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Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to...

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Autores principales: Li, Xin, Wang, Xiaocen, Gong, Pengtao, Zhang, Nan, Zhang, Xichen, Li, Jianhua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8393687/
https://www.ncbi.nlm.nih.gov/pubmed/34440343
http://dx.doi.org/10.3390/genes12081169
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author Li, Xin
Wang, Xiaocen
Gong, Pengtao
Zhang, Nan
Zhang, Xichen
Li, Jianhua
author_facet Li, Xin
Wang, Xiaocen
Gong, Pengtao
Zhang, Nan
Zhang, Xichen
Li, Jianhua
author_sort Li, Xin
collection PubMed
description Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.
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spelling pubmed-83936872021-08-28 Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB Li, Xin Wang, Xiaocen Gong, Pengtao Zhang, Nan Zhang, Xichen Li, Jianhua Genes (Basel) Article Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution. MDPI 2021-07-29 /pmc/articles/PMC8393687/ /pubmed/34440343 http://dx.doi.org/10.3390/genes12081169 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Li, Xin
Wang, Xiaocen
Gong, Pengtao
Zhang, Nan
Zhang, Xichen
Li, Jianhua
Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB
title Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB
title_full Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB
title_fullStr Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB
title_full_unstemmed Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB
title_short Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB
title_sort analysis of codon usage patterns in giardia duodenalis based on transcriptome data from giardiadb
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8393687/
https://www.ncbi.nlm.nih.gov/pubmed/34440343
http://dx.doi.org/10.3390/genes12081169
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