Comparative transcriptome analysis of early somatic embryo formation and seed development in Brazilian pine, Araucaria angustifolia (Bertol.) Kuntze

Somatic embryogenesis (SE) is a method for producing embryos in vitro and is considered a highly promising approach for micropropagation and germplasm conservation. However, the application of SE for genetic breeding and ex situ conservation of certain species, such as Brazilian pine, faces several technical challenges, including the difficulty of inducing embryogenic cultures using tissues of mature trees, the loss of embryogenic competence of cell cultures and incomplete development of somatic embryos. In order to understand the genetic factors governing embryogenesis, a comparative transcriptome analysis was performed to elucidate differences between distinct cell cultures, early zygotic and somatic embryos and, unorthodox seed developmental stages. A total of 64 GB of sequence derived from high-throughput Illumina RNA-seq profiling was used for de novo transcriptome assembly. The reference transcriptome resulted in 112,772 predicted unigenes with an average length of 825 bp and an N50 of 1,638 bp. Sequence similarity searches using a public protein database revealed 19,947 unigenes that could be annotated with gene descriptions and gene ontology terms. Analysis of differential gene expression allowed pinpointing of genes whose products are predicted to be involved in cell line embryogenic potential, early somatic embryo formation and unorthodox seed development. The results expand our understanding of the complex molecular events that control embryogenesis suggesting that the regeneration impairment of Araucaria angustifolia cultures is consequence of the auxin signaling failure. The generated data lay the foundation for future functional genomic and evolutionary studies that will advance the understanding of conifer biology and unorthodox seed physiology.