Analysis of codon usage bias reveals optimal codons in Elaeis guineensis

Abstract. Aditama R, Tanjung ZA, Sudania WM, Nugroho YA, Utomo C, Liwang T. 2020. Analysis of codon usage bias reveals optimal codons in Elaeis guineensis. Biodiversitas 21: 5331-5337. Codon usage bias of oil palm genome was reported employing several indices, including GC content, relative synonymo...

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Autores principales:	Redi Aditama, Zulfikar Achmad Tanjung, Widyartini Made Sudania, Yogo Adhi Nugroho, Condro Utomo, Tony Liwang
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2020
Materias:	elaeis guineensis, gc content, synonymous codons Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/f8cdb9ea6e0b4464b058b474c1007ce0
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spelling	oai:doaj.org-article:f8cdb9ea6e0b4464b058b474c1007ce02021-11-22T00:44:11ZAnalysis of codon usage bias reveals optimal codons in Elaeis guineensis1412-033X2085-472210.13057/biodiv/d211138https://doaj.org/article/f8cdb9ea6e0b4464b058b474c1007ce02020-10-01T00:00:00Zhttps://smujo.id/biodiv/article/view/6600https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Abstract. Aditama R, Tanjung ZA, Sudania WM, Nugroho YA, Utomo C, Liwang T. 2020. Analysis of codon usage bias reveals optimal codons in Elaeis guineensis. Biodiversitas 21: 5331-5337. Codon usage bias of oil palm genome was reported employing several indices, including GC content, relative synonymous codon usage (RSCU), the effective number of codons (ENC), and codon adaptation index (CAI). Unimodal distribution of GC content was observed and matched with non-grass monocots characteristics. Correspondence analysis (COA) on synonymous codon usage bias showed that the main axis was strongly driven by GC content. The ENC and neutrality plot of oil palm genes indicating that natural selection played more vital role compared to mutational bias on shaping codon usage bias. A positive correlation between calculated CAI and experimental data of oil palm gene expression was detected indicating good ability of this index. Finally, eighteen codons were defined as “optimal codons” that may provide a useful reference for heterogeneous expression and genome editing studies.Redi AditamaZulfikar Achmad TanjungWidyartini Made SudaniaYogo Adhi NugrohoCondro UtomoTony LiwangMBI & UNS Soloarticleelaeis guineensis, gc content, synonymous codonsBiology (General)QH301-705.5ENBiodiversitas, Vol 21, Iss 11 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	elaeis guineensis, gc content, synonymous codons Biology (General) QH301-705.5
spellingShingle	elaeis guineensis, gc content, synonymous codons Biology (General) QH301-705.5 Redi Aditama Zulfikar Achmad Tanjung Widyartini Made Sudania Yogo Adhi Nugroho Condro Utomo Tony Liwang Analysis of codon usage bias reveals optimal codons in Elaeis guineensis
description	Abstract. Aditama R, Tanjung ZA, Sudania WM, Nugroho YA, Utomo C, Liwang T. 2020. Analysis of codon usage bias reveals optimal codons in Elaeis guineensis. Biodiversitas 21: 5331-5337. Codon usage bias of oil palm genome was reported employing several indices, including GC content, relative synonymous codon usage (RSCU), the effective number of codons (ENC), and codon adaptation index (CAI). Unimodal distribution of GC content was observed and matched with non-grass monocots characteristics. Correspondence analysis (COA) on synonymous codon usage bias showed that the main axis was strongly driven by GC content. The ENC and neutrality plot of oil palm genes indicating that natural selection played more vital role compared to mutational bias on shaping codon usage bias. A positive correlation between calculated CAI and experimental data of oil palm gene expression was detected indicating good ability of this index. Finally, eighteen codons were defined as “optimal codons” that may provide a useful reference for heterogeneous expression and genome editing studies.
format	article
author	Redi Aditama Zulfikar Achmad Tanjung Widyartini Made Sudania Yogo Adhi Nugroho Condro Utomo Tony Liwang
author_facet	Redi Aditama Zulfikar Achmad Tanjung Widyartini Made Sudania Yogo Adhi Nugroho Condro Utomo Tony Liwang
author_sort	Redi Aditama
title	Analysis of codon usage bias reveals optimal codons in Elaeis guineensis
title_short	Analysis of codon usage bias reveals optimal codons in Elaeis guineensis
title_full	Analysis of codon usage bias reveals optimal codons in Elaeis guineensis
title_fullStr	Analysis of codon usage bias reveals optimal codons in Elaeis guineensis
title_full_unstemmed	Analysis of codon usage bias reveals optimal codons in Elaeis guineensis
title_sort	analysis of codon usage bias reveals optimal codons in elaeis guineensis
publisher	MBI & UNS Solo
publishDate	2020
url	https://doaj.org/article/f8cdb9ea6e0b4464b058b474c1007ce0
work_keys_str_mv	AT rediaditama analysisofcodonusagebiasrevealsoptimalcodonsinelaeisguineensis AT zulfikarachmadtanjung analysisofcodonusagebiasrevealsoptimalcodonsinelaeisguineensis AT widyartinimadesudania analysisofcodonusagebiasrevealsoptimalcodonsinelaeisguineensis AT yogoadhinugroho analysisofcodonusagebiasrevealsoptimalcodonsinelaeisguineensis AT condroutomo analysisofcodonusagebiasrevealsoptimalcodonsinelaeisguineensis AT tonyliwang analysisofcodonusagebiasrevealsoptimalcodonsinelaeisguineensis
_version_	1718418498395308032

Analysis of codon usage bias reveals optimal codons in Elaeis guineensis

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