Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants

The 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.Conifers 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.The evolution of xylem was a critical step that allowed vascular plants to colonize vast areas of the earth's terrestrial surface. Xylem plays an essential role in the transport of water and nutrients and provides mechanical support for vascular plants. Herbaceous vascular plants develop primary xylem, and woody plants also produce secondary xylem (or wood). Evolution from tracheids to vessels reflects a more efficient way for angiosperms to develop secondary xylem [1-3]. Primary xylem consists of cellulose, hemicellulose, pectin and proteins, while secondary xylem contains higher amounts