Identification of genes related to the phenotypic variations of a synthesized Paulownia (Paulownia tomentosa × Paulownia fortunei) autotetraploid

• We perform the de novo assembly of a transcriptome on P. tomentosa × P. fortunei.
• We have discovered various expressed genes involved in the pathways attributing to the organ enlargement of autotetraploid.
• The degrading enzymes for polysaccharides may cause the leaf enlargement in autotetraploid.
• Over expressed genes related to circadian rhythm may induce the growth rate in autotetraploid.
• Up-regulated genes involved in lignin biosynthesis may cause the organ size enlargement in autotetraploid.

Paulownia is a fast-growing deciduous tree native to China. It has great economic importance for the pulp and paper industries, as well as ecological prominence in forest ecosystems. Paulownia is of much interest to plant breeder keen to explore new plant varieties by selecting on the basis of phenotype. A newly synthesized autotetraploid Paulownia exhibited advanced characteristics, such as greater yield, and higher resistance than the diploid tree. However, tissue-specific transcriptome and genomic data in public databases are not sufficient to understand the molecular mechanisms associated with genome duplication. To evaluate the effects of genome duplication on the phenotypic variations in Paulownia tomentosa × Paulownia fortunei, the transcriptomes of the autotetraploid and diploid Paulownia were compared. Using Illumina sequencing technology, a total of 82,934 All-unigenes with a mean length of 1109 bp were assembled. The data revealed numerous differences in gene expression between the two transcriptomes, including 718 up-regulated and 667 down-regulated differentially expressed genes between the two Paulownia trees. An analysis of the pathway and gene annotations revealed that genes involved in nucleotide sugar metabolism in plant cell walls were down-regulated, and genes involved in the light signal pathway and the biosynthesis of structural polymers were up-regulated in autotetraploid Paulownia. The differentially expressed genes may contribute to the observed phenotypic variations between diploid and autotetraploid Paulownia. These results provide a significant resource for understanding the variations in Paulownia polyploidization and will benefit future breeding work.