Transcriptome sequencing of two phenotypic mosaic Eucalyptus trees reveals large scale transcriptome re-modelling

Abstract

Phenotypic mosaic trees offer an ideal system for studying differential gene expression. We have investigated two mosaic eucalypt trees from two closely related species (Eucalyptus melliodora and E. sideroxylon), which each support two types of leaves: one part of the canopy is resistant to insect herbivory and the remaining leaves are susceptible. Driving this ecological distinction are differences in plant secondary metabolites. We used these phenotypic mosaics to investigate genome wide patterns of foliar gene expression with the aim of identifying patterns of differential gene expression and the somatic mutation(s) that lead to this phenotypic mosaicism. We sequenced the mRNA pool from leaves of the resistant and susceptible ecotypes from both mosaic eucalypts using the Illumina HiSeq 2000 platform. We found large differences in pathway regulation and gene expression between the ecotypes of each mosaic. The expression of the genes in the MVA and MEP pathways is reflected by variation in leaf chemistry, however this is not the case for the terpene synthases. Apart from the terpene biosynthetic pathway, there are several other metabolic pathways that are differentially regulated between the two ecotypes, suggesting there is much more phenotypic diversity than has been described. Despite the close relationship between the two species, they show large differences in the global patterns of gene and pathway regulation.

Fig 1. A schematic of the E. melliodora (left) and the E. sideroxylon (right) mosaic trees.

The white areas in the canopy represent the leaves resistant to herbivory and the grey areas represent leaves that are susceptible to herbivory (graphic by Erin Walsh 2012).

Fig 2. Pathway analysis of genes expressed in the E. melliodora mosaic.

Blue squares indicate transcripts with higher levels of abundance in the leaves of the susceptible branch and red squares indicate transcripts more abundant in the leaves of the resistant branch. The intensity of the colour indicates the level of differential abundance of a transcript.

Fig 3. Pathway analysis of genes expressed in the E. sideroxylon mosaic.

Blue squares indicate transcripts with higher levels of abundant in the leaves of the susceptible branch and red squares indicate transcripts more abundant in the leaves of the resistant branch. THE intensity of the colour indicates the level of differential abundance of a transcript.