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 V Solovyev; Mohd Firdaus-Raih; Ravigadevi Sambanthamurthi; Denis Murphy; Leslie Low Eng Ti

doi:10.1186/s13062-017-0191-4

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 V Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy, Leslie Low Eng Ti

Faculty of Computing, Engineering and Science

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	English
Article number	21
Journal	Biology Direct
Volume	12:21
DOIs	https://doi.org/10.1186/s13062-017-0191-4
Publication status	Published - 8 Sep 2017

Keywords

oil palm
gene prediction
Seqping
intronless
genes

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Lim, C. K., Tatarinova, T. V., Rosli, R., Amiruddin, N., Azizi, N., Halim, M. A. A., Sanusi, N. S. N. M., Nagappan, J., Ponomarenko, P., Triska, M., Solovyev, V. V., Firdaus-Raih, M., Sambanthamurthi, R., Murphy, D., & Ti, L. L. E. (2017). Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct, 12:21, [21]. https://doi.org/10.1186/s13062-017-0191-4

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title = "Evidence-based gene models for structural and functional annotations of the oil palm genome",

abstract = "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.",

keywords = "oil palm, gene prediction, Seqping, intronless, genes",

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

note = "Availability of data and materials As part of the Malaysian Oil Palm Genome Program (MyOPGP), and to support post-genomics efforts, we developed the palmXplore system (http://palmxplore.mpob.gov.my), a public archive for oil palm (Elaeis guineensis) gene models hosted by MPOB. The collection includes 26,059 representative gene models and annotation information from different annotation methods: Enzyme Code (KEGG), Gene Ontology (Blast2GO) and PFAM. The gene models are downloadable from http://genomsawit.mpob.gov.my. The sequencing data can be accessed at the BioProject of the National Center for Biotechnology Information (NCBI) with accession ID PRJNA345530.",

year = "2017",

month = sep,

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doi = "10.1186/s13062-017-0191-4",

language = "English",

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journal = "Biology Direct",

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Lim, CK, Tatarinova, TV, Rosli, R, Amiruddin, N, Azizi, N, Halim, MAA, Sanusi, NSNM, Nagappan, J, Ponomarenko, P, Triska, M, Solovyev, VV, Firdaus-Raih, M, Sambanthamurthi, R, Murphy, D & Ti, LLE 2017, 'Evidence-based gene models for structural and functional annotations of the oil palm genome', Biology Direct, vol. 12:21, 21. https://doi.org/10.1186/s13062-017-0191-4

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T1 - Evidence-based gene models for structural and functional annotations of the oil palm genome

AU - Lim, Chan Kuang

AU - Tatarinova, Tatiana V.

AU - Rosli, Rozana

AU - Amiruddin, Nadzirah

AU - Azizi, Norazah

AU - Halim, Mohd Amin Ab

AU - Sanusi, Nik Shazana Nik Mohd

AU - Nagappan, Jayanthi

AU - Ponomarenko, Petr

AU - Triska, Martin

AU - Solovyev, Victor V

AU - Firdaus-Raih, Mohd

AU - Sambanthamurthi, Ravigadevi

AU - Murphy, Denis

AU - Ti, Leslie Low Eng

N1 - Availability of data and materials As part of the Malaysian Oil Palm Genome Program (MyOPGP), and to support post-genomics efforts, we developed the palmXplore system (http://palmxplore.mpob.gov.my), a public archive for oil palm (Elaeis guineensis) gene models hosted by MPOB. The collection includes 26,059 representative gene models and annotation information from different annotation methods: Enzyme Code (KEGG), Gene Ontology (Blast2GO) and PFAM. The gene models are downloadable from http://genomsawit.mpob.gov.my. The sequencing data can be accessed at the BioProject of the National Center for Biotechnology Information (NCBI) with accession ID PRJNA345530.

PY - 2017/9/8

Y1 - 2017/9/8

N2 - 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.

AB - 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.

KW - oil palm

KW - gene prediction

KW - Seqping

KW - intronless

KW - genes

U2 - 10.1186/s13062-017-0191-4

DO - 10.1186/s13062-017-0191-4

M3 - Article

C2 - 28886750

VL - 12:21

JO - Biology Direct

JF - Biology Direct

SN - 1745-6150

M1 - 21

ER -

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

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