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Gene conversion in angiosperm genomes with an emphasis on genes duplicated by polyploidization.

Wang XY, Paterson AH - Genes (Basel) (2011)

Bottom Line: The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution.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.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. wang.xiyin@gmail.com.

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.

No MeSH data available.


Related in: MedlinePlus

Homology pattern of chromosomes rice chromosomes R11, R12, and their respective sorghum orthologs S5 and S8. Chromosomes are shown with black curved lines, with ovals displaying centromeres. “L” and “S” show long and short arms of the chromosomes. The interior lines show the duplicated genes within genomes and orthologs between genomes. Colors of lines show Ks values (synonymous substitution rates between homologous genes), as illustrated in the right-bottom corner.
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f2-genes-02-00001: Homology pattern of chromosomes rice chromosomes R11, R12, and their respective sorghum orthologs S5 and S8. Chromosomes are shown with black curved lines, with ovals displaying centromeres. “L” and “S” show long and short arms of the chromosomes. The interior lines show the duplicated genes within genomes and orthologs between genomes. Colors of lines show Ks values (synonymous substitution rates between homologous genes), as illustrated in the right-bottom corner.

Mentions: One unusual duplicated genomic region in grasses has been subject to a remarkably high level of concerted gene evolution. Previously, it was suggested that rice chromosomes 11 and 12 share a segmental duplication near the termini of the short arms, dated to only 5–7 mya by various groups [8,26,35]. However, there have been suspicions about the date and origin of the duplicated segments, particularly based on the observation that no homoeologs from the 70-mya whole-genome doubling event could be identified [9]. With the availability of the sorghum genome sequence, a similar duplicated segment also appearing much younger than the 70-mya duplication was found on sorghum chromosomes 5 and 8, orthologous to rice chromosomes 11 and 12 (Figure 2). (Note: Homologous sequences are orthologous if they were separated by a speciation event). It seems prohibitively unlikely that two independent lineages would each experience recent segmental duplications in corresponding regions of one and only one pair of paleo-duplicated chromosomes. Much more probable is our alternative hypothesis that the region was not a pair of segmental duplications, but resulted from the pan-cereal whole-genome duplication and became differentiated from the remainder of the genome due to concerted evolution acting independently in sorghum, rice, and probably additional cereals. This hypothesis is strongly supported by an analysis of intra- and inter-species syntenic genes. While sorghum-sorghum and rice-rice paralogs from this region show Ks values of 0.44 and 0.22, respectively, sorghum-rice orthologs show Ks of 0.63, which seems to preclude the possibility of species-specific duplications but is very consistent with concerted evolution in these regions since the rice-sorghum split. “Parallel concerted evolution” may have also occurred in corresponding regions of other cereals. Indeed, physical and genetic maps suggest shared terminal segments of the corresponding chromosomes in wheat (Triticum aestivum, 4 and 5) [36], foxtail millet (Setaria italica, VII and VIII), and pearl millet (Pennisetum glaucum, linkage groups 1 and 4) [37].


Gene conversion in angiosperm genomes with an emphasis on genes duplicated by polyploidization.

Wang XY, Paterson AH - Genes (Basel) (2011)

Homology pattern of chromosomes rice chromosomes R11, R12, and their respective sorghum orthologs S5 and S8. Chromosomes are shown with black curved lines, with ovals displaying centromeres. “L” and “S” show long and short arms of the chromosomes. The interior lines show the duplicated genes within genomes and orthologs between genomes. Colors of lines show Ks values (synonymous substitution rates between homologous genes), as illustrated in the right-bottom corner.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3924838&req=5

f2-genes-02-00001: Homology pattern of chromosomes rice chromosomes R11, R12, and their respective sorghum orthologs S5 and S8. Chromosomes are shown with black curved lines, with ovals displaying centromeres. “L” and “S” show long and short arms of the chromosomes. The interior lines show the duplicated genes within genomes and orthologs between genomes. Colors of lines show Ks values (synonymous substitution rates between homologous genes), as illustrated in the right-bottom corner.
Mentions: One unusual duplicated genomic region in grasses has been subject to a remarkably high level of concerted gene evolution. Previously, it was suggested that rice chromosomes 11 and 12 share a segmental duplication near the termini of the short arms, dated to only 5–7 mya by various groups [8,26,35]. However, there have been suspicions about the date and origin of the duplicated segments, particularly based on the observation that no homoeologs from the 70-mya whole-genome doubling event could be identified [9]. With the availability of the sorghum genome sequence, a similar duplicated segment also appearing much younger than the 70-mya duplication was found on sorghum chromosomes 5 and 8, orthologous to rice chromosomes 11 and 12 (Figure 2). (Note: Homologous sequences are orthologous if they were separated by a speciation event). It seems prohibitively unlikely that two independent lineages would each experience recent segmental duplications in corresponding regions of one and only one pair of paleo-duplicated chromosomes. Much more probable is our alternative hypothesis that the region was not a pair of segmental duplications, but resulted from the pan-cereal whole-genome duplication and became differentiated from the remainder of the genome due to concerted evolution acting independently in sorghum, rice, and probably additional cereals. This hypothesis is strongly supported by an analysis of intra- and inter-species syntenic genes. While sorghum-sorghum and rice-rice paralogs from this region show Ks values of 0.44 and 0.22, respectively, sorghum-rice orthologs show Ks of 0.63, which seems to preclude the possibility of species-specific duplications but is very consistent with concerted evolution in these regions since the rice-sorghum split. “Parallel concerted evolution” may have also occurred in corresponding regions of other cereals. Indeed, physical and genetic maps suggest shared terminal segments of the corresponding chromosomes in wheat (Triticum aestivum, 4 and 5) [36], foxtail millet (Setaria italica, VII and VIII), and pearl millet (Pennisetum glaucum, linkage groups 1 and 4) [37].

Bottom Line: The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution.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.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. wang.xiyin@gmail.com.

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.

No MeSH data available.


Related in: MedlinePlus