Pseudogenization of<i>trnT-GGU</i>in chloroplast genomes of the plant family Asteraceae

Abdullah, Abdullah; Mehmood, Furrukh; Heidari, Parviz; Ahmed, Ibrar; Poczai, Péter

doi:10.1101/2021.02.01.429200

Cited by 4 publications

(2 citation statements)

References 37 publications

(52 reference statements)

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“…This phenomenon has been mostly observed in many sequenced chloroplast genomes of land plants and may be due to A/T-rich chloroplast genome content (Amiryousefi et al, 2018b;Abdullah I. et al, 2019, Abdullah et al, 2019Mehmood et al, 2020aMehmood et al, , 2020b. The high similarity exists in the codon usage of closely related species or of the same lineage, which provides insight into the evolution of plants, and the species of the same genus have high similarity compared with family-level comparison (Abdullah et al, 2020e;Abdullah et al, 2021). Hence, the high similarity in codon usage of Chimonanthus species showed their close evolutionary relationships.…”

Section: Chloroplast Genome Evolution Of Chimonanthusmentioning

confidence: 95%

Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification

Jamal

Wen

et al. 2021

Front. Genet.

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Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.

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Section: Chloroplast Genome Evolution Of Chimonanthusmentioning

confidence: 95%

Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification

Jamal

Wen

et al. 2021

Front. Genet.

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“…Plastid genomes are widely employed in plant evolutionary research, encompassing areas such as phylogenetics, taxonomic implications, population genetics, and phylogeography (Huang et al, 2019) (Abdullah et al, 2021). The reason for which plastomes are willingly used in this applications are the same that predestinate it to be applied in molecular identification of species, i.e.…”

Section: Introductionmentioning

confidence: 99%

The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification

Krawczyk,

Paukszto,

Maździarz

et al. 2023

Front. Plant Sci.

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Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.

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Pseudogenization of the chloroplast threonine (trnT-GGU) gene in the sunflower family (Asteraceae)

Abdullah

Mehmood

Heidari

et al. 2021

Sci Rep

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The chloroplast genome evolves through the course of evolution. Various types of mutational events are found within the chloroplast genome, including insertions-deletions (InDels), substitutions, inversions, gene rearrangement, and pseudogenization of genes. The pseudogenization of the chloroplast threonine (trnT-GGU) gene was previously reported in Cryptomeria japonica (Cupressaceae), Pelargonium × hortorum (Geraniaceae), and Anaphalis sinica and Leontopodium leiolepis of the tribe Gnaphalieae (Asteroideae, Asteraceae). Here, we performed a broad analysis of the trnT-GGU gene among the species of 13 subfamilies of Asteraceae and found this gene as a pseudogene in core Asteraceae (Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae), which was linked to an insertion event within the 5′ acceptor stem and is not associated with ecological factors such as habit, habitat, and geographical distribution of the species. The pseudogenization of trnT-GGU was not predicted in codon usage, indicating that the superwobbling phenomenon occurs in core Asteraceae in which a single transfer RNA (trnT-UGU) decodes all four codons of threonine. To the best of our knowledge, this is the first evidence of a complete clade of a plant species using the superwobbling phenomenon for translation.

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Pseudogenization oftrnT-GGUin chloroplast genomes of the plant family Asteraceae

Cited by 4 publications

References 37 publications

Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification

Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification

The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification

Pseudogenization of the chloroplast threonine (trnT-GGU) gene in the sunflower family (Asteraceae)

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