Evidence-based gene models for structural and functional annotations of the oil palm genome

The advent of rapid and inexpensive DNA sequencing has led to an explosion of data waiting to be transformed into knowledge about genome organization and function. Gene prediction is customarily the starting point for genome analysis. This paper presents a bioinformatics study of the oil palm genome, including comparative genomics analysis, database and tools development, and mining of biological data for genes of interest. We have annotated 26,059 oil palm genes integrated from two independent gene-prediction pipelines, Fgenesh++ and Seqping. This integrated annotation constitutes a significant improvement in comparison to the preliminary annotation published in 2013. We conducted a comprehensive analysis of intronless, resistance and fatty acid biosynthesis genes, and demonstrated that the high quality of the current genome annotation. 3,658 intronless genes were identified in the oil palm genome, an important resource for evolutionary study. Further analysis of the oil palm genes revealed 210 candidate resistance genes involved in pathogen defense. Fatty acids have diverse applications ranging from food to industrial feedstocks, and we identified 42 key genes involved in fatty acid biosynthesis in oil palm. These results provide an important resource for studies of plant genomes and a theoretical foundation for marker-assisted breeding of oil palm and related crops

Characterization of oil palm Acyl-CoA-Binding proteins and correlation of their gene expression with oil synthesis

Acyl-CoA-binding proteins (ACBPs) are involved in binding and trafficking acyl-CoA esters in eukaryotic cells. ACBPs contain a well-conserved acyl-CoA-binding domain (ACBD). Their various functions have been characterized in the model plant Arabidopsis and, to a lesser extent, in rice. In this study, genome-wide detection and expression analysis of ACBPs were performed on Elaeis guineensis (oil palm), the most important oil crop in the world. Seven E. guineensis ACBPs were identified and classified into four groups according to their deduced amino acid domain organization. Phylogenetic analysis showed conservation of this family with other higher plants. All seven EgACBPs were expressed in most tissues while their differential expression suggests various functions in specific tissues. For example, EgACBP3 had high expression in inflorescences and stalks while ACBP1 showed strong expression in leaves. Because of the importance of E. guineensis as an oil crop, expression of EgACBPs was specifically examined during fruit development. EgACBP3 showed high expression throughout mesocarp development, while EgACBP1 had enhanced expression during rapid oil synthesis. In endosperm, both EgACBP1 and EgACBP3 exhibited increased expression during seed development. These results provide important information for further investigations on the biological functions of EgACBPs in various tissues and, in particular, their roles in oil synthesis

Antioxidant and tyrosinase inhibition activities of α- mangostin and Garcinia mangostana Linn. pericarp extracts

The methanol, ethyl acetate and petroleum ether crude extracts of mangosteen pericarp and α- mangostin were evaluated for the antioxidant capacity and tyrosinase inhibition properties. The ferric reducing antioxidant power (FRAP) assay was used to investigate their antioxidant capacity. Tyrosinase inhibition effect was evaluated using mushroom tyrosinase inhibition assay. Methanol extract has higher antioxidant reducing capacity (m= 1.621), compared to the rest of the extracts. Meanwhile, ethyl acetate extract and α- mangostin showed potent tyrosinase inhibition activities as compared to Kojic acid, a well- known tyrosinase inhibitor. It is observed that tyrosinase inhibition effect is antioxidant independent as ethyl acetate extract possessed low antioxidant capacity. This study suggests direct tyrosinase inhibition by ethyl acetate extract of Garcinia mangostana

Analyses of hypomethylated oil palm gene space.

Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm

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

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

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 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