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

Chan Kuang Lim, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy, Leslie Low Eng Ti
doi: https://doi.org/10.1101/111120
Chan Kuang Lim
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
2Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
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Tatiana V. Tatarinova
3Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
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Rozana Rosli
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
4Genomics and Computational Biology research group, University of South Wales, Pontypridd, CF371DL, United Kingdom
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Nadzirah Amiruddin
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
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Norazah Azizi
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
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Mohd Amin Ab Halim
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
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Nik Shazana Nik Mohd Sanusi
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
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Jayanthi Nagappan
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
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Petr Ponomarenko
3Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
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Martin Triska
3Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
4Genomics and Computational Biology research group, University of South Wales, Pontypridd, CF371DL, United Kingdom
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Victor Solovyev
5Softberry Inc., 116 Radio Circle, Suite 400 Mount Kisco, NY 10549, USA.
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Mohd Firdaus-Raih
2Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
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Ravigadevi Sambanthamurthi
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
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Denis Murphy
4Genomics and Computational Biology research group, University of South Wales, Pontypridd, CF371DL, United Kingdom
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Leslie Low Eng Ti
1Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720 Kuala Lumpur, Malaysia
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  • For correspondence: lowengti@mpob.gov.my
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Abstract

The advent of rapid and inexpensive DNA sequencing has led to an explosion of data that must 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 a comparative genomics analysis, database and tools development, and mining of biological data for genes of interest. We annotated 26,087 oil palm genes integrated from two gene-prediction pipelines, Fgenesh++ and Seqping. As case studies, we conducted comprehensive investigations on intronless, resistance and fatty acid biosynthesis genes, and demonstrated that the current gene prediction set is of high quality. 3,672 intronless genes were identified in the oil palm genome, an important resource for evolutionary study. Further scrutiny of the oil palm genes revealed 210 candidate resistance genes involved in pathogen defense. Fatty acids have diverse applications ranging from food to industrial feedstock, and we identified 42 key genes involved in fatty-acid biosynthesis in oil palm mesocarp and kernel. These results provide an important resource for studies on plant genomes and a theoretical foundation for marker-assisted breeding of oil palm and related crops.

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Posted April 05, 2017.
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Evidence-based gene models for structural and functional annotations of the oil palm genome
Chan Kuang Lim, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy, Leslie Low Eng Ti
bioRxiv 111120; doi: https://doi.org/10.1101/111120
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Evidence-based gene models for structural and functional annotations of the oil palm genome
Chan Kuang Lim, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy, Leslie Low Eng Ti
bioRxiv 111120; doi: https://doi.org/10.1101/111120

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