Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera

<em>Juniperus flaccida</em> (drooping juniper) and <em>Pinus cembroides</em> (pinyon pine) are conifers native to North America, spanning Mexico and the Southwestern region of the United States. Although from two different lineages, both species exhibit heteroblastic growth. Morphologically, their leaves undergo a change between the juvenile and adult life stage. <em>J. flaccida</em> leaves appear needle-like at youth and scale-like at maturity, whereas the <em>P. cembroides</em> will transition from needle-like leaves to brown scale-like leaves. The objective was to perform a comparative transcriptomic analysis to quantify and examine differential expression in juvenile and adult individuals from both species. RNA from twelve samples was sequenced on HiSeq 1500 (100bp PE) and analyzed with available software. Because there are no reference genomes for these species, they were assembled<em> de novo </em>from the RNA-Seq reads. Following assembly, the coding regions were identified and redundant transcripts were removed. Quality filtered reads were aligned to the reference transcriptomes (one for each species), counts were generated from the alignment files, and differential expression analysis was performed with DESeq2 via Kallisto. Up and down-regulated genes (padj&lt;0.1) across both age classes (juvenile vs adult) were observed in each species and compared.