S A. 1990 Nov;87(22):8741-5. (PMID: 2247443)
Genome Res. 2007 Dec;17(12):1888-97. (PMID: 17989256)
Genetics. 2023 May 4;224(1):. (PMID: 36919976)
G3 (Bethesda). 2020 Jan 7;10(1):417-430. (PMID: 31757929)
Genome Res. 2018 Oct;28(10):1555-1565. (PMID: 30166407)
Genes (Basel). 2019 May 07;10(5):. (PMID: 31067804)
Mol Biol Evol. 2023 Nov 3;40(11):. (PMID: 37863047)
PLoS Genet. 2011 Apr;7(4):e1001376. (PMID: 21533076)
Cell Rep. 2016 Mar 22;14(11):2519-27. (PMID: 26972008)
Science. 2011 Feb 4;331(6017):555-61. (PMID: 21292972)
Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404)
Genome. 2008 Dec;51(12):988-1000. (PMID: 19088812)
Trends Genet. 2022 Jun;38(6):587-597. (PMID: 35272860)
Mol Ecol. 2015 Sep;24(17):4521-36. (PMID: 26190313)
Genetics. 2007 Feb;175(2):477-85. (PMID: 17322354)
Nat Comput Sci. 2021 Apr;1(4):262-271. (PMID: 38217170)
Nucleic Acids Res. 2000 Jan 1;28(1):175-6. (PMID: 10592217)
J Mol Biol. 1988 Dec 20;204(4):805-13. (PMID: 3065517)
Mol Biol Evol. 2022 Aug 3;39(8):. (PMID: 35895848)
Mol Biol Evol. 1987 Jul;4(4):406-25. (PMID: 3447015)
J Mol Evol. 2009 Aug;69(2):142-9. (PMID: 19582497)
Mob DNA. 2016 Jun 17;7:11. (PMID: 27330569)
Evolution. 1999 Jun;53(3):777-792. (PMID: 28565628)
BMC Genet. 2011 Jan 24;12:13. (PMID: 21261945)
Cell Mol Life Sci. 2011 Apr;68(8):1395-403. (PMID: 21207101)
Gigascience. 2021 Feb 16;10(2):. (PMID: 33590861)
Mob DNA. 2012 Mar 05;3(1):4. (PMID: 22390386)
PLoS One. 2017 Aug 17;12(8):e0183447. (PMID: 28817651)
Dev Biol. 1970 Jul;22(3):495-512. (PMID: 5463671)
Genetics. 1987 Oct;117(2):285-95. (PMID: 17246404)
J Biol. 2010;9(2):21. (PMID: 20478012)
PLoS Genet. 2012 Jan;8(1):e1002473. (PMID: 22291607)
Mol Cell Biol. 2015 Feb;35(3):544-54. (PMID: 25421713)
Genetics. 1992 Oct;132(2):619-33. (PMID: 1385266)
Plant J. 2007 May;50(4):710-22. (PMID: 17425718)
Mol Ecol. 2013 Feb;22(3):583-601. (PMID: 23174029)
Mol Ecol Resour. 2010 May;10(3):564-7. (PMID: 21565059)
Mol Biol Evol. 2021 Aug 23;38(9):3581-3592. (PMID: 33885820)
Annu Rev Genet. 2005;39:121-52. (PMID: 16285855)
Trends Genet. 2019 Oct;35(10):734-742. (PMID: 31395390)
Nat Commun. 2022 Nov 25;13(1):7245. (PMID: 36434003)
Genome Res. 2007 Feb;17(2):184-91. (PMID: 17200233)
PLoS One. 2014 Dec 09;9(12):e114773. (PMID: 25490398)
PLoS Genet. 2017 Jun 22;13(6):e1006771. (PMID: 28640831)
Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):2485-90. (PMID: 25583482)
Plant Cell. 2021 May 31;33(4):1135-1150. (PMID: 33793816)
Heredity (Edinb). 2009 Jul;103(1):54-61. (PMID: 19384343)
Genetics. 2008 Nov;180(3):1617-26. (PMID: 18791229)
Mol Cell. 2009 Aug 28;35(4):414-25. (PMID: 19716787)
Mol Biol Evol. 2008 Nov;25(11):2251-4. (PMID: 18728073)
Mol Biol Evol. 2021 Jun 25;38(7):3022-3027. (PMID: 33892491)
Proc Biol Sci. 2017 Jul 26;284(1859):. (PMID: 28747472)
Science. 2010 Feb 5;327(5966):693-6. (PMID: 20133573)
Gene. 1993 Dec 8;134(2):245-9. (PMID: 7916723)
Annu Rev Genet. 1999;33:261-311. (PMID: 10690410)
PLoS One. 2013 Oct 11;8(10):e78230. (PMID: 24147124)
Evolution. 1999 Feb;53(1):100-110. (PMID: 28565177)
PLoS Genet. 2013 Apr;9(4):e1003410. (PMID: 23593017)
Mol Biol Evol. 1990 Sep;7(5):444-58. (PMID: 2263195)
Proc Natl Acad Sci U S A. 2019 Jul 30;116(31):15602-15609. (PMID: 31320584)
Am J Hum Genet. 1999 Jan;64(1):24-30. (PMID: 9915939)
Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17829-34. (PMID: 19822756)
Proc Biol Sci. 2012 May 22;279(1735):1873-82. (PMID: 22298849)
Mol Biol Evol. 2001 Dec;18(12):2201-12. (PMID: 11719570)
Mol Cell Biol. 2006 Dec;26(23):8781-90. (PMID: 17000772)
Genetics. 2007 Jan;175(1):311-20. (PMID: 17110499)
Bioinformatics. 2010 Mar 15;26(6):841-2. (PMID: 20110278)
Aquat Toxicol. 2020 Sep;226:105556. (PMID: 32652413)
Evolution. 1998 Dec;52(6):1648-1670. (PMID: 28565305)
Genetics. 1984 Oct;108(2):501-21. (PMID: 6500260)

RGPIN-2017-03807 Libyan Ministry of Higher Education and Scientific Research

Keywords: Daphnia pulex; concerted evolution; copy number variation; intragenomic rDNA polymorphism; polymorphic nucleotide sites; ribosomal RNA gene

0 (DNA, Ribosomal)

Date Created: 20240521 Date Completed: 20240708 Latest Revision: 20240710

20240710

PMC11228840

10.1093/g3journal/jkae105

38771699