Deciphering Codon Usage Patterns in Genome of <i>Cucumis sativus</i> in Comparison with Nine Species of Cucurbitaceae

Cucumber is the most important vegetable crop in the Cucurbitaceae family. Condon usage bias (CUB) is a valuable character of species evolution. However, there is little research on the CUB of cucumber. Thus, this study analyzes the codon usage patterns of cucumber and its relatives within Cucurbita...

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Autores principales:	Yuan Niu, Yanyan Luo, Chunlei Wang, Weibiao Liao
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>Cucumis</i> Cucurbitaceae the synonymous codon usage patterns codon usage bias RSCU optimal codon Agriculture S
Acceso en línea:	https://doaj.org/article/bee29810f1b04b70a5165fde90354fee
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spelling	oai:doaj.org-article:bee29810f1b04b70a5165fde90354fee2021-11-25T16:10:27ZDeciphering Codon Usage Patterns in Genome of <i>Cucumis sativus</i> in Comparison with Nine Species of Cucurbitaceae10.3390/agronomy111122892073-4395https://doaj.org/article/bee29810f1b04b70a5165fde90354fee2021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4395/11/11/2289https://doaj.org/toc/2073-4395Cucumber is the most important vegetable crop in the Cucurbitaceae family. Condon usage bias (CUB) is a valuable character of species evolution. However, there is little research on the CUB of cucumber. Thus, this study analyzes the codon usage patterns of cucumber and its relatives within Cucurbitaceae on the genomic level. The analysis of fundamental indicators of codon characteristics shows that it was slightly GC poor, and there was weak codon usage bias in cucumber. We conduct the analysis of neutrality plot, ENC plot, P2 index, and COA indicates that the nucleotide composition, mutation pressure, and translational selection might play roles in CUB in cucumber and its relatives. Among these factors, nucleotide composition might play the most critical role. Based on these analyses, 30 optimal codons were identified in cucumber, most of them ending with U or A. Meanwhile, based on the RSCU values of species, a cluster tree was constructed, in which the situation of cucumber is consistent with the current taxonomic and evolutionary studies in Cucurbitaceae. This study systematically compared the CUB patterns and shaping factors of cucumber and its relatives, laying a foundation for future research on genetic engineering and evolutionary mechanisms in Cucurbitaceae.Yuan NiuYanyan LuoChunlei WangWeibiao LiaoMDPI AGarticle<i>Cucumis</i>Cucurbitaceaethe synonymous codon usage patternscodon usage biasRSCUoptimal codonAgricultureSENAgronomy, Vol 11, Iss 2289, p 2289 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>Cucumis</i> Cucurbitaceae the synonymous codon usage patterns codon usage bias RSCU optimal codon Agriculture S
spellingShingle	<i>Cucumis</i> Cucurbitaceae the synonymous codon usage patterns codon usage bias RSCU optimal codon Agriculture S Yuan Niu Yanyan Luo Chunlei Wang Weibiao Liao Deciphering Codon Usage Patterns in Genome of <i>Cucumis sativus</i> in Comparison with Nine Species of Cucurbitaceae
description	Cucumber is the most important vegetable crop in the Cucurbitaceae family. Condon usage bias (CUB) is a valuable character of species evolution. However, there is little research on the CUB of cucumber. Thus, this study analyzes the codon usage patterns of cucumber and its relatives within Cucurbitaceae on the genomic level. The analysis of fundamental indicators of codon characteristics shows that it was slightly GC poor, and there was weak codon usage bias in cucumber. We conduct the analysis of neutrality plot, ENC plot, P2 index, and COA indicates that the nucleotide composition, mutation pressure, and translational selection might play roles in CUB in cucumber and its relatives. Among these factors, nucleotide composition might play the most critical role. Based on these analyses, 30 optimal codons were identified in cucumber, most of them ending with U or A. Meanwhile, based on the RSCU values of species, a cluster tree was constructed, in which the situation of cucumber is consistent with the current taxonomic and evolutionary studies in Cucurbitaceae. This study systematically compared the CUB patterns and shaping factors of cucumber and its relatives, laying a foundation for future research on genetic engineering and evolutionary mechanisms in Cucurbitaceae.
format	article
author	Yuan Niu Yanyan Luo Chunlei Wang Weibiao Liao
author_facet	Yuan Niu Yanyan Luo Chunlei Wang Weibiao Liao
author_sort	Yuan Niu
title	Deciphering Codon Usage Patterns in Genome of <i>Cucumis sativus</i> in Comparison with Nine Species of Cucurbitaceae
title_short	Deciphering Codon Usage Patterns in Genome of <i>Cucumis sativus</i> in Comparison with Nine Species of Cucurbitaceae
title_full	Deciphering Codon Usage Patterns in Genome of <i>Cucumis sativus</i> in Comparison with Nine Species of Cucurbitaceae
title_fullStr	Deciphering Codon Usage Patterns in Genome of <i>Cucumis sativus</i> in Comparison with Nine Species of Cucurbitaceae
title_full_unstemmed	Deciphering Codon Usage Patterns in Genome of <i>Cucumis sativus</i> in Comparison with Nine Species of Cucurbitaceae
title_sort	deciphering codon usage patterns in genome of <i>cucumis sativus</i> in comparison with nine species of cucurbitaceae
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/bee29810f1b04b70a5165fde90354fee
work_keys_str_mv	AT yuanniu decipheringcodonusagepatternsingenomeoficucumissativusiincomparisonwithninespeciesofcucurbitaceae AT yanyanluo decipheringcodonusagepatternsingenomeoficucumissativusiincomparisonwithninespeciesofcucurbitaceae AT chunleiwang decipheringcodonusagepatternsingenomeoficucumissativusiincomparisonwithninespeciesofcucurbitaceae AT weibiaoliao decipheringcodonusagepatternsingenomeoficucumissativusiincomparisonwithninespeciesofcucurbitaceae
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Deciphering Codon Usage Patterns in Genome of <i>Cucumis sativus</i> in Comparison with Nine Species of Cucurbitaceae

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