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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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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. |
format | Online Article Text |
id | pubmed-8393687 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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