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

2020 ◽  
Author(s):  
Furrukh Mehmood ◽  
Abdullah ◽  
Zartasha Ubaid ◽  
Iram Shahzadi ◽  
Ibrar Ahmed ◽  
...  
Keyword(s):  
Selective Pressure ◽  
De Novo ◽  
Gc Content ◽  
Intergenic Spacer ◽  
Evolutionary Model ◽  
Cost Effective ◽  
Single Copy ◽  
Model Systems ◽  
Plastid Genomes ◽  
Worldwide Production

AbstractThe 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.

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

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9552
Author(s):  
Furrukh Mehmood ◽  
Abdullah ◽  
Zartasha Ubaid ◽  
Iram Shahzadi ◽  
Ibrar Ahmed ◽  
...  
Keyword(s):  
Selective Pressure ◽  
De Novo ◽  
Intergenic Spacer ◽  
Evolutionary Model ◽  
Cost Effective ◽  
Single Copy ◽  
Model Systems ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Worldwide Production

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 and gene content, codon usage, simple sequence and 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-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species.

scholarly journals Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria

2018 ◽  
Author(s):  
Jeffrey S. McLean ◽  
Batbileg Bor ◽  
Thao T. To ◽  
Quanhui Liu ◽  
Kristopher A. Kerns ◽  
...  
Keyword(s):  
Oral Cavity ◽  
De Novo ◽  
Gc Content ◽  
Single Copy ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Human Oral Cavity

ABSTRACTRecently, we discovered that a member of the Saccharibacteria/TM7 phylum (strain TM7x) isolated from the human oral cavity, has an ultra-small cell size (200-300nm), a highly reduced genome (705 Kbp) with limited de novo biosynthetic capabilities, and a very novel lifestyle as an obligate epibiont on the surface of another bacterium 1. There has been considerable interest in uncultivated phyla, particularly those that are now classified as the proposed candidate phyla radiation (CPR) reported to include 35 or more phyla and are estimated to make up nearly 15% of the domain Bacteria. Most members of the larger CPR group share genomic properties with Saccharibacteria including reduced genomes (<1Mbp) and lack of biosynthetic capabilities, yet to date, strain TM7x represents the only member of the CPR that has been cultivated and is one of only three CPR routinely detected in the human body. Through small subunit ribosomal RNA (SSU rRNA) gene surveys, members of the Saccharibacteria phylum are reported in many environments as well as within a diversity of host species and have been shown to increase dramatically in human oral and gut diseases. With a single copy of the 16S rRNA gene resolved on a few limited genomes, their absolute abundance is most often underestimated and their potential role in disease pathogenesis is therefore underappreciated. Despite being an obligate parasite dependent on other bacteria, six groups (G1-G6) are recognized using SSU rRNA gene phylogeny in the oral cavity alone. At present, only genomes from the G1 group, which includes related and remarkably syntenic environmental and human oral associated representatives1, have been uncovered to date. In this study we systematically captured the spectrum of known diversity in this phylum by reconstructing completely novel Class level genomes belonging to groups G3, G6 and G5 through cultivation enrichment and/or metagenomic binning from humans and mammalian rumen. Additional genomes for representatives of G1 were also obtained from modern oral plaque and ancient dental calculus. Comparative analysis revealed remarkable divergence in the host-associated members across this phylum. Within the human oral cavity alone, variation in as much as 70% of the genes from nearest oral clade (AAI 50%) as well as wide GC content variation is evident in these newly captured divergent members (G3, G5 and G6) with no environmental relatives. Comparative analyses suggest independent episodes of transmission of these TM7 groups into humans and convergent evolution of several key functions during adaptation within hosts. In addition, we provide evidence from in vivo collected samples that each of these major groups are ultra-small in size and are found attached to larger cells.

scholarly journals The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1179
Author(s):  
Ueric José Borges de Souza ◽  
Luciana Cristina Vitorino ◽  
Layara Alexandre Bessa ◽  
Fabiano Guimarães Silva
Keyword(s):  
Plastid Genome ◽  
Structural Characteristics ◽  
Gc Content ◽  
Single Copy ◽  
Chloroplast Genes ◽  
Artocarpus Heterophyllus ◽  
Plastid Genomes ◽  
The Family ◽  
High Degree ◽  
Degree Of Similarity

Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae.

scholarly journals Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 61 ◽  
Author(s):  
Huyen-Trang Vu ◽  
Ngan Tran ◽  
Thanh-Diem Nguyen ◽  
Quoc-Luan Vu ◽  
My-Huyen Bui ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Complete Chloroplast Genome ◽  
Critically Endangered Species ◽  
Plastid Genomes ◽  
Chloroplast Genomes

Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

scholarly journals Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

2020 ◽  
Author(s):  
Furrukh Mehmood ◽  
Abdullah . ◽  
Zartasha Ubaid ◽  
Yiming Bao ◽  
Peter Poczai ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
De Novo ◽  
Single Copy ◽  
Base Pairs ◽  
Insertion And Deletion ◽  
Plastid Genomes ◽  
Mutational Hotspots ◽  
The Family ◽  
Molecular Marker Development ◽  
Small Genus

Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled, complete, plastomed genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,198 base pairs (bp) to 154,361 bp and contained a pair of inverted repeats (IRa and IRb) of 25,027--25,071 bp that were separated by a large single-copy (LSC) region of 85,675--85,760 bp and a small single-copy (SSC) region of 18,457--18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastid genomes, which revealed close resemblance among the species. Both the substitution and insertion and deletion analyses confirmed that the IR region was significantly conserved compared with the LSC and SSC regions. Further comparative analysis among the Withania species highlighted 30 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification.

scholarly journals Comprehensive Analysis of Rhodomyrtus tomentosa Chloroplast Genome

Plants ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 89 ◽  
Author(s):  
Yuying Huang ◽  
Zerui Yang ◽  
Song Huang ◽  
Wenli An ◽  
Jing Li ◽  
...  
Keyword(s):  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Sister Relationship ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Plastid Genomes ◽  
Cp Genome ◽  
Rhodomyrtus Tomentosa

In the last decade, several studies have relied on a small number of plastid genomes to deduce deep phylogenetic relationships in the species-rich Myrtaceae. Nevertheless, the plastome of Rhodomyrtus tomentosa, an important representative plant of the Rhodomyrtus (DC.) genera, has not yet been reported yet. Here, we sequenced and analyzed the complete chloroplast (CP) genome of R. tomentosa, which is a 156,129-bp-long circular molecule with 37.1% GC content. This CP genome displays a typical quadripartite structure with two inverted repeats (IRa and IRb), of 25,824 bp each, that are separated by a small single copy region (SSC, 18,183 bp) and one large single copy region (LSC, 86,298 bp). The CP genome encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes and three pseudogenes (ycf1, rps19, ndhF). A considerable number of protein-coding genes have a universal ATG start codon, except for psbL and ndhD. Premature termination codons (PTCs) were found in one protein-coding gene, namely atpE, which is rarely reported in the CP genome of plants. Phylogenetic analysis revealed that R. tomentosa has a sister relationship with Eugenia uniflora and Psidium guajava. In conclusion, this study identified unique characteristics of the R. tomentosa CP genome providing valuable information for further investigations on species identification and the phylogenetic evolution between R. tomentosa and related species.

scholarly journals De Novo Assembly Discovered Novel Structures in Genome of Plastids and Revealed Divergent Inverted Repeats in Mammillaria (Cactaceae, Caryophyllales)

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 392 ◽  
Author(s):  
Solórzano ◽  
Chincoya ◽  
Sanchez-Flores ◽  
Estrada ◽  
Díaz-Velásquez ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Intergenic Spacer ◽  
Structural Diversity ◽  
Single Copy ◽  
Complete Sequence ◽  
Inverted Repeats ◽  
Total Size ◽  
Composition Structure ◽  
Novel Structures

The complete sequence of chloroplast genome (cpDNA) has been documented for single large columnar species of Cactaceae, lacking inverted repeats (IRs). We sequenced cpDNA for seven species of the short-globose cacti of Mammillaria and de novo assembly revealed three novel structures in land plants. These structures have a large single copy (LSC) that is 2.5 to 10 times larger than the small single copy (SSC), and two IRs that contain strong differences in length and gene composition. Structure 1 is distinguished by short IRs of <1 kb composed by rpl23-trnI-CAU-ycf2; with a total length of 110,189 bp and 113 genes. In structure 2, each IR is approximately 7.2 kb and is composed of 11 genes and one Intergenic Spacer-(psbK-trnQ)-trnQ-UUG-rps16-trnK-UUU-matK-trnK-UUU-psbA-trnH-GUG-rpl2-rpl23-trnI-CAU-ycf2; with a total size of 116,175 bp and 120 genes. Structure 3 has divergent IRs of approximately 14.1 kb, where IRA is composed of 20 genes: psbA-trnH-GUG-rpl23-trnI-CAU-ycf2-ndhB-rps7-rps12-trnV-GAC-rrn16-ycf68-trnI-GAU-trnA-AGC-rrn23-rrn4.5-rrn5-trnR-ACG-trnN-GUU-ndhF-rpl32; and IRB is identical to the IRA, but lacks rpl23. This structure has 131 genes and, by pseudogenization, it is shown to have the shortest cpDNA, of just 107,343 bp. Our findings show that Mammillaria bears an unusual structural diversity of cpDNA, which supports the elucidation of the evolutionary processes involved in cacti lineages.

The Complete Chloroplast Genome Sequence of Clerodendranthus Spicatus, A Medicinal Plant For Preventing And Treating Kidney Diseases From Lamiaceae Family

2021 ◽  
Author(s):  
Qing Du ◽  
Mei Jiang ◽  
Sihui Sun ◽  
Liqiang Wang ◽  
Shengyu Liu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Tandem Repeats ◽  
Kidney Diseases ◽  
Gc Content ◽  
Intergenic Spacer ◽  
Tectona Grandis ◽  
Single Copy ◽  
Complete Chloroplast Genome ◽  
Distance Analysis ◽  
Cistanche Deserticola

Abstract Clerodendranthus spicatus (Thunb.) C.Y.Wu is one of the most important medicine for the treatment of nephrology which distributes in south-east of China. In this study, we obtained the complete chloroplast genome of C. spicatus with a length of 152155bp, including a large single copy (LSC) region of 83098bp, small single copy (SSC) region of 17665bp and a pair of inverted repeat (IR) regions of 25696bp with the GC content of 37.86%. The genome contains 36 tRNA, 8 rRNA and 87 protein-coding genes. Most of them have one intron except the ycf3, rps12 and clpP genes. The length of rRNAs varies from 131bp to 2811bp and the GC contents are between 45.28% and 56.54%. The frequency of Isoleucine is fruitful accounting for 4.17%. The codons of AUG, UUA and AGA codon had presence of higher codon usage bias. For the repetitive sequence analysis, Thirty-six tandem repeats were identified with certain conditions. Forty interspersed repeats were identified, including 22 palindromic repeats and 18 direct repeats. The diverse positions of the specific rps19, ycf1, rpl2, trnH, psbA genes within the IR boundary analysis. The genetic distance analysis of the intergenic spacer regions for 5 relative species showed the areas of ndhG-ndhI, accD-psaI, rps15-ycf1, rpl20-clpP, ccsA-ndhD had high K2p value to distinguish the species through developing the molecular markers. From phylogenetic tree, C. spicatu was closely related to the genus of two Salvia speices, Tectona grandis, Cistanche deserticola and Glechoma longituba belonged to the Lamiales.

scholarly journals Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Junjun Yao ◽  
Fangyu Zhao ◽  
Yuanjiang Xu ◽  
Kaihui Zhao ◽  
Hong Quan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
De Novo ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Complete Chloroplast Genome ◽  
Ssr Analysis ◽  
Chloroplast Genomes

Dracocephalum tanguticum and Dracocephalum moldavica are important herbs from Lamiaceae and have great medicinal value. We used the Illumina sequencing technology to sequence the complete chloroplast genome of D. tanguticum and D. moldavica and then conducted de novo assembly. The two chloroplast genomes have a typical quadripartite structure, with the gene’s lengths of 82,221 bp and 81,450 bp, large single-copy region’s (LSC) lengths of 82,221 bp and 81,450 bp, and small single-copy region’s (SSC) lengths of 17,363 bp and 17,066 bp, inverted repeat region’s (IR) lengths of 51,370 bp and 51,352 bp, respectively. The GC content of the two chloroplast genomes was 37.80% and 37.83%, respectively. The chloroplast genomes of the two plants encode 133 and 132 genes, respectively, among which there are 88 and 87 protein-coding genes, respectively, as well as 37 tRNA genes and 8 rRNA genes. Among them, the rps2 gene is unique to D. tanguticum, which is not found in D. moldavica. Through SSR analysis, we also found 6 mutation hotspot regions, which can be used as molecular markers for taxonomic studies. Phylogenetic analysis showed that Dracocephalum was more closely related to Mentha.

scholarly journals The Complete Chloroplast Genome of Tamarix Ramosissima and Comparative Analysis of Tamaricaceae Species 

2020 ◽  
Author(s):  
Le Wang ◽  
Li Wang ◽  
Zhihong Guo
Keyword(s):  
Species Delimitation ◽  
De Novo ◽  
Gc Content ◽  
Single Copy ◽  
Tamarix Ramosissima ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Species Discrimination ◽  
Trna Genes ◽  
Cp Genome

Abstract Background: Tamarix ramosissima is a deciduous shrub resided in arid and semi-arid regions. Although of ecological and medicinal values, some Tamarix species are considered invasive as they have dominated the riparian zones of dryland in some parts of the world. Chloroplast (cp) DNA is highly conserved in structure and gene arrangement, making cp genomic data valuable resources for species delimitation and phylogenetics. The cp genome of T. ramosissima was de novo assembled with the aim of providing reference and data resource for further cp-derived marker development and species delimitation of Tamarix.Results: Here, the complete chloroplast (CP) genome of T. ramosissima was sequenced and analyzed, showing a size of 156150 bp and a GC content of 36.5%. The plastome displayed a typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions of 26554 bp, separated by a large single copy (LSC) region of 84795 bp, and a small single copy (SSC) region of 18247 bp. The cp genome encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 32 repeat sequences and 64 simple sequence repeats (SSR) were identified in the plastome, and an obvious A/T bias was observed in the majority of the SSRs detected. By comparing the T. ramosissima cp genome with those of four other Tamaricaceae species, a number of divergence hotspots were identified among these plastomes. Together with the SSRs and long repeats identified, these divergence hotspots could be developed as potential molecular markers facilitating species discrimination and evolutionary studies. Using plastome sequences, we re-investigated the phylogenetic relationship among 19 species, and T. ramosissima was found to be a sister of Tamarix chinensis.Conclusions: Taken together, our study provides valuable genomic resources to deepen the understanding of the plant photosynthetic mechanism and phylogenomics.

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