Background Single copy genes are common across angiosperm genomes. single copy

Background Single copy genes are common across angiosperm genomes. single copy genes was partially confirmed by the RNA-seq data, rather than the Codon Adaptation Index (CAI). Unlike in most other species, a strongly negatively correlation occurs between Nc and GC3 among single copy genes in grass genomes. When compared to all non-single copy genes, single copy genes indicate more conservation (as indicated Enzastaurin by and values). But our alternative splicing (AS) results reveal that selective constraints are weaker in single copy genes than in low copy family genes (1C10 in-paralogs) and stronger than high copy family genes (>10 in-paralogs). Using concatenated shared single copy genes, we obtained a well-resolved phylogenetic tree. With the addition of intron sequences, the branch support is improved, but striking incongruences are also evident. Therefore, it is noteworthy that inclusion of intron sequences seems more appropriate for the phylogenetic reconstruction at Sstr3 lower taxonomic levels. Conclusions Our analysis provides insight into the evolutionary characteristics of single copy genes across 29 angiosperm genomes. The results suggest that there are key differences in evolutionary constraints between single copy genes and non-single copy genes. And to some extent, these evolutionary constraints show some species-specific differences, especially between eudicots and monocots. Our preliminary evidence also suggests that the concatenated shared single copy genes are well suited for use in resolving phylogenetic relationships. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-504) contains supplementary material, which is available to authorized users. and and (Oxalidaceae) are used as a phylogenetic marker at lower taxonomic levels [15]. It is therefore important to further evaluate the effects of intron on phylogeny reconstruction when Enzastaurin using single copy genes. In this present study, single copy genes were identified and characterized from the previously sequenced genomes of 29 angiosperms. Codon choice may affect various molecular mechanisms, including protein folding, exon splicing, translational accuracy and efficiency [16C19]. Thus to evaluate codon bias, codon usage indices were measured among the single copy genes. In addition, the selective constraints imposed on single copy genes were also examined. We also assessed the reliability of phylogeny developed from identified single copy genes. Results Identification of single copy genes The percentage of single copy genes identified in 29 angiosperm genomes ranged widely, from approximately 8%-35% (details in Table?1). The lower percentage was for and and and (Additional file 3). However, the opposite was true for and and where higher CAI values occurred among non-single copy genes (Additional file 5). Several studies indicated that there is either a weak or strong negative correlation between gene expression level and GC3 content [23C27]. Our results partially revealed that the GC3 values were significantly lower for single copy genes than for non-single copy genes in the 22 plant species examined (Additional file 3). Alternative splicing (AS) Alternative splicing is a major factor in increasing species diversity and regulatory complexity [28], and has significant effects on the evolution of coding exons [29, 30]. To assess the AS difference between single copy genes and non-single copy genes, AS data sets from different growth and developmental stages, or multiple organs of and were analyzed. Single copy genes had on average, increased levels of AS relative to gene families containing at least 10 in-paralogs. In contrast, those gene families with 1C10 in-paralogs had a higher proportion of AS than did single copy genes (Figure?2). Figure 2 Distribution of alternative splicing (AS) events between single copy genes and other family genes. The vertical axis represents the proportion of genes for which AS is found. The horizontal axis represents the different numbers of AS. The significance … Phylogeny reconstruction using single copy genes Twelve shared single copy genes of 29 angiosperm genomes Enzastaurin were used to evaluate the power of phylogenetic reconstruction. Maximum likelihood phylogenetic trees were reconstructed using individual and concatenated twelve shared single copy genes. When an individual single copy gene was used, relatively high incongruence was observed among the individual single copy genes, except that the grass species possessed consistent topology with high bootstrap values (data not shown). The concatenated twelve shared single copy genes recovered an identical topology with proposed by APG III [31] (Figure?3). Figure 3 Maximum likelihood (ML) phylogenetic tree bases on the 12 shared single copy genes. Numbers above nodes are bootstrap proportions from 1000 pseudoreplicates. and were used as outgroups. The letters embedded … To assess the role of introns in phylogenetic reconstruction, a second set of phylogenetic trees were recovered using single copy genes with the inclusion of introns. Again, high incongruence was observed among the individual single copy genes. Similarly, grass.

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