Codon usage and codon pair patterns in non-grass monocot genomes

Mazumdar, Purabi; Othman, RofinaYasmin Binti; Mebus, Katharina; Ramakrishnan, N.; Harikrishna, Jennifer Ann

doi:10.1093/aob/mcx112

Cited by 63 publications

(53 citation statements)

References 107 publications

(151 reference statements)

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“…In addition, we also noticed that GC-rich trinucleotide motifs (CCG/CGG, AGG/CCT, AAG/CTT, AGC/CTG, ACG/CGT, and ACC/GGT > 67%) were more abundant than AT-rich trinucleotide (AAC/GTT, AAG/CTT, AAT/ATT, ACT/AGT, ATC/ATG < 33%). The fact that high GC content and consequent codon usage bias can be considered specific features of monocot genomes is strongly supported by these results 44,70 .…”

Section: Discussionmentioning

confidence: 55%

De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing

Taheri

Abdullah

Rafii

et al. 2019

Sci Rep

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Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C . alismatifolia cvs, ‘Chiang Mai Pink’ and ‘UB Snow 701’, to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C . alismatifolia cultivars, one hybrid, three Curcuma , and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma .

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Section: Discussionmentioning

confidence: 55%

De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing

Taheri

Abdullah

Rafii

et al. 2019

Sci Rep

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show abstract

“…Hence, knowledge of the codon usage and codon-pair context patterns of plants and underlying evolutionary forces will be useful to understand the molecular mechanism of environmental adaptation and biological diversity of each species [43]. In addition, this information can be applied for codon optimizations of diverse sets of genes to be used in plant transformation programs.…”

Section: Introductionmentioning

confidence: 99%

Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study

et al. 2020

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We studied the correlation of synonymous codon usage (SCU) on gene expression levels under drought stress in rice. Sixty genes related to drought stress (with high, intermediate and low expression) were selected from rice meta-analysis data and various codon usage indices such as the effective number of codon usage (ENC), codon adaptation index (CAI) and relative synonymous codon usage (RSCU) were calculated. We found that in genes highly expressing under drought 1) GC content was higher, 2) ENC value was lower, 3) the preferred codons of some amino acids changed and 4) the RSCU ratio of GC-end codons relative to AT-end codons for 18 amino acids increased significantly compared with those in other genes. We introduce ARSCU as the Average ratio of RSCUs of GC-end codons to AT-end codons in each gene that could significantly separate high-expression genes under drought from low-expression genes. ARSCU is calculated using the program ARSCU-Calculator developed by our group to help predicting expression level of rice genes under drought. An index above ARSCU threshold is expected to indicate that the gene under study may belong to the "high expression group under drought". This information may be applied for codon optimization of genes for rice genetic engineering. To validate these findings, we further used 60 other genes (randomly selected subset of 43233 genes studied for their response to drought stress). ARSCU value was able to predict the level of expression at 88.33% of the cases. Using third set of 60 genes selected amongst high expressing genes not related to drought, only 31.65% of the genes showed ARSCU value of higher than the set threshold. This indicates that the phenomenon we described in this report may be unique for drought related genes. To justify the observed correlation between CUB and high expressing genes under drought, possible role of tRNA post transcriptional modification and tRFs was hypothesized as possible underlying biological mechanism.

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“…The gBGC hypothesis was proposed based on the observation of the rapid increment of local GC content over genomic hotspots of recombination (Clément and Arndt 2013) and whole genome GC content over the high recombination rates of some species (Figuet et al 2014;Weber et al 2014). The gBGC hypothesis was successfully explained the codon usage patterns of some non-grass monocot species, including Musa acuminata, Musa balbisiana, Phoenix dactylifera, and Spirodela polyrhiza (Mazumdar et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Analysis of codon usage bias reveals optimal codons in Elaeis guineensis

Aditama¹,

Tanjung²,

Sudania³

et al. 2020

Biodiversitas

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Abstract. Aditama R, Tanjung ZA, Sudania WM, Nugroho YA, Utomo C, Liwang T. 2020. Analysis of codon usage bias reveals optimal codons in Elaeis guineensis. Biodiversitas 21: 5331-5337. Codon usage bias of oil palm genome was reported employing several indices, including GC content, relative synonymous codon usage (RSCU), the effective number of codons (ENC), and codon adaptation index (CAI). Unimodal distribution of GC content was observed and matched with non-grass monocots characteristics. Correspondence analysis (COA) on synonymous codon usage bias showed that the main axis was strongly driven by GC content. The ENC and neutrality plot of oil palm genes indicating that natural selection played more vital role compared to mutational bias on shaping codon usage bias. A positive correlation between calculated CAI and experimental data of oil palm gene expression was detected indicating good ability of this index. Finally, eighteen codons were defined as “optimal codons” that may provide a useful reference for heterogeneous expression and genome editing studies.

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Codon usage and codon pair patterns in non-grass monocot genomes

Abstract: Optimal codons in these non-grass monocots show a preference for G/C in the third codon position. These results support the concept that codon usage and nucleotide composition in non-grass monocots are mainly driven by gBGC.

Cited by 63 publications

References 107 publications

De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing

De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing

Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study

Analysis of codon usage bias reveals optimal codons in Elaeis guineensis

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