Comprehensive Analysis of Codon Usage in Quercus Chloroplast Genome and Focus on psbA Gene

Sheng, Shi; Liu, Yan-Qun; Xia, Run-Xi; Qin, Li

doi:10.3390/genes13112156

Cited by 15 publications

(10 citation statements)

References 67 publications

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“…Codon usage bias is an important evolutionary characteristic that is common in many organisms. It is in uenced by natural selection, base mutations, and other factors [88], and has been extensively studied in many plant species [89][90][91][92]. In this study, the GC content decreased in the following order: GC1 > GC2 > GC3 (Table 3).…”

Section: Discussionmentioning

confidence: 68%

Structural conservation and functional genetic adaptive evolution of chloroplast genomes in Cycle-cup Oaks

Li,

Zheng,

Wang

et al. 2023

Preprint

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Background: Cycle-cup oaks (Quercus section Cyclobalanopsis) are one of the principal components of forests in the tropical and subtropical climates of East and Southeast Asia. They have experienced relatively recent increases in the diversification rate, driven by changing climates and the Himalayan orogeny. However, the course, tempo, and mode of genome evolution in cycle-cup oaks remain largely unknown; in particular, how plant plastome genes and genomes evolve during rapid speciation. To address this question, we analyzed the complete plastomes of 50 species of Quercus section Cyclobalanopsis, 36 newly sequenced and 14 published species. Results: Based on a series of analyses, including genome structure, genome annotation, GC content, repeat sequences, SSR components, codon usage bias, and comparative genomics, we found that Quercus section Cyclobalanopsishad a conserved plastome structure. Highly divergent regions, such as the ndhFand ycf1 gene regions and the petN—psbM and rpoB—trnC-GCA gene spacer regions, provided potential molecular markers for subsequent analysis. The maximum likelihood phylogenetic tree based on complete chloroplast genomes, coding DNA sequences, and highly divergent regions produced a poorly resolved genetic relationship of the plastid lineages of section Cyclobalanopsis. We identified nine protein-coding genes containing sites for positive selection: ndhA, ndhD, ndhF, ndhH, rbcL, rpl32, accD, ycf1, and ycf2. Conclusions: We compared and analyzed the chloroplast genomes of 50 species of Quercus section Cyclobalanopsis to explore their diversity structure, phylogenetic relationships, and ecological adaptative evolution. These chloroplast genome data provide valuable information for deep insights into phylogenetic relationships and intraspecific diversity in Quercus.

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Section: Discussionmentioning

confidence: 68%

Structural conservation and functional genetic adaptive evolution of chloroplast genomes in Cycle-cup Oaks

Li,

Zheng,

Wang

et al. 2023

Preprint

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“…Six Euphorbiaceae plant species 31 and seven Miscanthus species 32 were biased towards A/T bases and A/T-ending codons. Quercus chloroplast genomes prefer A/T-ending codons and avoid C/G-ending codons 33 . Additionally, the Ka/Ks revealed selection pressure on protein-coding genes 34 , Ka/Ks ratios > 1, close to 1, or < 1 indicate that the gene has undergone positive selection, neutral selection, or purifying selection, respectively 35 .…”

Section: Discussionmentioning

confidence: 99%

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Xiao,

Zhao,

Wang

et al. 2024

Sci Rep

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The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of Gleditsia species has been limited. Using the Illumina sequencing, we assembled and annotated the whole chloroplast genomes of seven Gleditsia species (Gleditsia sinensis, Gleditsia japonica var. delavayi (G. delavayi), G. fera, G. japonica, G. microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), G. microphylla mutant). The assembled genomes revealed that Gleditsia species have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative genomic analysis showed that most (65.8–75.8%) of the abundant simple sequence repeats in Gleditsia and Gymnocladus species were located in the large single copy region. The Gleditsia chloroplast genome prefer T/A-ending codons and avoid C/G-ending codons, positive selection was acting on the rpoA, rpl20, atpB, ndhA and ycf4 genes, most of the chloroplast genes of Gleditsia species underwent purifying selection. Expansion and contraction of the inverted repeat (IR)/single copy (SC) region showed similar patterns within the Gleditsia genus. Polymorphism analysis revealed that coding regions were more conserved than non-coding regions, and the IR region was more conserved than the SC region. Mutational hotspots were mostly found in intergenic regions such as “rps16-trnQ”, “trnT-trnL”, “ndhG-ndhI”, and "rpl32-trnL” in Gleditsia. Phylogenetic analysis showed that G. fera is most closely related to G. sinensis,G. japonica and G. delavayi are relatively closely related. Zhū Yá Zào can be considered a bud mutation of the G. sinensis. The albino phenotype of G. microphylla mutant is not caused by variations in the chloroplast genome, and that the occurrence of the albino phenotype may be due to mutations in chloroplast-related genes involved in splicing or localization functions. This study will help us enhance our exploration of the genetic evolution and geographical origins of the Gleditsia genus.

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“…Codon usage preference is usually considered to be the result of the tendency to develop relative equilibrium within cells during species evolution, and codons with a RSCU greater than 1 are considered to be used by amino acid preference [ 17 , 39 – 41 ]. The result indicated that Phe, Ile and Glu were the most common amino acids, and Met and Ter were much less common in the P. granatum mitogenome.…”

Section: Discussionmentioning

confidence: 99%

Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

Feng,

Wang,

Wang

et al. 2023

BMC Plant Biol

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Background Punica granatum is a fundamentally important fruit tree that has important economic, medicinal and ornamental properties. At present, there are few reports on the mitochondrial genome of pomegranate. Hence, in this study the P. granatum mitogenome was sequenced and assembled to further understanding of organization, variation, and evolution of mitogenomes of this tree species. Results The genome structure was multi-chromosomes with seven circular contigs, measuring 382,774 bp in length with a 45.91% GC content. It contained 74 genes, including 46 protein-coding genes, 25 tRNA genes, and three rRNA genes. There were 188 pairs of dispersed repeats with lengths of 30 or greater, primarily consisting of reverse complementary repeats. The mitogenome analysis identified 114SSRs and 466 RNA editing sites. Analyses of codon usage, nucleotide diversity and gene migration from chloroplast to mitochondrial were also conducted. The collinear and comparative analysis of mitochondrial structures between P. granatum and its proximal species indicated that P. granatum ‘Taishanhong’ was closely related to P. granatum ‘Qingpitian’ and Lagerstroemia indica. Phylogenetic examination based on the mitogenome also confirmed the evolutionary relationship. Conclusion The results offered crucial information on the evolutionary biology of pomegranate and highlighted ways to promote the utilization of the species’ germplasm.

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Comprehensive Analysis of Codon Usage in Quercus Chloroplast Genome and Focus on psbA Gene

Cited by 15 publications

References 67 publications

Structural conservation and functional genetic adaptive evolution of chloroplast genomes in Cycle-cup Oaks

Structural conservation and functional genetic adaptive evolution of chloroplast genomes in Cycle-cup Oaks

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

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