Identifier | Total | Download | Reference(s) | Last Updated | |||||||||||||||||
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Pisifera5 (P5) Genome Build | p5_sc***** (e.g. p5_sc00001) |
40,360 | p5_scaffolds.na.gz 329.78M |
Malaysian Oil Palm Genome Programme Sequences V2.0Introduction The oil palm genomes were assembled using Newbler. The pisifera genome (P5-build) was assembled from 154.8 million reads from genomic and BAC pool DNA fragment and paired-end linker libraries. This represents ~30-fold raw sequence coverage of the genome. In addition, ~235,000 BAC end reads generated using Sanger sequencing were also included in the P5-build.
Description Genome Data Usage Policy Please cite the following publication: Rajinder Singh, Meilina Ong-Abdullah, Eng-Ti L Low, Mohamad Arif Abdul Manaf, Rozana Rosli, Rajanaidu Nookiah, Leslie C-L Ooi, Siew-Eng Ooi, Kuang-Lim Chan, Mohd Amin Halim, Norazah Azizi, Jayanthi Nagappan, Blaire Bacher, Nathan Lakey, Steven W Smith, Dong He, Michael Hogan, Muhammad A Budiman, Ernest K Lee, Rob DeSalle, David Kudrna, Jose L Goicoechea, Rod Wing, Richard K Wilson, Robert S Fulton, Jared M Ordway, Robert A Martienssen and Ravigadevi Sambanthamurthi (2013) Oil palm genome sequence reveals divergence of interfertile species in Old and New Worlds. Nature 500, 335–339 (15 August 2013)
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July 7, 2018 | ||||||||||||||||
E. guineensis (EG5.1) Genome Build | Eg_Chr** (e.g. Eg_Chr1) |
16 chromosomes | EG5.1_linked.na.gz 329.50M |
Malaysian Oil Palm Genome Programme Sequences V2.0Introduction The oil palm genomes were assembled using Newbler. The pisifera genome (P5-build) was assembled from 154.8 million reads from genomic and BAC pool DNA fragment and paired-end linker libraries. This represents ~30-fold raw sequence coverage of the genome. In addition, ~235,000 BAC end reads generated using Sanger sequencing were also included in the P5-build.
Description Genome Data Usage Policy Please cite the following publication: Rajinder Singh, Meilina Ong-Abdullah, Eng-Ti L Low, Mohamad Arif Abdul Manaf, Rozana Rosli, Rajanaidu Nookiah, Leslie C-L Ooi, Siew-Eng Ooi, Kuang-Lim Chan, Mohd Amin Halim, Norazah Azizi, Jayanthi Nagappan, Blaire Bacher, Nathan Lakey, Steven W Smith, Dong He, Michael Hogan, Muhammad A Budiman, Ernest K Lee, Rob DeSalle, David Kudrna, Jose L Goicoechea, Rod Wing, Richard K Wilson, Robert S Fulton, Jared M Ordway, Robert A Martienssen and Ravigadevi Sambanthamurthi (2013) Oil palm genome sequence reveals divergence of interfertile species in Old and New Worlds. Nature 500, 335–339 (15 August 2013)
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July 7, 2018 | ||||||||||||||||
E. guineensis (AM_EG5.1) Genome Build | 16 chromosomes | AM_EG5.1.na.gz 193.50M AM_EG5.1.agp 49.0K |
Malaysian Oil Palm Genome Programme Sequences V2.0Introduction The chromosomal-level assembly of the African oil palm has been improved by integrating multiple genetic maps and maximizing the collinearity between the input maps and order of the genomic scaffolds. About 828 Mb (~54%) of the African oil palm genome has been successfully incorporated into 16 pseudo-chromosomes.
Description Genome Data Usage Policy The genome data was temporarily made available for manuscript evaluation purposes. |
October 6, 2021 | |||||||||||||||||
Representative Gene Models | p5.00_sc*****_p**** (e.g. p5.00_sc00001_p00001) |
26,059 | EG5.1_Genes.V3.gff3.gz 5.87M EG5.1_Genes.V3.na.gz 10M EG5.1_Genes.V3.aa.gz 6.4M |
Malaysian Oil Palm Genome Programme Sequences V2.0Introduction This file contains oil palm predicted genes Version 3 on EG build version 5.1. The framework is a combination of the Seqping pipeline developed by MPOB, and the Fgenesh++ pipeline by Softberry. A set of 26,059 oil palm genes has been identified.
Genome Data Usage Policy Please cite the following publication: CHAN, K L; TATARINOVA, T V; ROSLI, R; AMIRUDDIN, N; AZIZI, N; AB HALIM, M A; NIK MOHD SANUSI, N S; JAYANTHI, N; PONOMARENKO, P; TRISKA, M; SOLOVYEV, V; FIRDAUS-RAIH, M; SAMBANTHAMURTHI,R; MURPHY, D and LESLIE, E T L (2017). Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct, 12:21.
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July 7, 2018 | ||||||||||||||||
Fgenesh++ Predicted Genes | 27,915 | fgenesh.supported.gff3.gz 4.6M |
Malaysian Oil Palm Genome Programme Sequences V2.0Genome Data Usage Policy Please cite the following publication: CHAN, K L; TATARINOVA, T V; ROSLI, R; AMIRUDDIN, N; AZIZI, N; AB HALIM, M A; NIK MOHD SANUSI, N S; JAYANTHI, N; PONOMARENKO, P; TRISKA, M; SOLOVYEV, V; FIRDAUS-RAIH, M; SAMBANTHAMURTHI,R; MURPHY, D and LESLIE, E T L (2017). Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct, 12:21.
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July 7, 2018 | |||||||||||||||||
Seqping Predicted Genes | 17,680 | maker.supported.gff3.gz 4.6M |
Malaysian Oil Palm Genome Programme Sequences V2.0Genome Data Usage Policy Please cite the following publication: CHAN, K L; TATARINOVA, T V; ROSLI, R; AMIRUDDIN, N; AZIZI, N; AB HALIM, M A; NIK MOHD SANUSI, N S; JAYANTHI, N; PONOMARENKO, P; TRISKA, M; SOLOVYEV, V; FIRDAUS-RAIH, M; SAMBANTHAMURTHI,R; MURPHY, D and LESLIE, E T L (2017). Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct, 12:21.
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July 7, 2018 | |||||||||||||||||
Intronless Genes | EgIG_* (e.g. EgIG_1) |
3,539 |
Malaysian Oil Palm Genome Programme Sequences V2.0Genome Data Usage Policy Please cite the following publication: CHAN, K L; TATARINOVA, T V; ROSLI, R; AMIRUDDIN, N; AZIZI, N; AB HALIM, M A; NIK MOHD SANUSI, N S; JAYANTHI, N; PONOMARENKO, P; TRISKA, M; SOLOVYEV, V; FIRDAUS-RAIH, M; SAMBANTHAMURTHI,R; MURPHY, D and LESLIE, E T L (2017). Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct, 12:21.
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March 12, 2019 | |||||||||||||||||
Fatty Acid Biosynthesis (FAB) Genes | Eg*****_* (e.g. EgACC_1) |
42 |
Malaysian Oil Palm Genome Programme Sequences V2.0Genome Data Usage Policy Please cite the following publication: CHAN, K L; TATARINOVA, T V; ROSLI, R; AMIRUDDIN, N; AZIZI, N; AB HALIM, M A; NIK MOHD SANUSI, N S; JAYANTHI, N; PONOMARENKO, P; TRISKA, M; SOLOVYEV, V; FIRDAUS-RAIH, M; SAMBANTHAMURTHI,R; MURPHY, D and LESLIE, E T L (2017). Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct, 12:21.
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July 7, 2018 | |||||||||||||||||
Resistance (R) Genes | Eg_rgh_***_* (e.g. Eg_rgh_cnl_1) |
210 |
Malaysian Oil Palm Genome Programme Sequences V2.0Genome Data Usage Policy Please cite the following publication: CHAN, K L; TATARINOVA, T V; ROSLI, R; AMIRUDDIN, N; AZIZI, N; AB HALIM, M A; NIK MOHD SANUSI, N S; JAYANTHI, N; PONOMARENKO, P; TRISKA, M; SOLOVYEV, V; FIRDAUS-RAIH, M; SAMBANTHAMURTHI,R; MURPHY, D and LESLIE, E T L (2017). Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct, 12:21.
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July 7, 2018 | |||||||||||||||||
ACBP Genes | EgACBP* (e.g. EgACBP1) |
7 |
Malaysian Oil Palm Genome Programme Sequences V2.0Genome Data Usage Policy N/A |
December 25, 2018 | |||||||||||||||||
Shell Gene | SHELL |
1 | n/a |
Malaysian Oil Palm Genome Programme Sequences V2.0Genome Data Usage Policy Please cite the following publication: Singh, R., Low, E-T.L., Ooi, L.C-L., Ong-Abdullah, M., Ting, N.C., Nagappan, J., Nookiah, R., Amiruddin, M.D., Rosli, R., Manaf, M.A.A. et al. (2013) The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. Nature, 500, 340–344.
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July 7, 2018 | ||||||||||||||||
Virescens Gene | VIRESCENS |
1 | n/a |
Malaysian Oil Palm Genome Programme Sequences V2.0Genome Data Usage Policy Please cite the following publication: Singh, R., Low, E-T.L., Ooi, L.C-L., Ong-Abdullah, M., Nookiah, R., Ting, N.C., Marjuni, M., Chan, P-L., Ithnin, M., Manaf, M.A.A. et al. (2014) The oil palm VIRESCENS gene controls fruit colour and encodes a R2R3-MYB. Nat. Commun., 5, 4106.
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July 7, 2018 | ||||||||||||||||
Mantled Gene | EgDEF1 |
1 | n/a |
Malaysian Oil Palm Genome Programme Sequences V2.0Genome Data Usage Policy Please cite the following publication: Ong-Abdullah, M., Ordway, J.M., Jiang, N., Ooi, S.E., Kok, S-Y., Sarpan, N., Azimi, N., Hashim, A.T., Ishak, Z., Rosli, S.K. et al. (2015) Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature, 525, 533–537.
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July 7, 2018 |
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