Comparative analyses of chloroplast genomes among three Firmiana species: Identification of mutational hotspots and phylogenetic relationship with other species of Malvaceae

Abdullah, Abdullah; Shahzadi, Iram; Mehmood, Furrukh; Ali, Zain; Malik, Muhammad Suleman; Waseem, Shahid; Mirza, Bushra; Ahmed, Ibrar; Waheed, Mohammad Tahir

doi:10.1016/j.plgene.2019.100199

Cited by 74 publications

(86 citation statements)

References 49 publications

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“…Our finding of increased transition substitutions compared to transversion substitutions is consistent with other findings (Wakeley 1996;Cao et al 2018). Contradictory findings of more transversion than transition findings have also been documented previously (Cai et al 2015;Abdullah et al 2019a;Shahzadi et al 2020). This bias of higher transversions might be due to the composition of genomes and the genetic characteristics of codons (Morton et al 1997).…”

Section: Discussionsupporting

confidence: 92%

“…After quality confirmation, the Fast-Plast v. 1.2.2 pipeline (https ://githu b.com/mrmck ain/Fast-Plast ) was initially used to assemble the raw reads following similar parameters previously employed for the assembly of chloroplast genomes of subfamilies Aroideae and Monsteroideae (Henriquez et al 2020a,b). The resulting assembly from Fast-Plast was further confirmed by de novo assembly using Velvet v.1.2.10 following Abdullah et al (2019aAbdullah et al ( , 2020b using Kmer values of 61, 71, and 81. Validation and coverage depth analyses of de novo assembled genomes were performed by mapping short reads to their respective assembled chloroplast genomes.…”

Section: De Novo Assembly and Annotationmentioning

confidence: 99%

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Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution

et al. 2020

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The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae: Anthurium huixtlense (size: 163,116 bp) and Pothos scandens (size: 164,719 bp). The chloroplast genome of P. scandens showed unique contraction and expansion of inverted repeats (IRs), thereby increasing the size of the large single-copy region (LSC: 102,956 bp) and decreasing the size of the small singlecopy region (SSC: 6779 bp). This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as compared to those in IRs. We found a 2.3-fold increase of oligonucleotide repeats in P. scandens when compared with A. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 in P. scandens and 2.12 in A. huixtlense. Transversion mutations mostly translated in non-synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.

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Section: Discussionsupporting

confidence: 92%

Section: De Novo Assembly and Annotationmentioning

confidence: 99%

Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution

et al. 2020

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“…To understand the molecular evolution, it is important to know about the nucleotide substitution rates (Muse & Gaut, 1994). LSC and SSC regions are more prone to substitutions and indels whereas the IR regions are more conserved in the chloroplast genome (Ahmed et al, 2012; Abdullah et al, 2019b). Our results also showed similar results in that the IR region is mostly conserved, and most of the substitutions occurs in the LSC and SSC regions.…”

Section: Discussionmentioning

confidence: 99%

“…The plastid genome exists in circular and linear forms (Oldenburg & Bendich, 2015) and the percentage of each form varies within plant cells (Oldenburg & Bendich, 2016). 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).…”

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

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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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“…The plastid genome exists in circular and linear forms (Oldenburg & Bendich, 2015) and the percentage of each form varies within plant cells (Oldenburg & Bendich, 2016). 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%

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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Comparative analyses of chloroplast genomes among three Firmiana species: Identification of mutational hotspots and phylogenetic relationship with other species of Malvaceae

Cited by 74 publications

References 49 publications

Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution

Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution

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

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)"

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