Browsing by Subject "Chloroplast genome"

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  • Abdullah,; Henriquez, Claudia L.; Mehmood, Furrukh; Hayat, Aamir; Sammad, Abdul; Waseem, Shahid; Waheed, Mohammad Tahir; Matthews, Peter J.; Croat, Thomas B; Poczai, Péter; Ahmed, Ibrar (2021)
    Chloroplast (cp) genomes are considered important for the study of lineage-specific molecular evolution, population genetics, and phylogenetics. Our aim here was to elucidate the molecular evolution in cp genomes of species in the Dracunculus clade (Aroideae, Araceae). We report de novo assembled cp genomes for eight species from eight genera and also retrieved cp genomes of four species from the National Center for Biotechnology Information (NCBI). The cp genomes varied in size from 162,424 bp to 176,835 bp. Large Single Copy (LSC) region ranged in size from 87,141 bp to 95,475 bp; Small Single Copy (SSC) from 14,338 bp to 23,981 bp; and Inverted Repeats (IRa and IRb) from 25,131 bp to 32,708 bp. The expansion in inverted repeats led to duplication of ycf1 genes in four species. The genera showed high similarity in gene content and yielded 113 unique genes (79 protein-coding, 4 rRNA, and 30 tRNA genes). Codon usage, amino acid frequency, RNA editing sites, microsatellites repeats, transition and transversion substitutions, and synonymous and non-synonymous substitutions were also similar across the clade. A previous study reported deletion of ycf1, accD, psbE, trnL-CAA, and trnG-GCC genes in four Amorphophallus species. Our study supports conservative structure of cp genomes in the Dracunculus clade including Amorphophallus species and does not support gene deletion mentioned above. We also report suitable polymorphic loci based on comparative analyses of Dracunculus clade species, which could be useful for phylogenetic inference. Overall, the current study broad our knowledge about the molecular evolution of chloroplast genome in aroids.
  • Poczai, Péter; Amiryousefi, Ali; Hyvönen, Jaakko (2017)
    In this study, we announce the complete chloroplast genome sequence of Nicotiana attenuata. The genome sequence of 155,941 bp consists of two inverted repeat (IRa and IRb) regions of 25,438 bp each, a large single-copy (LSC) region of 86,513 bp and a small single-copy (SSC) region of 18,524 bp. The overall GC content is 37.9% and the GC contents of LSC, IRs, and SSC are 36%, 43.2%, and 32.1%, respectively. The plastome with 129 annotated unique genes includes 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Using the whole chloroplast genome sequences alignment of 16 Solanaceae species a phylogenetic hypothesis is presented validating the position of N. attenuata within Nicotianeae.
  • Mehmood, Furrukh; Abdullah,; Ubaid, Zartasha; Shahzadi, Iram; Ahmed, Ibrar; Waheed, Mohammad Tahir; Poczai, Péter; Mirza, Bushra (2020)
    The genus Nicotiana of the family Solanaceae, commonly referred to as tobacco plants, are a group cultivated as garden ornamentals. Besides their use in the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history, which is tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species, namely N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes showed typical quadripartite structure, consisting of a pair of inverted repeats (IR) regions (25,323–25,369 bp each) separated by a large single copy (LSC) region (86,510 –86,716 bp) and a small single copy (SSC) region (18,441–18,555 bp). Comparative analyses of Nicotiana plastid genomes showed similar GC content, gene content, codon usage, simple sequence repeats, oligonucleotide repeats, RNA editing sites and substitutions with currently available Solanaceae genomes sequences. We identified twenty highly polymorphic regions mostly belonging to intergenic spacer regions (IGS), which could be appropriate for the development of robust and cost-effective markers to infer the phylogeny of genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. The relaxed molecular clock analyses estimated that the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65–0.46). The biogeographical analysis showed a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicated that four genes involved in different plastid functions, such as DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations of the following genes might have contributed to the survival and better adaptation during the evolutionary history of tobacco species.
  • Amiryousefi, Ali; Hyvönen, Jaakko; Poczai, Péter (2017)
  • Amiryousefi, Ali; Hyvönen, Jaakko; Poczai, Péter (2017)