Genome Size Evolution in Pufferfish: a Comparative Analysis of Diodontid and Tetraodontid Pufferfish Genomes

Overview

Journal Genome Res

Specialty Genetics

Date 2003 May 3

PMID 12727902

Citations 28

Authors

Daniel E Neafsey

Stephen R Palumbi

Affiliations

Soon will be listed here.

Abstract

Smooth pufferfish of the family Tetraodontidae have the smallest vertebrate genomes yet measured. They have a haploid genome size of approximately 400 million bp (Mb), which is almost eight times smaller than the human genome. Given that spiny pufferfish from the sister family Diodontidae and a fish from the outgroup Molidae have genomes twice as large as smooth puffers, it appears that the genome size of smooth puffers has contracted in the last 50-70 million years since their divergence from the spiny puffers. Here we use renaturation kinetics to compare the repetitive nature of the smooth and spiny puffer genomes. We also estimate the rates of small (<400 bp) insertions and deletions in smooth and spiny puffers using defunct non-LTR retrotransposons. We find a significantly greater abundance of a transposon-like repetitive DNA class in spiny puffers relative to smooth puffers, in addition to nearly identical indel rates. We comment on the role that large insertions may play in the evolution of genome size in these two groups.

Citing Articles

High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes of .

Wang B, Saleh A, Yang N, Asare E, Chen H, Wang Q Animals (Basel). 2024; 14(10).

PMID: 38791643 PMC: 11117352. DOI: 10.3390/ani14101425.

The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history.

Eaton K, Krabbenhoft T, Backenstose N, Bernal M G3 (Bethesda). 2024; 14(7).

PMID: 38739549 PMC: 11228864. DOI: 10.1093/g3journal/jkae096.

Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure.

Villarreal F, Burguener G, Sosa E, Stocchi N, Somoza G, Turjanski A BMC Genomics. 2024; 25(1):297.

PMID: 38509481 PMC: 10956332. DOI: 10.1186/s12864-024-10081-z.

Transposon Mining in the Small Genomes of Animals.

Guo M, Addy G, Yang N, Asare E, Wu H, Saleh A Biology (Basel). 2024; 13(1).

PMID: 38248455 PMC: 10813416. DOI: 10.3390/biology13010024.

Comparative genomics reveals insights into anuran genome size evolution.

Zuo B, Micah Nneji L, Sun Y BMC Genomics. 2023; 24(1):379.

PMID: 37415107 PMC: 10324214. DOI: 10.1186/s12864-023-09499-8.

References

Robertson H . The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses. Genome Res. 2000; 10(2):192-203. DOI: 10.1101/gr.10.2.192. View

Petrov D, Lozovskaya E, Hartl D . High intrinsic rate of DNA loss in Drosophila. Nature. 1996; 384(6607):346-9. DOI: 10.1038/384346a0. View

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

Thompson J, Gibson T, Plewniak F, Jeanmougin F, Higgins D . The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1998; 25(24):4876-82. PMC: 147148. DOI: 10.1093/nar/25.24.4876. View

Petrov D, Hartl D . Trash DNA is what gets thrown away: high rate of DNA loss in Drosophila. Gene. 1998; 205(1-2):279-89. DOI: 10.1016/s0378-1119(97)00516-7. View

SantaLucia Jr J . A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A. 1998; 95(4):1460-5. PMC: 19045. DOI: 10.1073/pnas.95.4.1460. View

Vinogradov A . Genome size and GC-percent in vertebrates as determined by flow cytometry: the triangular relationship. Cytometry. 1998; 31(2):100-9. DOI: 10.1002/(sici)1097-0320(19980201)31:2<100::aid-cyto5>3.0.co;2-q. View

Petrov D, Hartl D . High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Mol Biol Evol. 1998; 15(3):293-302. DOI: 10.1093/oxfordjournals.molbev.a025926. View

Poulter R, Butler M, Ormandy J . A LINE element from the pufferfish (fugu) Fugu rubripes which shows similarity to the CR1 family of non-LTR retrotransposons. Gene. 1999; 227(2):169-79. DOI: 10.1016/s0378-1119(98)00600-3. View

10.

Elgar G, Clark M, Meek S, Smith S, Warner S, Edwards Y . Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res. 1999; 9(10):960-71. PMC: 310822. DOI: 10.1101/gr.9.10.960. View

11.

Petrov D, Sangster T, Johnston J, Hartl D, Shaw K . Evidence for DNA loss as a determinant of genome size. Science. 2000; 287(5455):1060-2. DOI: 10.1126/science.287.5455.1060. View

12.

Crollius H, Jaillon O, Dasilva C, Ozouf-Costaz C, Fizames C, Fischer C . Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. Genome Res. 2000; 10(7):939-49. PMC: 310905. DOI: 10.1101/gr.10.7.939. View

13.

Bensasson D, Petrov D, Zhang D, Hartl D, Hewitt G . Genomic gigantism: DNA loss is slow in mountain grasshoppers. Mol Biol Evol. 2001; 18(2):246-53. DOI: 10.1093/oxfordjournals.molbev.a003798. View

14.

Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J . Initial sequencing and analysis of the human genome. Nature. 2001; 409(6822):860-921. DOI: 10.1038/35057062. View

15.

Gregory T . Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev Camb Philos Soc. 2001; 76(1):65-101. DOI: 10.1017/s1464793100005595. View

16.

Brainerd E, Slutz S, Hall E, Phillis R . Patterns of genome size evolution in tetraodontiform fishes. Evolution. 2002; 55(11):2363-8. DOI: 10.1111/j.0014-3820.2001.tb00750.x. View

17.

Petrov D . Mutational equilibrium model of genome size evolution. Theor Popul Biol. 2002; 61(4):531-44. DOI: 10.1006/tpbi.2002.1605. View

18.

Aparicio S, Chapman J, Stupka E, Putnam N, Chia J, Dehal P . Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002; 297(5585):1301-10. DOI: 10.1126/science.1072104. View

19.

Dasilva C, Hadji H, Ozouf-Costaz C, Nicaud S, Jaillon O, Weissenbach J . Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome. Proc Natl Acad Sci U S A. 2002; 99(21):13636-41. PMC: 129727. DOI: 10.1073/pnas.202284199. View

20.

Blumenstiel J, Hartl D, Lozovsky E . Patterns of insertion and deletion in contrasting chromatin domains. Mol Biol Evol. 2002; 19(12):2211-25. DOI: 10.1093/oxfordjournals.molbev.a004045. View