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

Abstract

BackgroundOil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools.ResultsUsing two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures.ConclusionsWe present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database (http://palmxplore.mpob.gov.my), will provide important resources for studies on the genomes of oil palm and related crops.ReviewersThis article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-017-0191-4) contains supplementary material, which is available to authorized users.

In silico characterization and expression profiling of the diacylglycerol acyltransferase gene family (DGAT1, DGAT2, DGAT3 and WS/DGAT) from oil palm, Elaeis guineensis

“…A list of curated DGAT genes from Arabidopsis was used as a reference to identify DGAT orthologs from the Orthomcl data (Supplementary S1 file). To search for other E. guineensis DGAT genes especially those which are singletons, a hidden Markov model (HMM) profile was built from orthologous amino acid sequences and used as a query for hmmsearch from the HMMER3 package [60] against our E. guineensis gene models [7]. Sequence similarity searches, using BLASTP program [61] against reference sequence protein database (Viridiplantae), were performed to identify additional DGAT genes in E. guineensis.…”

“…TBlastN was used to identify the DGAT scaffold sequence from our genome assembly data. The Exonerate program (version 2.2.0) [70] with protein2genome model parameters was used to find the number of exons and introns and to predict the location of DGAT gene in our EG5.1 Genome build [7]. Gene structures between the detected orthologs were generated using WebScipio interface version Scipio v1.5 [71,72].…”

“…RNA seq data from endosperm, mesocarp and vegetative tissues were read mapped to the E. guineensis genome P5-build using the Tuxedo suite [74] and linked to our E. guineensis gene model [7]. Sequencing of transcriptome libraries was performed using Roche/454 and Illumina HiSeq 2000 machines.…”

“…While DGAT1 ranged from about 500 -540 amino acids (aa), DGAT2 was much shorter at about 330 aa. Two types of DGAT1 were characterized when we compared the three annotated sequences from the latest E. guineensis gene model [7] with those described in [81]. Using tblastn searches it was found that EgDGAT1_2 [7] is similar to EgDGAT1-1 [81], while EgDGAT1_3 [7] were similar to EgDGAT1-2 [81].…”

“…Further information about palm oil has been reviewed by Sambanthamurthi et al (2000) and Murphy (2014). Two key recent developments in oil palm research have been the publication of the genome sequence in 2013 [6] and the compilation of an updated gene model dataset for the species in 2017 [7].…”