Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots

Abdullah, Abdullah; Mehmood, Furrukh; Shahzadi, Iram; Waseem, Shahid; Mirza, Bushra; Ahmed, Ibrar; Waheed, Mohammad Tahir

doi:10.1016/j.ygeno.2019.04.010

Cited by 133 publications

(140 citation statements)

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“…Manuscript to be reviewed trnL-F spacer, trnS-G spacer and two genes, ndhF and matK (Clarkson et al, 2004). Recently, inference of phylogeny based on complete plastid genomes has provided deep insight into the phylogeny of certain families and genera (Henriquez et al, 2014;Amiryousefi, Hyvönen & Poczai, 2018a;Abdullah et al, 2020). Here, we reconstructed a phylogenetic tree for eleven species of genus Nicotiana that belong to nine sections (Clarkson et al, 2004) analyses support the previous classification of genus Nicotiana, and corroborates that plastid genomic resources can provide further support for highly resolved phylogenies.…”

Section: Phylogenetic Relationships and The Origin Of Tetraploid Nicosupporting

confidence: 80%

“…Circular-plastid genomes typically quadripartite structure, consisting of two inverted repeat regions (IRa and IRb), separated by one large single-copy (LSC) and one small single-copy (SSC) region (Palmer, 1985;Amiryousefi, Hyvönen & Poczai, 2018a;Abdullah et al, 2019a). Numerous mutational events occur in plastid genomes, including variations in tandem repeats, insertions and deletions (indels), and point mutations; inversions and translocations are also common (Jheng et al, 2012;Xu et al, 2015;Abdullah et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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Peer Review #1 of "Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica) (v0.2)"

2020

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Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history, tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (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 with currently available Solanaceae genome sequences showed similar GC content, gene content, codon usage, simple sequence repeats, oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the 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. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65-0.46). Biogeographical analysis supported 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

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Section: Phylogenetic Relationships and The Origin Of Tetraploid Nicosupporting

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica) (v0.2)"

2020

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“…trnL intron and trnL-F spacer , trnS-G spacer and two genes , ndhF and matK (Clarkson et al, 2004). Recently, inference of phylogeny based on complete chloroplast genomes has provided deep insight into the phylogeny of certain families and genera (Henriquez et al, 2014; Amiryousefi, Hyvönen & Poczai, 2018a; Abdullah et al, 2019a). Here, we reconstructed a phylogenetic tree among eleven species of genus Nicotiana that belong to nine sections (Clarkson et al, 2004) based on 75 protein-coding genes by using S. dulcamara as an outgroup which attests the previous classification of genus Nicotiana with high bootstrapping values.…”

Section: Discussionmentioning

confidence: 99%

“…Circular formed plastomes have a typical quadripartite structure, with two inverted repeat regions (IRa and IRb), separated by one large single-copy (LSC) and one small single-copy (SSC) region (Palmer, 1985; Amiryousefi, Hyvönen & Poczai, 2018a; Abdullah et al, 2019b). Numerous mutational events occur in plastid genomes: variations in tandem repeats, insertion and deletions (indels), and point mutations, but inversions and translocations are also common (Jheng et al, 2012; Xu et al, 2015; Abdullah et al, 2019a). The plastid genome of angiosperms have a uniparental maternal inheritance (Daniell, 2007) but paternal inheritance has been recorded in a few gymnosperm species (Neale & Sederoff, 1989).…”

Section: Introductionmentioning

confidence: 99%

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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“…Chloroplasts are important organelles in photosynthesis (Li et al 2018;Santos and Almeida 2019;Yan et al 2019). Compared with the nuclear genome, the chloroplast genome size is smaller, with very conservative gene composition, gene sequence and gene type, lower nucleotide replacement frequency, and the cp genomes are inherited uniparentally (maternally in most angiosperms plants) (Abdullaha et al 2019;Song et al 2019;Zhang et al 2019), which is widely used in studying phylogeny of plant species. The plants of Ulmus in the family Ulmaceae are mostly positive and sunloving plant, which are characterized by drought tolerance, cold tolerance, barren tolerance, pruning tolerance, fast growth, strong adaptability, and other characteristics (Zhang 2016;Shi et al 2017).…”

mentioning

confidence: 99%

The complete chloroplast genome sequence of Ulmus elongata (Ulmaceae)

Yinran¹,

Xiaoxu

Shuxiang³

et al. 2020

Mitochondrial DNA Part B

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Ulmus elongata is a species of Sect. Chaetoptelea (Liemb.) S chneid in Ulmaceae, and it is an endangered wild plant listed in the second class of the Protected Plants in China. The complete chloroplast genome (cp) of U. elongata was reported in this study. The result showed that the cp genome was 159,230 bp in length including a large single-copy (LSC) 87,718 bp and a small single-copy (SSC) 18,690 bp, which were separated by two inverted repeats (IRs) of 26,411 bp with the typical quadripartite structure, respectively. The genome encoded 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The GC content was 35.57%. Chloroplast sequences were used for constructing phylogenetic tree to determine the evolutionary status of U. elongata. The maximum-likelihood phylogenetic analysis showed that U. elongata was clustered with five other Ulmus species, and the relationship between Ulmus and Zelkova was closest. The success of cp genome assembly of U. elongata has laid a foundation for the study of chloroplast molecular biology and can effectively promote the study of genetic breeding and molecular evolution of U. elongata. ARTICLE HISTORY

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Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots

Cited by 133 publications

References 57 publications

Peer Review #1 of "Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica) (v0.2)"

Peer Review #1 of "Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica) (v0.2)"

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

The complete chloroplast genome sequence of Ulmus elongata (Ulmaceae)

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