Abstract
BackgroundWood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution.ResultsThe xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution.ConclusionsConifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.
Highlights
IntroductionWood formation is an important developmental process in vascular plants which played a crucial role in plant evolution
Wood is a valuable natural resource and a major carbon sink
The xylem transcriptome is highly conserved in conifer species We compared the xylem transcriptomes among different conifer species, and analysed the homologs between conifer xylem transcriptomes and the xylem transcriptomes or genomes of angiosperms, lycophytes and moss (Additional file 1A-D and Figure 1A-B)
Summary
Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. Herbaceous vascular plants develop primary xylem, and woody plants produce secondary xylem (or wood). Genes involved in wood formation have been identified in many plant species [8,9,10,11,12,13], allowing investigation of xylem evolution at the transcriptome level. The expanding genomic resources of model plant species [15,16,17,18] are invaluable for exploring many aspects of plant development and evolution, including xylem formation and evolution. Recent studies suggest whole-genome duplication and reorganization [15,16,17] have been a major driving force in plant evolution
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