Limits...
CenH3 evolution in diploids and polyploids of three angiosperm genera.

Masonbrink RE, Gallagher JP, Jareczek JJ, Renny-Byfield S, Grover CE, Gong L, Wendel JF - BMC Plant Biol. (2014)

Bottom Line: Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification.Since the N terminus is subject to diversifying selection but the DNA binding domains do not appear to be, rapidly evolving centromere sequences are unlikely to be the primary driver of CenH3 sequence diversification.At present, the functional explanation for the diversity generated by both conventional protein evolution in the N terminal domain, as well as alternative splicing, remains unexplained.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification. The centromere specific histone, CenH3, evolves rapidly in many species, perhaps as a coevolutionary response to rapidly evolving centromeric DNA. To gain insight into CenH3 evolution, we characterized patterns of nucleotide and protein diversity among diploids and allopolyploids within three diverse angiosperm genera, Brassica, Oryza, and Gossypium (cotton), with a focus on evidence for diversifying selection in the various domains of the CenH3 gene. In addition, we compare expression profiles and alternative splicing patterns for CenH3 in representatives of each genus.

Results: All three genera retain both duplicated CenH3 copies, while Brassica and Gossypium exhibit pronounced homoeologous expression level bias. Comparisons among genera reveal shared and unique aspects of CenH3 evolution, variable levels of diversifying selection in different CenH3 domains, and that alternative splicing contributes significantly to CenH3 diversity.

Conclusions: Since the N terminus is subject to diversifying selection but the DNA binding domains do not appear to be, rapidly evolving centromere sequences are unlikely to be the primary driver of CenH3 sequence diversification. At present, the functional explanation for the diversity generated by both conventional protein evolution in the N terminal domain, as well as alternative splicing, remains unexplained.

Show MeSH
Episodic diversifying selection inBrassicaandOryza, as inferred using MEME. Each phylogeny represents a single codon exhibiting diversifying selection in the specified genus. The scale bar represents distance and EBF is the empirical Bayes factor, which signifies diversifying selection with warm colors and stabilizing selection with cool colors. Particular branches are labeled with numbers, which correspond to the Ka:Ks of a single codon on the right of each phylogeny.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4308911&req=5

Fig3: Episodic diversifying selection inBrassicaandOryza, as inferred using MEME. Each phylogeny represents a single codon exhibiting diversifying selection in the specified genus. The scale bar represents distance and EBF is the empirical Bayes factor, which signifies diversifying selection with warm colors and stabilizing selection with cool colors. Particular branches are labeled with numbers, which correspond to the Ka:Ks of a single codon on the right of each phylogeny.

Mentions: 3D structures of CenH3 proteins from a single species in each genus. a. Brassica napus (AC8). b. Oryza australiensis isolate (EE). c. Gossypium raimondii (D5). The secondary protein structures are depicted below each 3D model containing nonsynonymous SNPs within each genus mapped to the secondary structure of the CenH3 protein. The different shades of blue signify the borders of each protein domain; α signifies an alpha helix and L signifies a loop. Black rectangles signify nonsynonymous SNPs, while yellow rectangles signify nonsynonymous SNPs under positive selection (Figure 3). The N terminus was the primary site of length variation among the three genera and the long black rectangle in the N terminus of the Brassica CenH3 signifies gaps in the alignment among Brassica species.


CenH3 evolution in diploids and polyploids of three angiosperm genera.

Masonbrink RE, Gallagher JP, Jareczek JJ, Renny-Byfield S, Grover CE, Gong L, Wendel JF - BMC Plant Biol. (2014)

Episodic diversifying selection inBrassicaandOryza, as inferred using MEME. Each phylogeny represents a single codon exhibiting diversifying selection in the specified genus. The scale bar represents distance and EBF is the empirical Bayes factor, which signifies diversifying selection with warm colors and stabilizing selection with cool colors. Particular branches are labeled with numbers, which correspond to the Ka:Ks of a single codon on the right of each phylogeny.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4308911&req=5

Fig3: Episodic diversifying selection inBrassicaandOryza, as inferred using MEME. Each phylogeny represents a single codon exhibiting diversifying selection in the specified genus. The scale bar represents distance and EBF is the empirical Bayes factor, which signifies diversifying selection with warm colors and stabilizing selection with cool colors. Particular branches are labeled with numbers, which correspond to the Ka:Ks of a single codon on the right of each phylogeny.
Mentions: 3D structures of CenH3 proteins from a single species in each genus. a. Brassica napus (AC8). b. Oryza australiensis isolate (EE). c. Gossypium raimondii (D5). The secondary protein structures are depicted below each 3D model containing nonsynonymous SNPs within each genus mapped to the secondary structure of the CenH3 protein. The different shades of blue signify the borders of each protein domain; α signifies an alpha helix and L signifies a loop. Black rectangles signify nonsynonymous SNPs, while yellow rectangles signify nonsynonymous SNPs under positive selection (Figure 3). The N terminus was the primary site of length variation among the three genera and the long black rectangle in the N terminus of the Brassica CenH3 signifies gaps in the alignment among Brassica species.

Bottom Line: Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification.Since the N terminus is subject to diversifying selection but the DNA binding domains do not appear to be, rapidly evolving centromere sequences are unlikely to be the primary driver of CenH3 sequence diversification.At present, the functional explanation for the diversity generated by both conventional protein evolution in the N terminal domain, as well as alternative splicing, remains unexplained.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification. The centromere specific histone, CenH3, evolves rapidly in many species, perhaps as a coevolutionary response to rapidly evolving centromeric DNA. To gain insight into CenH3 evolution, we characterized patterns of nucleotide and protein diversity among diploids and allopolyploids within three diverse angiosperm genera, Brassica, Oryza, and Gossypium (cotton), with a focus on evidence for diversifying selection in the various domains of the CenH3 gene. In addition, we compare expression profiles and alternative splicing patterns for CenH3 in representatives of each genus.

Results: All three genera retain both duplicated CenH3 copies, while Brassica and Gossypium exhibit pronounced homoeologous expression level bias. Comparisons among genera reveal shared and unique aspects of CenH3 evolution, variable levels of diversifying selection in different CenH3 domains, and that alternative splicing contributes significantly to CenH3 diversity.

Conclusions: Since the N terminus is subject to diversifying selection but the DNA binding domains do not appear to be, rapidly evolving centromere sequences are unlikely to be the primary driver of CenH3 sequence diversification. At present, the functional explanation for the diversity generated by both conventional protein evolution in the N terminal domain, as well as alternative splicing, remains unexplained.

Show MeSH