Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

<div><p>Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, <i>Arabidopsis thaliana</i>. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops.</p></div

A list of gene model sources from six plant species.

<p>A list of gene model sources from six plant species.</p

Venn diagram of orthologous groups in six plant genomes.

<p>Venn diagram generated by ClusterVenn from <a href="http://www.bioinfogenome.net/OrthoVenn/clustervenn.php" target="_blank">http://www.bioinfogenome.net/OrthoVenn/clustervenn.php</a>.</p

Phylogenetic and alignment analysis of selected candidate thioesterase (FAT) genes.

<p>(A) Phylogenetic tree of FATA and FATB sequences. (B) Phylogenetic tree of six putative oil palm acyl-ACP thioesterases that separated into subfamily A (red circle), subfamily B (green square) and subfamily C (blue triangle). A full list of sequences is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194792#pone.0194792.s003" target="_blank">S3 Table</a>. (C) Classification of FATB genes. Classes 1, 2 and 3 are represented by a blue square, pink diamond and brown circle respectively. A full list of sequences is available in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194792#pone.0194792.s003" target="_blank">S3 Table</a>.</p

Phylogenetic and expression analysis of selected candidate R genes.

<p>(A) Heatmap of the six R genes expressed in 22 oil palm transcriptome libraries. (B) Phylogenetic tree between <i>M. acuminata</i> and <i>O. sativaorthologs</i> with eight oil palm R genes constructed using Mega7.</p

Number of genes and clusters identified between five different plant species and oil palm.

<p>Number of genes and clusters identified between five different plant species and oil palm.</p