Complete chloroplast genome sequences of <i>Dioscorea</i>: Characterization, genomic resources, and phylogenetic analyses

Zhao, Zhenyu; Wang, Xin; YiXin, Yu; Yuan, Subo; Jiang, Dan; Zhang, Yujun; Zhang, Teng; Zhong, Wenhao; Yuan, Qingjun; Huang, Luqi

doi:10.7717/peerj.6032

Cited by 29 publications

(48 citation statements)

References 50 publications

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“…As shown in the previous studies, our comparison also confirmed that the IR region was more conserved than the LSC and SSC regions within these species ( Fig. 3; Zhao et al, 2018;Ma et al, 2018).…”

Section: Comparative Analysissupporting

confidence: 90%

“…The GC contents of the LSC and SSC regions are 31.5% and 31.4%, respectively, whereas that of the IR regions is 42.2%. Similar to other closely related species, the high GC content in IR region is due to the high GC content in four rRNA genes in this region (54.6%; Zhao et al, 2018).…”

Section: Resultsmentioning

confidence: 52%

“…The intron and intergenic spacer region covered 36.1% of the genome (intron 7%, and intergenic spacer 29%). Overall guanine-cytosine (GC) content of T. zeylanicus chloroplast genome was 37.24% which is similar to closely related species (Zhao et al, 2018;Ma et al, 2018). The GC contents of the LSC and SSC regions are 31.5% and 31.4%, respectively, whereas that of the IR regions is 42.2%.…”

Section: Resultsmentioning

confidence: 66%

“…The comparison of chloroplast genome of three families of Dioscoreales (Dioscoreaceae, Burmanniaceae, and Nartheciaceae) and their evolutionary relationship was previously reported (Zhao et al, 2018;Ma et al, 2018). In this study, we extended the comparative analysis by including 11 Dioscoreales representing five families (Dioscoreaceae, Nartheciaceae, Taccaceae, Burmanniaceae, and Trichopodaceae; Table 2).…”

Section: Comparative Analysismentioning

confidence: 83%

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The Complete Chloroplast Genome of Trichopus zeylanicus, And Phylogenetic Analysis with Dioscoreales

et al. 2019

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The Plant Genome C hloroplasts are important organelles that are responsible for photosynthesis and play a vital role in plant physiology and development in green plants and algae (Raven and Allen, 2003). Chloroplasts have their own DNA, and for most of the land plants, the chloroplast genome exists in circular form with a quadripartite structure comprised of a large single copy (LSC) and a small single copy (SSC) region separated by two inverted repeats (IR; Sugiura, 2003; Wicke et al., 2011). The size of the chloroplast genome varies from 120 to 170 Kb and possessed 60 to 130 genes which are primarily involved in photosynthesis and other metabolic process (Sugiura, 2003; Wicke et al., 2011). The haploid nature, low level of recombination, and maternal inheritance of the chloroplast genome, as well as its low substitution rate compared with the nuclear genome, present chloroplast genomes as valuable

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Section: Comparative Analysissupporting

confidence: 90%

Section: Resultsmentioning

confidence: 52%

Section: Resultsmentioning

confidence: 66%

Section: Comparative Analysismentioning

confidence: 83%

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The Complete Chloroplast Genome of Trichopus zeylanicus, And Phylogenetic Analysis with Dioscoreales

et al. 2019

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“…The GC content of the Nicotiana species referred to above were similar to those of other Nicotiana species (Sugiyama et al, 2005; Yukawa, Tsudzuki & Sugiura, 2006) i.e. the GC content in the IR is high, which might be a result of the existence of ribosomal RNA (Qian et al, 2013; Cheng et al, 2017; Zhao et al, 2018). The genome organization, gene order and content and of these Nicotiana species were also similar for N. slyvestris and N. tabacum (Sugiyama et al, 2005; Yukawa, Tsudzuki & Sugiura, 2006).…”

Section: Discussionsupporting

confidence: 56%

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

Mehmood

Abdullah

Ubaid

et al. 2020

Preprint

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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 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.

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Chemotaxonomic studies of 12 Dioscorea species from China by UHPLC‐QTOF‐MS/MS analysis

Wang

Sun

et al. 2019

Phytochemical Analysis

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Introduction Dioscorea species, which contain abundant steroidal saponins, have been used as folk medicines or raw materials to synthesise steroid drugs. Objective To establish a rapid chemotaxonomic method that will comprehensively resolve confusions about genetic relationships of genus Dioscorea. Methods A comprehensive strategy using ultra‐high‐performance liquid chromatography coupled with quadrupole time‐of‐flight tandem mass spectrometry (UHPLC‐QTOF‐MS/MS) was firstly proposed to evaluate the chemotaxonomy of 12 species (27 taxa) from China by hierarchical cluster analysis (HCA) based on the variations of the identified metabolites. Results Twenty‐eight secondary metabolites (mainly steroidal saponins) were identified. The MSn fragmentation patterns of DA (a new acetylated steroidal saponin at C‐7 position) were firstly reported. Moreover, eight major steroidal saponins were further quantified simultaneously by UPLC‐QTOF‐MS method. According to HCA results, D. bulbifera L. was distinguished with species of sect. Stenophora Uline for pennogenin‐type steroidal saponins. Dioscorea zingiberensis exhibited far distance from other members of sect. Stenophora Uline for two unique saponins. Dioscorea banzhuana may be reclassified into sect. Stenophora. Dioscorea nipponica subsp. rosthornii and D. collettii var. hypoglauca might be separated from their original subspecies/varieties as new species, respectively. Conclusion The chemotaxonomic method was successfully applied in the study of genetic relationships of Dioscorea species. This study not only enhanced the understanding of chemical constituents, but also laid basic theoretical foundations for the rational utilisation and chemotaxonomy of genus Dioscorea.

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Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

Cited by 29 publications

References 50 publications

The Complete Chloroplast Genome of Trichopus zeylanicus, And Phylogenetic Analysis with Dioscoreales

The Complete Chloroplast Genome of Trichopus zeylanicus, And Phylogenetic Analysis with Dioscoreales

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

Chemotaxonomic studies of 12 Dioscorea species from China by UHPLC‐QTOF‐MS/MS analysis

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