Frequent recombination in <i>Cynoglossus</i> <i>abbreviatus</i> (Pleuronectiformes: Cynoglossidae) ribosomal 18S rDNA

Li Gong; Tingqi Jiang; Bilin Hu; Kaixin Wang; Nannan Zhang; Zengliang Miao

doi:10.1007/s13131-024-2291-1

Volume 43 Issue 8

Aug. 2024

Turn off MathJax

Article Contents

Abstract

References

Supplements

Article Navigation > Acta Oceanologica Sinica > 2024 > 43(8): 98-103

Ruifang Wang, Mengmeng Tong, Shiwen Zhou, Junjie Zheng, Wenguang Zhang, Xinfeng Dai, Douding Lu, Jiarong Hu, Tianze Leng, Qinglin Mu, Zhongyong Yan, Jiangning Zeng, Pengbin Wang. Morphological, phylogenetic and metabolite profile of Prorocentrum clipeus, a newly recorded epiphytic dinoflagellate in the northern Yellow Sea[J]. Acta Oceanologica Sinica, 2024, 43(8): 128-141. doi: 10.1007/s13131-024-2302-2

Citation:

Li Gong, Tingqi Jiang, Bilin Hu, Kaixin Wang, Nannan Zhang, Zengliang Miao. Frequent recombination in Cynoglossus abbreviatus (Pleuronectiformes: Cynoglossidae) ribosomal 18S rDNA[J]. Acta Oceanologica Sinica, 2024, 43(8): 98-103. doi: 10.1007/s13131-024-2291-1

Citation:

PDF( 657 KB)

Frequent recombination in Cynoglossus abbreviatus (Pleuronectiformes: Cynoglossidae) ribosomal 18S rDNA

doi: 10.1007/s13131-024-2291-1

Li Gong^{1, 2},
Tingqi Jiang^{1, 2},
Bilin Hu^{1, 2},
Kaixin Wang^{1, 2},
Nannan Zhang^{1, 2},
Zengliang Miao^{1, 2
,
,}

1.
National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan 316022, China
2.
Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China

Funds: The Basic Scientific Research Operating Expenses of Zhejiang Provincial Universities under contract 2021JZ003; the Zhoushan Science and Technology Bureau under contract No. 2021C21007; the Natural Science Foundation of Zhejiang Province under contract Y21C190023; the National Natural Science Foundation of China under contract 31272273.

More Information

Corresponding author: miaozl@zjou.edu.cn
Received Date: 2023-09-22
Accepted Date: 2023-11-11

Available Online: 2024-04-22

Publish Date: 2024-08-25

Abstract

Abstract

The conventional theory of concerted evolution has been used to explain the lack of sequence variation in ribosomal RNA (rRNA) genes across diverse eukaryotic species. However, recent investigations into rRNA genes in flatfish genome have resulted in controversial findings. This study focuses on 18S rRNA genes of the widely distributed tongue sole, Cynoglossus abbreviatus (Pleuronectiformes: Cynoglossidae), aiming to explore sequence polymorphism. Five distinct 18S rDNA sequence types (Type A, B, R1, R2, and R3) were identified, suggesting a departure from concerted evolution. A combination of general criteria and variations in highly conserved regions were employed to detect pseudogenes. The results pinpointed Type A sequences as potential pseudogenes due to significant sequence variations and deviations in secondary structure within highly conserved regions. Three types (Type R1, R2, and R3) were identified as recombinants between Type A and B sequences, with simple crossing over and gene conversion as the most likely recombination mechanisms. These findings not only contribute to rRNA pseudogene identification but also shed light on the evolutionary dynamics of rRNA genes in teleost genomes.
- ribosomal RNA,
- tongue sole,
- non-concerted evolution,
- pseudogene,
- crossing over,
- gene conversion

FullText(HTML)

References(36)

References

Alaeddini, R. , S. J. Walsh & A. Abbas, 2010. Forensic implications of genetic analyses from degraded DNA—a review. Forensic science international: genetics 4(3): 148–157.

Bailey, C. D. , T. G. Carr, S. A. Harris, et al. , 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Mol Phylogenet Evol 29(3): 435–455.

Edger, P. P. , M. Tang, K. A. Bird, et al., 2014. Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment ofits phylogenetic utility across the Brassicaceae (Mustards). Plos One 9(7), doi: 10.1371/journal.pone.0101341

Gong, L. , H. Luo, W. Shi, et al. , 2019. Intra-individual variation and transcribed pseudogenes in the ribosomal ITS1-5.8S-ITS2 rDNA of Paraplagusia japonica (Pleuronectiformes: Cynoglossidae). Biochem Bioph Res Co 513(3): 726–731, doi: 10.1016/j.bbrc.2019.04.064

Gong, L. , W. Shi, M. Yang, et al. , 2018a. Characterization of 18S-ITS1-5.8S rDNA in eleven species in Soleidae: implications for phylogenetic analysis. Hydrobiologia 819(1): 161–175, doi: 10.1007/s10750-018-3634-8

Gong, L. , W. Shi, M. Yang, et al. , 2018b. Marked intra-genomic variation and pseudogenes in the ITS1-5.8S-ITS2 rDNA of Symphurus plagiusa (Pleuronectiformes: Cynoglossidae). Animal Biology 68(4): 353–365, doi: 10.1163/15707563-17000134

Gong, L. , W. Shi, M. Yang, et al. , 2021. Variations in the conserved 18S and 5.8 S reveal the putative pseudogenes in 18S-ITS1-5.8 S rDNA of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae). Biochem Bioph Res Co 534: 233–239.

Gong, L. , W. Shi, M. Yang, et al. , 2016a. Long duplication of 18S ribosomal DNA in Cynoglossus lineolatus (Pleuronectiformes: Cynoglossidae): novel molecular evidence for unequal crossing over model. Acta Oceanologica Sinica 35(12): 38–50.

Gong, L. , W. Shi, M. Yang, et al. , 2016b. Non-concerted evolution in ribosomal ITS2 sequence in Cynoglossus zanzibarensis (Pleuronectiformes: Cynoglossidae). Biochem Syst Ecol 66: 181–187, doi: 10.1016/j.bse.2016.04.002

Guo, Z. S. , Z. Wang & X. G. Hou, 2021. Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria. FISHES 6(3), doi: 10.3390/fishes6030042

Hall, T. A. , 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41(41): 95–98.

Harpke, D. & A. Peterson, 2008. Extensive 5.8 S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions. J Plant Res 121(3): 261–270.

Hillis, D. M. & M. T. Dixon, 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol 66(4): 411–453.

Kolarik, M. , I. C. Wei, S. Y. Hsieh, et al. , 2021. Nucleotide composition bias of rDNA sequences as a source of phylogenetic artifacts in Basidiomycota-a case of a new lineage of a uredinicolous Ramularia-like anamorph with affinities to Ustilaginomycotina. Mycological Progress 20(12): 1553–1571, doi: 10.1007/s11557-021-01749-x

Kumar, S. , G. Stecher, M. Li, et al. , 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6): 1547–1549, doi: 10.1093/molbev/msy096

Larkin, M. A. , G. Blackshields, N. P. Brown, et al. , 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23(21): 2947–2948, doi: 10.1093/bioinformatics/btm404

Lee, M. O. , S. Bornelov, L. Andersson, et al. , 2016. Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination. P Natl Acad Sci Usa 113(48): 13815–13820, doi: 10.1073/pnas.1616948113

Li, Y. , R. H. Yang, L. Jiang, et al. , 2017. rRNA Pseudogenes in Filamentous Ascomycetes as Revealed by Genome Data. G3-Genes Genom Genet 7(8): 2695–2703, doi: 10.1534/g3.117.044016

Librado, P. & J. Rozas, 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451–1452.

Luo, H. , 2020. Study on Validity in Species of Cynoglossidae and Mechanisms of Gene Rearrangement in Mitogenomes of Bothidae Living in Coastal Waters off China (Teleostei: Pleuronectiformes). University of Chinese Academy of Sciences.

Martin, D. P. , B. Murrell, M. Golden, et al. , 2015. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus evolution 1(1): vev003.

Meng, L. , Y. Gao & L. Gong, 2022. Recombination and incomplete concerted evolution of the ribosomal 18S (partial) -ITS1-5.8S-ITS2-28S (partial) rDNA in Cynoglossus trigrammus genome. Biochem Syst Ecol 105: 104513, doi: 10.1016/j.bse.2022.104513

Mighell, A. , N. Smith, P. Robinson, et al. , 2000. Vertebrate pseudogenes. Febs Lett 468(2): 109–114.

Nagylaki, T. & T. D. Petes, 1982. Intrachromosomal Gene Conversion and the Maintenance of Sequence Homogeneity among Repeated Genes. Genetics 100(2): 315–337.

Navarro, A. , E. Betrán, A. Barbadilla, et al. , 1997. Recombination and Gene Flux Caused by Gene Conversion and Crossing Over in Inversion Heterokaryotypes. Genetics 146(2): 695–709, doi: 10.1093/genetics/146.2.695

Nei, M. , X. Gu & T. Sitnikova, 1997. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. P Natl Acad Sci 94(15): 7799–7806.

Nei, M. & A. P. Rooney, 2005. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39: 121–152, doi: 10.1146/annurev.genet.39.073003.112240

Pääbo, S. , D. M. Irwin & A. C. Wilson, 1990. DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 265(8): 4718-4721.

Prudkovsky, A. , A. Vetrova & S. Kremnyov, 2023. What Does “ITS” Say about Hybridization in Lineages of Sarsia (Corynidae, Hydrozoa) from the White Sea? Diversity 15(5): 675.

Roman, H. , 1985. Gene conversion and crossing-over. Environmental Mutagenesis 7(6): 923–932, doi: 10.1002/em.2860070614

Smith, G. P. , 1974. Unequal crossover and the evolution of multigene families. Cold Spring Harb Sym 38: 507–513.

Smith, G. P. , 1976. Evolution of repeated DNA sequences by unequal crossover. Science 191(4227): 528–535, doi: 10.1126/science.1251186

Stadler, D. R. , 1959. The relationship of gene conversion to crossing over in Neurospora. P Natl Acad Sci 45(11): 1625–1629, doi: 10.1073/pnas.45.11.1625

Wu, Z. W. , Q. M. Wang, X. Z. Liu, et al. , 2016. Intragenomic polymorphism and intergenomic recombination in the ribosomal RNA genes of strains belonging to a yeast species Pichia membranifaciens. Mycology 7(3): 102–111, doi: 10.1080/21501203.2016.1204369

Xu, J. , Q. Zhang & X. Xu, 2009. Intragenomic variability and pseudogenes of ribosomal DNA in Stone flounder Kareius bicoloratus. Mol Phylogenet Evol 52(1): 157–166.

Zuriaga, M. A., S. Mas-Coma & M. D. Bargues. 2015. A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease. Mem I Oswaldo Cruz, 110(3): 353–362

Relative Articles