De novo characterization of Larix gmelinii (Rupr.) Rupr. transcriptome and analysis of its gene expression induced by jasmonates

Abstract

Background: Larix gmelinii is a dominant tree species in China's boreal forests and plays an important role in the coniferous ecosystem. It is also one of the most economically important tree species in the Chinese timber industry due to excellent water resistance and anti-corrosion of its wood products. Unfortunately, in Northeast China, L. gmelinii often suffers from serious attacks by diseases and insects. The application of exogenous volatile semiochemicals may induce and enhance its resistance against insect or disease attacks; however, little is known regarding the genes and molecular mechanisms related to induced resistance.

Results: We performed de novo sequencing and assembly of the L. gmelinii transcriptome using a short read sequencing technology (Illumina). Chemical defenses of L. gmelinii seedlings were induced with jasmonic acid (JA) or methyl jasmonate (MeJA) for 6 hours. Transcriptomes were compared between seedlings induced by JA, MeJA and untreated controls using a tag-based digital gene expression profiling system. In a single run, 25,977,782 short reads were produced and 51,157 unigenes were obtained with a mean length of 517 nt. We sequenced 3 digital gene expression libraries and generated between 3.5 and 5.9 million raw tags, and obtained 52,040 reliable reference genes after removing redundancy. The expression of disease/insect-resistance genes (e.g., phenylalanine ammonialyase, coumarate 3-hydroxylase, lipoxygenase, allene oxide synthase and allene oxide cyclase) was up-regulated. The expression profiles of some abundant genes under different elicitor treatment were studied by using real-time qRT-PCR.The results showed that the expression levels of disease/insect-resistance genes in the seedling samples induced by JA and MeJA were higher than those in the control group. The seedlings induced with MeJA elicited the strongest increases in disease/insect-resistance genes.

Conclusions: Both JA and MeJA induced seedlings of L. gmelinii showed significantly increased expression of disease/insect-resistance genes. MeJA seemed to have a stronger induction effect than JA on expression of disease/insect-resistance related genes. This study provides sequence resources for L. gmelinii research and will help us to better understand the functions of disease/insect-resistance genes and the molecular mechanisms of secondary metabolisms in L. gmelinii.

Figure 1

Histogram presentation of gene ontology classification. The results are summarized in three main categories: biological process, cellular component and molecular function. The left y-axis indicates the percentage of genes for each function belonging to a main category of genes in that main category; the right y-axis indicates the correspondent number of genes.

Figure 2

Phenylalanine, tyrosine and tryptophan biosynthesis pathway induced by MeJA treatment. Black borders: Pathway; up-regulated genes are marked with red; down-regulated genes are marked with green.

Figure 3

qRT-PCR validation of DGE tag data. The x-axis indicates treatment method. The y-axis indicates relative expression level. The following selection of genes were tested with their description. (A) phenylalanine ammonialyase (Unigene 46956), (B) cinnamate 4-hydroxylase (Unigene 47342). (C) 4-coumarate-CoA ligase (Unigene 11155), (D)  trans-cinnamate 4-monooxygenase (Unigene 20026), (E) caffeic acid 3-O-methyltransferase (Unigene 15709), (F) caffeoyl-CoA O-methyltransferase (Unigene 16480).