Analysis of codon usage patterns in<i>Morus notabilis</i>based on genome and transcriptome data

Wen, Yan; Zou, Ziliang; Li, Hongshun; Xiang, Zhonghuai; He, Ningjia

doi:10.1139/gen-2016-0129

Cited by 20 publications

(13 citation statements)

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“…Codon usage and amino acid usage patterns may also show interstrain variation and can reveal the molecular basis of evolution of A. hydrophila [ 21 ]. Exploring these parameters may also reveal the type of natural selection pressure on genes, as found in previous studies [ 22 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative genome analysis provides deep insights into Aeromonas hydrophila taxonomy and virulence-related factors

et al. 2018

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BackgroundAeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and misclassified. Moreover, the potential pathogenic factors among the publicly available genomes in A. hydrophila strains of different origins have not yet been investigated.ResultsTo identify the valid strains of A. hydrophila and their pathogenic factors, we performed a pan-genomic study. It revealed that there were 13 mislabelled strains and 49 valid strains that were further verified by Average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and in silico multiple locus strain typing (MLST). Multiple numbers of phages were detected among the strains and among them Aeromonas phi 018 was frequently present. The diversity in type III secretion system (T3SS) and conservation of type II and type VI secretion systems (T2SS and T6SS, respectively) among all the strains are important to study for designing future strategies. The most prevalent antibiotic resistances were found to be beta-lactamase, polymyxin and colistin resistances. The comparative analyses of sequence type (ST) 251 and other ST groups revealed that there were higher numbers of virulence factors in ST-251 than in other STs group.ConclusionPublicly available genomes have 13 mislabelled organisms, and there are only 49 valid A. hydrophila strains. This valid pan-genome identifies multiple prophages that can be further utilized. Different A. hydrophila strains harbour multiple virulence factors and antibiotic resistance genes. Identification of such factors is important for designing future treatment regimes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5100-4) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Comparative genome analysis provides deep insights into Aeromonas hydrophila taxonomy and virulence-related factors

et al. 2018

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“…The slope of the plot regression was zero indicates no effects of directional mutation pressure (complete selective constraints). The slope 1 depicted that the codon usage bias is completely affected by directional mutation pressure representing complete neutrality (Sueoka, 1988;Wen et al, 2017).…”

Section: Analysis Of Neutrality Plotmentioning

confidence: 99%

Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species

Wang

et al. 2020

PeerJ

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Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.

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“…The slope of the plot regression is zero which indicates that there is no effect on directional mutation pressure (complete selection constraint). Slope 1 indicates that the codon usage bias is completely affected by the directional mutation pressure, and represents complete neutrality [59]. RSCU (Relative synonymous codon usage) for CDS was calculated using CodonW v1.4.4 [55].…”

Section: Codon Usage Analysesmentioning

confidence: 99%

Comparative chloroplast genome s: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

li¹,

Hu²,

He³

et al. 2021

Preprint

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Background: Chloroplast genome resources can provide useful information for the evolution of plant species. Tea plant (Camellia sinensis) is among the most economically valuable member of Camellia. Here, we determined the chloroplast genome of the first natural triploid Chinary type tea (‘Wuyi narcissus’ cultivar of Camellia sinensis var. sinensis, CWN) and conducted the genome comparison with the diploid Chinary type tea (Camellia sinensis var. sinensis, CSS) and two types of diploid Assamica type teas (Camellia sinensis var. assamica: Chinese Assamica type tea, CSA and Indian Assamica type tea, CIA). Further, the evolutionary mechanism of the chloroplast genome of Camellia sinensis and the relationships of Camellia species based on chloroplast genome were discussed.Results: Comparative analysis showed the evolutionary dynamics of chloroplast genome of Camellia sinensis were the repeats and insertion-deletions (indels), and distribution of the repeats, indels and substitutions were significantly correlated. Chinese tea and Indian tea had significant differences in the structural characteristic and the codon usage of the chloroplast genome. Analysis of sequence characterized amplified region (SCAR) using sequences of the intergenic spacers (trnE/trnT) showed none of 292 different Camellia sinensis cultivars had similar sequence characteristic to triploid CWN, but the other four Camellia species did. Estimations of the divergence time showed that CIA diverged from the common ancestor of two Assamica type teas about 6.2 Mya (CI: 4.4-8.1 Mya). CSS and CSA diverged to each other about 0.8 Mya (CI: 0.4-1.5 Mya). Moreover, phylogenetic clustering was not exactly consistent with the current taxonomy of Camellia. Conclusions: The repeat-induced and indel-induced mutations were two important dynamics contributed to the diversification of the chloroplast genome in Camellia sinensis, which were not mutually exclusive. Chinese tea and Indian tea might have undergone different selection pressures. Chloroplast transfer occurred during the polyploid evolution in Camellia sinensis. In addition, our results supported the three different domestication origins of Chinary type tea, Chinese Assamica type tea and Indian Assamica type tea. And, the current classification of some Camellia species might need to be further discussed.

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Analysis of codon usage patterns inMorus notabilisbased on genome and transcriptome data

Cited by 20 publications

References 62 publications

Comparative genome analysis provides deep insights into Aeromonas hydrophila taxonomy and virulence-related factors

Comparative genome analysis provides deep insights into Aeromonas hydrophila taxonomy and virulence-related factors

Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species

Comparative chloroplast genome s: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

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