Nonconcerted evolution of histone 3 genes in a liverwort, Conocephalum conicum

Abstract

To estimate the extent of genetic variation at the DNA level, the histone 3 (H3) genes were sequenced from single individual each from the three cryptic species recognized based on allozyme analyses, YFS, J and T types of Conocephalum conicum and two closely related species, C. japonicum and Marchantia polymorpha . Although the H3 genes are known to be highly conserved, the nucleotide diversities were 0.128, 0.109, 0.108, 0.049 and 0.034. These values are 30 to 100 times higher than that in Drosophila melanogaster (0.001). Besides, there were considerable differences in the position, length and number of introns among the loci of H3 genes. The observed high level of nucleotide diversities was explained by the fixation of many random mutations, and non-concerted evolution that resulted from low rates of unequal crossing-over and gene conversion probably due to the dispersed structure of H3 genes on genome in this species. The non-concerted evolutionary pattern was established by the analysis of phylogenetic tree and divergence rates. This study confirmed previous results suggesting that natural populations of liverwort maintains high extent of variation at DNA level.

Evolution of histone H3: emergence of variants and conservation of post-translational modification sites1This article is part of Special Issue entitled Asilomar Chromatin and has undergone the Journal’s usual peer review process.

“…Excluded from analysis were known and suspected centromeric histone H3 sequences (Baker and Rogers 2006;Dalal et al 2007;Talbert et al 2004), pseudo genes, tissue-specific H3 variants such as histone H3t, found in human testes (Tachiwana et al 2008), and sequence records with high apparent error rates that precluded identification of established histone H3 features (Luger et al 1997). Histone sequences, deposited as plant histones (Kim and Yamazaki 2004) but obviously arising from fungal or insect contaminants, were identified ( Fig. S2A) 2 and excluded from TOL analyses.…”