Gene Conversion in Angiosperm Genomes with an Emphasis on Genes Duplicated by Polyploidization

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2014 Apr 9

PMID 24710136

Citations 19

Authors

Xi-Yin Wang

Andrew H Paterson

Affiliations

Soon will be listed here.

Abstract

Angiosperm genomes differ from those of mammals by extensive and recursive polyploidizations. The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution. Though most genes may escape conversion by their homologs, concerted evolution of duplicated genes can last for millions of years or longer after their origin. Indeed, paralogous genes on two rice chromosomes duplicated an estimated 60-70 million years ago have experienced gene conversion in the past 400,000 years. Gene conversion preserves similarity of paralogous genes, but appears to accelerate their divergence from orthologous genes in other species. The mutagenic nature of recombination coupled with the buffering effect provided by gene redundancy, may facilitate the evolution of novel alleles that confer functional innovations while insulating biological fitness of affected plants. A mixed evolutionary model, characterized by a primary birth-and-death process and occasional homoeologous recombination and gene conversion, may best explain the evolution of multigene families.

Citing Articles

Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow.

Wang J, Zhang L, Wang J, Hao Y, Xiao Q, Teng J BMC Plant Biol. 2022; 22(1):298.

PMID: 35710333 PMC: 9205023. DOI: 10.1186/s12870-022-03684-9.

Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus .

Shen S, Li Y, Wang J, Wei C, Wang Z, Ge W Genes (Basel). 2021; 12(12).

PMID: 34946893 PMC: 8701993. DOI: 10.3390/genes12121944.

Genome-Wide Identification and Gene Expression Analysis of Acyl-Activating Enzymes Superfamily in Tomato () Under Aluminum Stress.

Jin J, He Q, Li P, Lou H, Chen W, Yang J Front Plant Sci. 2021; 12:754147.

PMID: 34925406 PMC: 8674732. DOI: 10.3389/fpls.2021.754147.

Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence.

Wei C, Wang Z, Wang J, Teng J, Shen S, Xiao Q BMC Genomics. 2021; 22(1):460.

PMID: 34147070 PMC: 8214281. DOI: 10.1186/s12864-021-07776-y.

Comprehensive characterization of the and families on and gene co-expression network analysis of its members during aluminium toxicity and phosphate starvation stresses.

Cardoso T, Pinto R, Paiva L 3 Biotech. 2020; 10(12):525.

PMID: 33214973 PMC: 7658292. DOI: 10.1007/s13205-020-02528-3.

References

Ohta T . Population genetics theory of concerted evolution and its application to the immunoglobulin V gene tree. J Mol Evol. 1984; 20(3-4):274-80. DOI: 10.1007/BF02104733. View

Nei M, Rogozin I, Piontkivska H . Purifying selection and birth-and-death evolution in the ubiquitin gene family. Proc Natl Acad Sci U S A. 2000; 97(20):10866-71. PMC: 27115. DOI: 10.1073/pnas.97.20.10866. View

Chapman B, Bowers J, Feltus F, Paterson A . Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc Natl Acad Sci U S A. 2006; 103(8):2730-5. PMC: 1413778. DOI: 10.1073/pnas.0507782103. View

Carels N, Bernardi G . Two classes of genes in plants. Genetics. 2000; 154(4):1819-25. PMC: 1461008. DOI: 10.1093/genetics/154.4.1819. View

James S, OKelly M, Carter D, Davey R, van Oudenaarden A, Roberts I . Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Res. 2009; 19(4):626-35. PMC: 2665781. DOI: 10.1101/gr.084517.108. View

Sun Q, Collins N, Ayliffe M, Smith S, Drake J, Pryor T . Recombination between paralogues at the Rp1 rust resistance locus in maize. Genetics. 2001; 158(1):423-38. PMC: 1461629. DOI: 10.1093/genetics/158.1.423. View

Innan H . A method for estimating the mutation, gene conversion and recombination parameters in small multigene families. Genetics. 2002; 161(2):865-72. PMC: 1462133. DOI: 10.1093/genetics/161.2.865. View

Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A . The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007; 449(7161):463-7. DOI: 10.1038/nature06148. View

Zhang L, Vision T, Gaut B . Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol Biol Evol. 2002; 19(9):1464-73. DOI: 10.1093/oxfordjournals.molbev.a004209. View

10.

Nicolas S, Le Mignon G, Eber F, Coriton O, Monod H, Clouet V . Homeologous recombination plays a major role in chromosome rearrangements that occur during meiosis of Brassica napus haploids. Genetics. 2006; 175(2):487-503. PMC: 1800630. DOI: 10.1534/genetics.106.062968. View

11.

Kadyk L, Hartwell L . Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae. Genetics. 1992; 132(2):387-402. PMC: 1205144. DOI: 10.1093/genetics/132.2.387. View

12.

Bagnall R, Ayres K, Green P, Giannelli F . Gene conversion and evolution of Xq28 duplicons involved in recurring inversions causing severe hemophilia A. Genome Res. 2005; 15(2):214-23. PMC: 546521. DOI: 10.1101/gr.2946205. View

13.

Stambuk S, Radman M . Mechanism and control of interspecies recombination in Escherichia coli. I. Mismatch repair, methylation, recombination and replication functions. Genetics. 1998; 150(2):533-42. PMC: 1460348. DOI: 10.1093/genetics/150.2.533. View

14.

Carvalho A . The advantages of recombination. Nat Genet. 2003; 34(2):128-9. DOI: 10.1038/ng0603-128. View

15.

Griffiths S, Sharp R, Foote T, Bertin I, Wanous M, Reader S . Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature. 2006; 439(7077):749-52. DOI: 10.1038/nature04434. View

16.

Paterson A, Bowers J, Chapman B, Peterson D, Rong J, Wicker T . Comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity. Curr Opin Biotechnol. 2004; 15(2):120-5. DOI: 10.1016/j.copbio.2004.03.001. View

17.

Jenczewski E, Eber F, Grimaud A, Huet S, Lucas M, Monod H . PrBn, a major gene controlling homeologous pairing in oilseed rape (Brassica napus) haploids. Genetics. 2003; 164(2):645-53. PMC: 1462591. DOI: 10.1093/genetics/164.2.645. View

18.

Nicolas S, Leflon M, Monod H, Eber F, Coriton O, Huteau V . Genetic regulation of meiotic cross-overs between related genomes in Brassica napus haploids and hybrids. Plant Cell. 2009; 21(2):373-85. PMC: 2660629. DOI: 10.1105/tpc.108.062273. View

19.

Datta A, Hendrix M, Lipsitch M . Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast. Proc Natl Acad Sci U S A. 1997; 94(18):9757-62. PMC: 23263. DOI: 10.1073/pnas.94.18.9757. View

20.

Tang H, Bowers J, Wang X, Paterson A . Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A. 2009; 107(1):472-7. PMC: 2806719. DOI: 10.1073/pnas.0908007107. View