Genome-wide analysis of codon usage in sesame (Sesamum indicum L.)

Andargie, Mebeaselassie; Zhu, Changqing

doi:10.1016/j.heliyon.2021.e08687

Cited by 13 publications

(8 citation statements)

References 86 publications

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“…Plots with slopes close to zero indicate the absence of neutrality, and that selection pressure might be a strong force in shaping codon composition, i.e. selective constraints ( Andargie and Congyi 2022 ; Bahiri-Elitzur and Tuller 2021 ; Muthabathula et al . 2018 ).…”

Section: Resultsmentioning

confidence: 99%

The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss

Benson,

Sheltra,

Huff

2023

G3: Genes, Genomes, Genetics

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To complete its parasitic lifecycle, Salmacisia buchloëana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides; Poaceae). To gain insight into S. buchloëana’s ability to manipulate its host, we sequenced and assembled the 20.1 Mb genome of S. buchloëana into 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests that S. buchloëana is nested within the genus Tilletia and diverged from T. caries and T. walkeri ∼40 million years ago. We find that S. buchloëana contains a novel chromosome arm with no syntenic relationship to other publicly available Tilletia genomes and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role in S. buchloëana’s evolution and host specificity. Salmacisia buchloëana has one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation and that S. buchloëana has a unique bias for the serine codon UCG. Finally, we identify three inteins within the S. buchloëana genome, two of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.

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Section: Resultsmentioning

confidence: 99%

The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss

Benson,

Sheltra,

Huff

2023

G3: Genes, Genomes, Genetics

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“…PR2 analysis revealed that TdEXPs and TtEXPs were greatly influenced by the C frequency in the 3rd codon of amino acids. The codon adaptation index (CAI, 0–1.0) was used to estimate the adaptation of genes to codon usage of highly expressed genes [ 52 , 53 ]. Higher CAI values represent a potentially higher level of expression and potentially greater codon usage bias [ 54 , 55 ].…”

Section: Discussionmentioning

confidence: 99%

Evolution and Expression of the Expansin Genes in Emmer Wheat

Li,

Liu,

Cao

et al. 2023

IJMS

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Expansin proteins, a crucial class of intracellular proteins, are known to play a vital role in facilitating processes like cell wall relaxation and cell growth. Recent discoveries have revealed that expansin proteins also have significant functions in plant growth, development, and response to resistance. However, the expansin gene family, particularly in emmer wheat, has not been thoroughly studied, particularly in terms of evolution. In this study, we identified 63 TdEXPs and 49 TtEXPs from the latest genome versions of wild emmer wheat (WEW) and durum wheat (DW), respectively. The physicochemical properties of the encoded expansin proteins exhibited minimal differences, and the gene structures remained relatively conserved. Phylogenetic analysis categorized the proteins into three subfamilies, namely EXPA, EXPB, and EXLA, in addition to the EXLB subfamily. Furthermore, codon preference analysis revealed an increased usage frequency of the nucleotide “T” in expansin proteins throughout the evolution of WEW and DW. Collinearity analysis demonstrated higher orthology between the expansin proteins of WEW and DW, with a Ka/Ks ratio ranging from 0.4173 to 0.9494, indicating purifying selection during the evolution from WEW to DW. Haplotype analysis of the expansin gene family identified five genes in which certain haplotypes gradually became dominant over the course of evolution, enabling adaptation for survival and improvement. Expression pattern analysis indicated tissue-specific expression of expansin genes in emmer wheat, and some of these genes were quantified through qRT-PCR to assess their response to salt stress. These comprehensive findings present the first systematic analysis of the expansin protein gene family during the evolution from WEW to DW, providing a foundation for further understanding the functions and biological roles of expansin protein genes in emmer wheat.

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“…Researchers have reported mixed results on the effects of gene length on codon bias. This correlation is strongly positive for E. coli genes; strongly negative for D. melanogaster and S. cerevisiae genes ( Moriyama and Powell, 1998 ), Caenorhabditis elegans , and Arabidopsis thaliana ( Duret and Mouchiroud, 1999 ); and weak for sesame ( Andargie and Congyi, 2022 ). Codon bias was significantly positively correlated ( p < 0.001) with gene length in both up-regulated and down-regulated gene sets, indicating that with an increase in length, bias also increased.…”

Section: Discussionmentioning

confidence: 99%

Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities

Khandia

Pandey

Zaki

et al. 2023

Front. Mol. Neurosci.

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IntroductionNeurodegeneration and cancer present in comorbidities with inverse effects due to the expression of genes and pathways acting in opposition. Identifying and studying the genes simultaneously up or downregulated during morbidities helps curb both ailments together.MethodsThis study examines four genes. Three of these (Amyloid Beta Precursor Protein (APP), Cyclin D1 (CCND1), and Cyclin E2 (CCNE2) are upregulated, and one protein phosphatase 2 phosphatase activator (PTPA) is simultaneously downregulated in both disorders. We investigated molecular patterns, codon usage, codon usage bias, nucleotide bias in the third codon position, preferred codons, preferred codon pairs, rare codons, and codon context.ResultsParity analysis revealed that T is preferred over A, and G is preferred over C in the third codon position, suggesting composition plays no role in nucleotide bias in both the upregulated and downregulated gene sets and that mutational forces are stronger in upregulated gene sets than in downregulated ones. Transcript length influenced the overall %A composition and codon bias, and the codon AGG exerted the strongest influence on codon usage in both the upregulated and downregulated gene sets. Codons ending in G/C were preferred for 16 amino acids, and glutamic acid-, aspartic acid-, leucine-, valine-, and phenylalanine-initiated codon pairs were preferred in all genes. Codons CTA (Leu), GTA (Val), CAA (Gln), and CGT (Arg) were underrepresented in all examined genes.DiscussionUsing advanced gene editing tools such as CRISPR/Cas or any other gene augmentation technique, these recoded genes may be introduced into the human body to optimize gene expression levels to augment neurodegeneration and cancer therapeutic regimens simultaneously.

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Genome-wide analysis of codon usage in sesame (Sesamum indicum L.)

Cited by 13 publications

References 86 publications

The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss

The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss

Evolution and Expression of the Expansin Genes in Emmer Wheat

Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities

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