Recent relaxation of purifying selection on the tandem-repetitive early-stage histone H3 gene in brooding sea stars

AbstractBackgroundTransposable elements (TEs) can be key drivers of evolution, but the mechanisms and scope of how they impact gene and genome function are largely unknown. Previous analyses revealed that TE-mediated gene amplifications can have variable effects on fungal genomes, from inactivation of function to production of multiple active copies. For example, a DNA methyltransferase gene in the wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) was amplified to tens of copies, all of which were inactivated by Repeat-Induced Point mutation (RIP) including the original, resulting in loss of cytosine methylation. In another wheat pathogen, Pyrenophora tritici-repentis, a histone H3 gene was amplified to tens of copies with little evidence of RIP, leading to many potentially active copies. To further test the effects of transposon-aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded Pseudocercospora fijiensis genome was analyzed in greater detail.ResultsThese analyses identified a housekeeping gene, histone H3, which was captured and amplified to hundreds of copies by a hAT DNA transposon, all of which were inactivated by RIP, except for the original. In P. fijiensis the original H3 gene probably was not protected from RIP, but most likely was maintained intact due to strong purifying selection. Comparative analyses revealed that a similar event occurred in five additional genomes representing the fungal genera Cercospora, Pseudocercospora and Sphaerulina.ConclusionsThese results indicate that the interplay of TEs and RIP can result in different and unpredictable fates of amplified genes, with variable effects on gene and genome evolution.

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Difference in larval type explains patterns of nonsynonymous substitutions in two ancient paralogs of the histone H3 gene in sea stars

Evolution & Development ◽

10.1111/j.1525-142x.2010.00406.x ◽

2010 ◽

Vol 12 (2) ◽

pp. 222-230 ◽

Cited By ~ 4

Author(s):

David W. Foltz ◽

Christopher L. Mah

Keyword(s):

Histone H3 ◽

Sea Stars ◽

Nonsynonymous Substitutions ◽

Larval Type ◽

Histone H3 Gene

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Faculty Opinions recommendation of Transformation vector based on promoter and intron sequences of a replacement histone H3 gene. A tool for high, constitutive gene expression in plants.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1004708.51106 ◽

2002 ◽

Author(s):

Steven Spiker

Keyword(s):

Gene Expression ◽

Histone H3 ◽

Transformation Vector ◽

Constitutive Gene Expression ◽

Histone H3 Gene

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Sea urchin early histone H2A modulator binding factor 1 is a positive transcription factor also for the early histone H3 gene.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.90.14.6854 ◽

1993 ◽

Vol 90 (14) ◽

pp. 6854-6858 ◽

Cited By ~ 16

Author(s):

F. Palla ◽

C. Bonura ◽

L. Anello ◽

C. Casano ◽

M. Ciaccio ◽

...

Keyword(s):

Transcription Factor ◽

Sea Urchin ◽

Histone H3 ◽

Histone H2a ◽

Binding Factor ◽

Histone H3 Gene

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Identification of Histone H3 (HH3) Genes in Gossypium hirsutum Revealed Diverse Expression During Ovule Development and Stress Responses

Genes ◽

10.3390/genes10050355 ◽

2019 ◽

Vol 10 (5) ◽

pp. 355

Author(s):

Ghulam Qanmber ◽

Faiza Ali ◽

Lili Lu ◽

Huijuan Mo ◽

Shuya Ma ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Stress Responses ◽

Functional Divergence ◽

Histone H3 ◽

Purifying Selection ◽

Histone Variants ◽

Biological Information ◽

Amino Acid Residues ◽

Sequence Logos ◽

Indole 3 Acetic Acid

Histone acts as the core for nucleosomes and is a key protein component of chromatin. Among different histone variants, histone H3 (HH3) variants have been reported to play vital roles in plant development. However, biological information and evolutionary relationships of HH3 genes in cotton remain to be elucidated. The current study identified 34 HH3 genes in Gossypium hirsutum. Phylogenetic analysis classified HH3 genes of 19 plant species into eight distinct clades. Sequence logos analysis among Arabidopsis, rice, and G. hirsutum amino acid residues showed higher conservation in amino acids. Using collinearity analysis, we identified 81 orthologous/paralogous gene pairs among the four genomes (A, D, At, and Dt) of cotton. Further, orthologous/paralogous and the Ka/Ks ratio demonstrated that cotton HH3 genes experienced strong purifying selection pressure with restricted functional divergence resulting from segmental and whole genome duplication. Expression pattern analysis indicated that GhHH3 genes were preferentially expressed in cotton ovule tissues. Additionally, GhHH3 gene expression can be regulated by abiotic stresses (cold, heat, sodium chloride (NaCl), and polyethylene glycol (PEG)) and phytohormonal (brassinolide (BL), gibberellic acid (GA), indole-3-acetic acid (IAA), salicylic acid (SA), and methyl jasmonate (MeJA)) treatments, suggesting that GhHH3 genes might play roles in abiotic and hormone stress resistance. Taken together, this work provides important information to decipher complete molecular and physiological functions of HH3 genes in cotton.

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