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

Kuang Lim Chan, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Nagappan Jayanthi, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus Mohd Raih, Ravigadevi Sambanthamurthi, Denis Murphy, Eng Ti Leslie Low

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Background: Oil 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. Results: Using 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. Conclusions: We 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. Reviewers: This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov.

Original languageEnglish
Article number21
JournalBiology Direct
Volume12
Issue number1
DOIs
Publication statusPublished - 8 Sep 2017

Fingerprint

Palm oil
Structural Models
Elaeis guineensis
Annotation
Oils
Genome
genome
Genes
Gene
gene
oil
genes
Fatty Acids
Biosynthesis
fatty acid
Disease Resistance
disease resistance
fatty acids
Model
Genomics

Keywords

  • Fatty acids
  • Gene prediction
  • Intronless
  • Oil palm
  • Resistance genes
  • Seqping

ASJC Scopus subject areas

  • Immunology
  • Ecology, Evolution, Behavior and Systematics
  • Modelling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

Cite this

Chan, K. L., Tatarinova, T. V., Rosli, R., Amiruddin, N., Azizi, N., Halim, M. A. A., ... Low, E. T. L. (2017). Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct, 12(1), [21]. https://doi.org/10.1186/s13062-017-0191-4

Evidence-based gene models for structural and functional annotations of the oil palm genome. / Chan, Kuang Lim; Tatarinova, Tatiana V.; Rosli, Rozana; Amiruddin, Nadzirah; Azizi, Norazah; Halim, Mohd Amin Ab; Sanusi, Nik Shazana Nik Mohd; Jayanthi, Nagappan; Ponomarenko, Petr; Triska, Martin; Solovyev, Victor; Mohd Raih, Mohd Firdaus; Sambanthamurthi, Ravigadevi; Murphy, Denis; Low, Eng Ti Leslie.

In: Biology Direct, Vol. 12, No. 1, 21, 08.09.2017.

Research output: Contribution to journalArticle

Chan, KL, Tatarinova, TV, Rosli, R, Amiruddin, N, Azizi, N, Halim, MAA, Sanusi, NSNM, Jayanthi, N, Ponomarenko, P, Triska, M, Solovyev, V, Mohd Raih, MF, Sambanthamurthi, R, Murphy, D & Low, ETL 2017, 'Evidence-based gene models for structural and functional annotations of the oil palm genome', Biology Direct, vol. 12, no. 1, 21. https://doi.org/10.1186/s13062-017-0191-4
Chan KL, Tatarinova TV, Rosli R, Amiruddin N, Azizi N, Halim MAA et al. Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct. 2017 Sep 8;12(1). 21. https://doi.org/10.1186/s13062-017-0191-4
Chan, Kuang Lim ; Tatarinova, Tatiana V. ; Rosli, Rozana ; Amiruddin, Nadzirah ; Azizi, Norazah ; Halim, Mohd Amin Ab ; Sanusi, Nik Shazana Nik Mohd ; Jayanthi, Nagappan ; Ponomarenko, Petr ; Triska, Martin ; Solovyev, Victor ; Mohd Raih, Mohd Firdaus ; Sambanthamurthi, Ravigadevi ; Murphy, Denis ; Low, Eng Ti Leslie. / Evidence-based gene models for structural and functional annotations of the oil palm genome. In: Biology Direct. 2017 ; Vol. 12, No. 1.
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AU - Azizi, Norazah

AU - Halim, Mohd Amin Ab

AU - Sanusi, Nik Shazana Nik Mohd

AU - Jayanthi, Nagappan

AU - Ponomarenko, Petr

AU - Triska, Martin

AU - Solovyev, Victor

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N2 - Background: Oil 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. Results: Using 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. Conclusions: We 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. Reviewers: This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov.

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