GC3-biased gene domains in mammalian genomes

Shen, Wenlong; Wang, Dong; Ye, Bingyu; Shi, Minglei; Ma, Lei; Zhang, Yan; Zhao, Zhihu

doi:10.1093/bioinformatics/btv329

Cited by 34 publications

(24 citation statements)

References 31 publications

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“…Similar results were also reported for mitochondrial CYB gene , ND1 gene (Uddin, Choudhury, & Chakraborty, 2018), and CHIKV genes (Butt, Nasrullah, & Tong, 2014). In a comparative study of mitogenomes (Shen et al, 2015). Genes with elevated GC3 undergo methylation which, in due course of time, leads to mutation (Tatarinova, Alexandrov, Bouck, & Feldmann, 2010).…”

Section: Discussionsupporting

confidence: 76%

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Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

Barbhuiya

Uddin²,

Chakraborty

2019

J Exp Zool Pt B

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The biological phenomenon where some synonymous codons are repeatedly preferred to others in gene transcripts is called codon usage bias (CUB). The analysis of CUB is not only helpful in evolutionary biology but also in improving the expression level of exogenous genes in the host cell by codon optimization. The overall nucleotide composition analysis demonstrated an unequal distribution of four nucleobases and T% was the highest in all seven species. The genes were AT‐rich, evident from overall low GC content. In addition, third codon position analysis indicated that in four Bombina species namely, Bombina fortinuptialis, Bombina lichuanensis, Bombina maxima, Bombina microdeladigitora, nucleobase A3/T3 was the preferred one, whereas A3/C3 was favored in Bombina bombina, Bombina orientalis, and Bombina variegata. Influence of mutation pressure on codon distribution and codon bias was evident from correlation analysis. Correspondence analysis demonstrated that compositional bias driven by mutation pressure along with natural selection acted on CUB of mitochondrial genes. Neutrality plot revealed that natural selection played a major role whereas mutation pressure had a minor but significant role. Our phylogenetic analyses showed that closely linked species belonging to the same genus were noticeably separated in different clades.

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Section: Discussionsupporting

confidence: 76%

“…Zhang, Liu, Wang, Han, & Zhang, ). The content of guanine and cytosine at the third codon position (GC3) is an indicator of the extent of CUB (Shen et al, ). Genes with elevated GC3 undergo methylation which, in due course of time, leads to mutation (Tatarinova, Alexandrov, Bouck, & Feldmann, ).…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

Barbhuiya

Uddin²,

Chakraborty

2019

J Exp Zool Pt B

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“…Since synonymous codons mostly differ at the third position of codon for encoding the corresponding amino acid, GC composition at the third codon position (GC3) is an excellent parameter for analyzing synonymous CUB . The genes that possess higher GC3 are usually more susceptible to cellular methylation and finally lead to a greater probability of mutation compared with the genes with lower GC3 .…”

Section: Discussionmentioning

confidence: 99%

“…28 Since synonymous codons mostly differ at the third position of codon for encoding the corresponding amino acid, GC composition at the third codon position (GC3) is an excellent parameter for analyzing synonymous CUB. 50 The genes that possess higher GC3 are usually more susceptible to cellular methylation and finally lead to a greater probability of mutation compared with the genes with lower GC3. 51 Duan et al (2015) reported that GC composition at third codon position (GC3) was higher than GC composition at the first codon position (GC1) in fishes and mammals, while lower in amphibians, reptiles, and birds with the exception of Taeniopygia guttata.…”

Section: Discussionmentioning

confidence: 99%

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Uddin¹,

Mazumder

Barbhuiya

et al. 2020

IUBMB Life

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In this study, we used bioinformatic approach to analyze the compositional features and codon usage bias (CUB) of ATP6 and ATP8 genes among three groups, namely, fishes, aves, and mammals which thrive in three different habitats as no work was reported yet. The coding sequences of these genes were retrieved from the National Center for Biotechnology Information to explore the similarities and dissimilarities of codon usage of each gene among these groups. Low values of synonymous codon usage order in fishes, aves, and mammals for ATP6 and ATP8 genes suggested that the CUB of ATP6 and ATP8 genes was low. In ATP6 gene, overall GC contents in fishes, aves and mammals were (mean ± SD) 44.09 ± 3.10, 46.65 ± 1.90, and 39.41 ± 2.89%, respectively, whereas in ATP8 gene, the overall GC contents were 42.76 ± 4.38, 44.16 ± 2.43, and 34.19 ± 3.82% in fishes, aves, and mammals, that is, both genes were found to be AT rich. In ATP6 gene, the codon AGC was overrepresented in fishes but under‐represented in aves and mammals, whereas in ATP8 gene, the codon GCC was overrepresented in fishes but underrepresented in aves and mammals. The pattern of codon usage was different in these genes and varied among groups as evident from correspondence analysis. The slope of the regression line in neutrality plot was lower than 0.5, which revealed that the role of natural selection was higher than mutation pressure in shaping the CUB in ATP6 and ATP8 genes.

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“…Jellyfish have two primary muscle types: the epitheliomuscular cells, which are the predominant muscle cells found in sessile cnidarians; and the striated muscle cells located in the medusa bell that are essential for swimming. To understand the evolution of active-swimming in jellyfish, we examined their codon bias compared to other metazoans by calculating the guanine and cytosine content at the third codon position (GC3) [12, 13] (Additional file 1: Figure S13). It has been suggested that genes with high level of GC3 are more adaptable to external stresses (e.g., environmental changes) [14].…”

Section: Resultsmentioning

confidence: 99%

The jellyfish genome sheds light on the early evolution of active predation

Kim

Lee

et al. 2018

Preprint

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59Background: Unique among cnidarians, jellyfish have remarkable morphological and 60 biochemical innovations that allow them to actively hunt in the water column. One of the first 61 animals to become free-swimming, jellyfish employ pulsed jet propulsion and venomous 62 tentacles to capture prey. 63Results: To understand these key innovations, we sequenced the genome of the giant Nomura's 64 jellyfish (Nemopilema nomurai), the transcriptomes of its bell and tentacles, and transcriptomes 65 across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of 66 Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, 67 marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with 68 expanded Myosin type II family and venom domains; possibly contributing to jellyfish mobility 69 and active predation. We also identified gene family expansions of Wnt and posterior Hox genes, 70 and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, 71 which together may be related to the unique jellyfish body plan (medusa formation).72 Conclusions: Taken together, the jellyfish genome and transcriptomes genetically confirm their 73 unique morphological and physiological traits that have combined to make these animals one of 74 the world's earliest and most successful multi-cellular predators. 75 76 Background 80 Cnidarians, including jellyfish and their predominantly sessile relatives the coral, sea anemone, 81 and hydra, first appeared in the Precambrian Era and are now key members of aquatic 82 ecosystems worldwide [1]. Between 500 and 700 million years ago, jellyfish developed novel 83 physiological traits that allowed them to become one of the first free-swimming predators. The 84 life cycle of the jellyfish includes a small polypoid, sessile stage which reproduces asexually to 85 form the mobile medusa form that can reproduce both sexually and asexually [2]. The class 86 Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a 87 bell and venomous tentacles used for hunting and defense [3]. Jellyfish medusae feature a 88 radially symmetric body structure, powered by readily identifiable cell types such as motor 89neurons and striated muscles that expand and contract to create the most energy-efficient 90 swimming method in the animal kingdom [4, 5]. Over 95% water, jellyfish are osmoconformers 91 that use ion gradients to deliver solutes to cells and tissues where sodium and calcium ions 92 activate the muscle contractions that power their propulsion. Notably, many jellyfish species can 93 survive in habitats with varying levels of salinity and are successful in low-oxygen environments, 94 allowing them to bloom even in dead zones [6]. These innovations have allowed them to 95 colonize aquatic habitats across the globe both in brackish and marine environments, spanning 96 the shallow surface waters to the depths of the seas. 97 98 Results and discussion 99

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GC3-biased gene domains in mammalian genomes

Cited by 34 publications

References 31 publications

Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

The jellyfish genome sheds light on the early evolution of active predation

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