Transcriptome Analysis of Yellow Horn (<i>Xanthoceras sorbifolia</i> Bunge): A Potential Oil-Rich Seed Tree for Biodiesel in China

<div><p>Background</p><p>Yellow horn (<i>Xanthoceras sorbifolia</i> Bunge) is an oil-rich seed shrub that grows well in cold, barren environments and has great potential for biodiesel production in China. However, the limited genetic data means that little information about the key genes involved in oil biosynthesis is available, which limits further improvement of this species. In this study, we describe sequencing and <i>de novo</i> transcriptome assembly to produce the first comprehensive and integrated genomic resource for yellow horn and identify the pathways and key genes related to oil accumulation. In addition, potential molecular markers were identified and compiled.</p><p>Methodology/Principal Findings</p><p>Total RNA was isolated from 30 plants from two regions, including buds, leaves, flowers and seeds. Equal quantities of RNA from these tissues were pooled to construct a cDNA library for 454 pyrosequencing. A total of 1,147,624 high-quality reads with total and average lengths of 530.6 Mb and 462 bp, respectively, were generated. These reads were assembled into 51,867 unigenes, corresponding to a total of 36.1 Mb with a mean length, N50 and median of 696, 928 and 570 bp, respectively. Of the unigenes, 17,541 (33.82%) were unmatched in any public protein databases. We identified 281 unigenes that may be involved in <i>de novo</i> fatty acid (FA) and triacylglycerol (TAG) biosynthesis and metabolism. Furthermore, 6,707 SSRs, 16,925 SNPs and 6,201 InDels with high-confidence were also identified in this study.</p><p>Conclusions</p><p>This transcriptome represents a new functional genomics resource and a foundation for further studies on the metabolic engineering of yellow horn to increase oil content and modify oil composition. The potential molecular markers identified in this study provide a basis for polymorphism analysis of Xanthoceras, and even Sapindaceae; they will also accelerate the process of breeding new varieties with better agronomic characteristics.</p></div

Enzymes/protein related to FA biosynthesis and metabolism identified by annotation of the yellow horn unigenes.

<p>Enzymes/protein related to FA biosynthesis and metabolism identified by annotation of the yellow horn unigenes.</p

Clusters of orthologous groups (COG) classifications of yellow horn unigenes.

<p>Clusters of orthologous groups (COG) classifications of yellow horn unigenes.</p

Functional annotation of yellow horn unigenes in public protein databases.

<p>Functional annotation of yellow horn unigenes in public protein databases.</p

Distribution of putative single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) in the yellow horn transcriptome.

<p>Distribution of putative single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) in the yellow horn transcriptome.</p

Overview of de novo fatty acid (FA) and triacylglycerol(TAG) biosynthesis pathways.

<p>Indentified enzymes include: ACCase, α-acetyl-CoA carboxylase carboxyl transferase (EC:6.4.1.2); MAT, Malonyl-CoA-ACP transacylase (EC:2.3.1.39); KAS, 3-Ketoacyl ACP synthase (KASII, EC: 2.3.1.179; KAS III, EC: 2.3.1.180); KAR, 3-Ketoacyl ACP reductase (EC:1.1.1.100); HAD, 3R-hydroxymyristoyl ACP dehydrase (EC:4.2.1.-); EAR, enoyl-ACP reductase I (EC:1.3.1.9); FATA/B, fatty acyl-ACP thioesterase A/B (EC:3.1.2.14 3.1.2.-); AAD, acyl-ACP desaturase (EC:1.14.19.2); PCH, palmitoyl-CoA hydrolase (EC:3.1.2.2); ACSL, long-chain acyl-CoA synthetase (EC:6.2.1.3); FAD2/6, Δ12(ω6)-Desaturase (EC:1.14.19.-); FAD3/7/8, Δ15(ω3)-Desaturase (EC:1.14.19.-); GK, glycerol kinase (EC:2.7.1.30); ATS1/GPAT, glycerol-3-phosphate acyltransferase (EC:2.3.1.15); LPAT, lysophosphatidyl acyltransferase (EC:2.3.1.51); PP, phosphatidate phosphatase (EC:3.1.3.4); DGAT1, diacylglycerol <i>O</i>-acyltransferase 1 (EC:2.3.1.20); PDAT1, phospholipid: diacylglycerol acyltransferase 1 (EC:2.3.1.158); LPCAT, lysophosphatidylcholine acyltransferase (EC:2.3.1.23 2.3.1.67); PLA2, Phospholipase A2 (EC:3.1.1.4). Lipid substrates are abbreviated: 16∶0, palmitic acid; 18∶0, stearic acid; 18∶1, oleic acid; 18∶2, linoleic acid.</p

Number of floral visitors to 46 <i>Magnolia sprengeri</i> flowers observed during the five floral stages.

<p>Number of floral visitors to 46 <i>Magnolia sprengeri</i> flowers observed during the five floral stages.</p

Gene Ontology (GO) categories assigined to the yellow horn unigenes.

<p>Gene Ontology (GO) categories assigined to the yellow horn unigenes.</p

Unigenes functional annotation results.

<p>(A) Top-hit species distribution for BLASTx matches for yellow horn unigenes using the following order of priority: NR, TrEMBL and Swiss-Prot. (B) E-value distribution of top BLASTx hits for each unigene. (C) Distribution of unigenes in length with BLASTx hits compared with those without hits.</p

Summary of yellow horn 454 sequencing and assembly.

<p>Summary of yellow horn 454 sequencing and assembly.</p