Analysis of codon usage in the mitochondrion genome of Spirodela polyrhiza

Huang, Mingxing; Zhong, Yuxin; Ma, Xiaoyu; Hu, Qinxia; Fu, Minghui; Han, Yuping

doi:10.1016/j.aquabot.2019.03.002

Cited by 3 publications

(2 citation statements)

References 46 publications

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“…The number of genes in each group was 10% of the total number of genes in the dataset. The codon bias of the total codon usage from both sets of genes was estimated using ENC and the set of genes with the lower ENC (more highly biased) was putatively identified as the more highly expressed (Huang et al 2019). Significance was assessed by a two way chi-squared contingency test with the criterion of 0.01.…”

Section: Determination Of Optimal Codonsmentioning

confidence: 99%

Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes

Chen

Zhao

Qiao

et al. 2020

Mitochondrial DNA Part B

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Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly correlated with codon usage. In general, both mitochondrial genomes favor codons that end in A or U, with a secondary preference for pyrimidine rich codons. These observations are similar to previous reports of codon usage in cotton nuclear genomes, possibly suggestive of a general bias spanning genomic compartment. Although evidence for codon usage bias is weak for most genes, we identified six genes (i.e. atp8, atp9, sdh3, sdh4, mttB and rpl2) with significant nonrandom codon usage. In general, we find multiple factors that influence cotton mitochondrial genome codon usage, which may include selection in a subset of genes.

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Section: Determination Of Optimal Codonsmentioning

confidence: 99%

Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes

Chen

Zhao

Qiao

et al. 2020

Mitochondrial DNA Part B

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“…SPX proteins are receptors for InsP(8), and release Phosphate Starvation Response (PHR) proteins (AtPHR1 in Arabidopsis and OsPHR2 in rice) into nucleus to promoting the expression of PSR genes (Y. N. Cui et al, 2019; M. X. Huang et al, 2019;Medici et al, 2019;Osorio et al, 2019). Nitrate-Inducible Garp-Type Transcriptional Repressor 1 (NIGT1) proteins are induced by environmental nitrate and low Pi stress, are involved in both N and P sensing, uptake, and assimilation to balance N and P content in plants (Maeda et al, 2018;.…”

Section: Introductionmentioning

confidence: 99%

Physiological and transcriptomic analysis reveal the response mechanisms to nutrient deficiencies in aquatic plant Spirodela polyrhiza

Hou

Zhao

et al. 2022

Preprint

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Macrophytes are critical primary producers in freshwater ecosystem and provide potential crop output to feed the expanding human population, they also have been used to mitigate eutrophication and upgrade the water quality. Aquatic plants adapt themselves to the more complicated, changeable and unstable conditions compared to terrestrial plants, especially the fluctuated nutrient environments. Nitrogen (N) and phosphorus (P) are the key nutrient elements for plants, and their cycles have been massively altered by anthropogenic activities in diverse ecosystems. However, there is still a lack of comprehensive understanding about the adapt mechanisms of N and P stress in aquatic plants. Therefore, we investigated the response mechanisms at the molecular, physiological, and morphological levels in the macrophyte Spirodela polyrhiza under N deficiency, P deficiency, combined N and P deficiency, and total nutrient deficiency using RNA-seq, physiological, and biochemical measurements in this study. We found that the similar response mechanisms are shared between terrestrial plants and this tiny aquatic plant, such as nutrient deficiency-induced root system architecture (RSA) changes and photosynthetic inhibition, interacting of N/P signaling networks and uptake, and the consistent changes of gene expression profiles at transcriptional level. Encouragingly, novel findings have been found in S. polyrhiza. The dramatic accumulation of starch or protein without significantly growth inhibition under nutrient deficiencies, improve the crop output of S. polyrhiza. It has a more complex P-signaling network, which is made up of miR399, PHO2, PHT1 and lncRNAs, and miR399 should be a dual-function regulator in Pi homeostasis of S. polyrhiza. The N assimilation process explained the prioritizing usage of ammonium (NH )-N in duckweed, enhancing its application to phytoremediation of NH waste water.

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DNA barcoding and molecular phylogeny of genus Pseudagrion (Odonata: Coenagrionidae) based on mitochondrial COI, ND1 and 16S rRNA genes

Walia,

Dhillon

2024

Int J Trop Insect Sci

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Analysis of codon usage in the mitochondrion genome of Spirodela polyrhiza

Cited by 3 publications

References 46 publications

Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes

Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes

Physiological and transcriptomic analysis reveal the response mechanisms to nutrient deficiencies in aquatic plant Spirodela polyrhiza

DNA barcoding and molecular phylogeny of genus Pseudagrion (Odonata: Coenagrionidae) based on mitochondrial COI, ND1 and 16S rRNA genes

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