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

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.

Download Full-text

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

Plants ◽

10.3390/plants9060752 ◽

2020 ◽

Vol 9 (6) ◽

pp. 752

Author(s):

Furrukh Mehmood ◽

Abdullah ◽

Zartasha Ubaid ◽

Yiming Bao ◽

Peter Poczai ◽

...

Keyword(s):

Tandem Repeats ◽

De Novo ◽

Single Copy ◽

Large Single Copy ◽

Base Pairs ◽

Mutational Hotspots ◽

The Family ◽

Molecular Marker Development ◽

Small Genus ◽

Small Single Copy

Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635–85,765 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 plastomes, which revealed high similarities among the species. Comparative analysis among the Withania species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (rps4-trnT, trnM-atpE, and rps15) were sufficient to discriminate the Withania species included in current study.

Download Full-text

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

Frontiers in Genetics ◽

10.3389/fgene.2020.560368 ◽

2020 ◽

Vol 11 ◽

Author(s):

Peninah Cheptoo Rono ◽

Xiang Dong ◽

Jia-Xin Yang ◽

Fredrick Munyao Mutie ◽

Millicent A. Oulo ◽

...

Keyword(s):

Tandem Repeats ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Coding Region ◽

Base Pairs ◽

Protein Coding ◽

Chloroplast Genomes ◽

The Family ◽

Cp Genome

The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.

Download Full-text

Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

PeerJ ◽

10.7717/peerj.7500 ◽

2019 ◽

Vol 7 ◽

pp. e7500 ◽

Cited By ~ 4

Author(s):

Mikhail I. Schelkunov ◽

Maxim S. Nuraliev ◽

Maria D. Logacheva

Keyword(s):

Plant Species ◽

Mutation Rate ◽

Plastid Genome ◽

Gene Content ◽

High Mutation Rate ◽

Base Pairs ◽

Plastid Genomes ◽

The Family

Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

Download Full-text

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

Forests ◽

10.3390/f11111179 ◽

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.

Download Full-text

Nuclear and mitochondrial genomic resources for the meltwater stonefly, Lednia tumana Ricker, 1952 (Plecoptera: Nemouridae)

10.1101/360180 ◽

2018 ◽

Cited By ~ 1

Author(s):

Scott Hotaling ◽

Joanna L. Kelley ◽

David W. Weisrock

Keyword(s):

Aquatic Insects ◽

National Park ◽

De Novo ◽

Nuclear Genome ◽

Base Pairs ◽

Aquatic Biodiversity ◽

The Family ◽

Complete Form ◽

Alpine Streams ◽

The U.S

AbstractWith more than 3,700 described species, stoneflies (Order Plecoptera) are an important component of global aquatic biodiversity. The meltwater stonefly Lednia tumana (Ricker, 1952; Family Nemouridae) is endemic to alpine streams of Glacier National Park and has been petitioned for listing under the U.S. Endangered Species Act (ESA) due to climate change-induced loss of alpine glaciers and snowfields. Here, we present de novo assemblies of the nuclear (~520 million base pairs [bp]) and mitochondrial (15,014-bp) genomes for L. tumana. The L. tumana nuclear genome is the most complete stonefly genome reported to date, with ~71% of genes present in complete form and more than 4,600 contigs longer than 10-kilobases (kb). The L. tumana mitochondrial genome is the second for the family Nemouridae and the first from North America. Together, both genomes represent important foundational resources, setting the stage for future efforts to understand the evolution of L. tumana, stoneflies, and aquatic insects worldwide.

Download Full-text

The complete plastid genomes of four species from Brassicales

10.1101/458000 ◽

2018 ◽

Author(s):

Weixue Mu ◽

Ting Yang ◽

Xin Liu

Keyword(s):

Single Copy ◽

Data Sets ◽

Base Pairs ◽

Typical Structure ◽

Protein Coding ◽

Protein Coding Genes ◽

Phylogenetic Studies ◽

Plastid Genomes ◽

Cleome Rutidosperma ◽

Small Single Copy

AbstractBrassicales is a diverse angiosperm order with about 4,700 recognized species. Here, we assembled and described the complete plastid genomes from four species of Brassicales: Capparis urophylla F.Chun (Capparaceae), Carica papaya L. (Caricaceae), Cleome rutidosperma DC. (Cleomaceae), and Moringa oleifera Lam. (Moringaceae), including two plastid genomes newly assembled for two families (Capparaceae and Moringaceae). The four plastid genomes are 159,680 base pairs on average in length and encode 78 protein-coding genes. The genomes each contains a typical structure of a Large Single-Copy (LSC) region and a Small Single-Copy (SSC) region separated by two Inverted Repeat (IR) regions. We performed the maximum-likelihood (ML) phylogenetic analysis using three different data sets of 66 protein-coding genes (ntAll, ntNo3rd and AA). Our phylogenetic results from different dataset are congruent, and are consistent with previous phylogenetic studies of Brassiales.

Download Full-text

Plastome Diversity and Phylogenomic Relationships in Asteraceae

Plants ◽

10.3390/plants10122699 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2699

Author(s):

Joan Pere Pascual-Díaz ◽

Sònia Garcia ◽

Daniel Vitales

Keyword(s):

Ribosomal Rna ◽

Evolutionary Rate ◽

Plastid Dna ◽

Single Copy ◽

Phylogenomic Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Plastid Genomes ◽

The Family ◽

Rna Genes

Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae—as well as in the sister family Calyceraceae—lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family’s phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

Download Full-text

Plasmid-Encoded Anthranilate Synthase (TrpEG) inBuchnera aphidicola from Aphids of the Family Pemphigidae

Applied and Environmental Microbiology ◽

10.1128/aem.65.1.117-125.1999 ◽

1999 ◽

Vol 65 (1) ◽

pp. 117-125 ◽

Cited By ~ 32

Author(s):

Roeland C. H. J. Van Ham ◽

David Martínez-Torres ◽

Andrés Moya ◽

Amparo Latorre

Keyword(s):

Tandem Repeats ◽

Single Copy ◽

Essential Amino Acids ◽

Replication Initiation ◽

Anthranilate Synthase ◽

Broad Host Range ◽

Unexpected Finding ◽

Origin Of Replication ◽

The Family ◽

Putative Origin

ABSTRACT Buchnera aphidicola is an obligate intracellular symbiont of aphids. One of its proposed functions is the synthesis of essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. The genetic organization of the tryptophan pathway in Buchnera from proliferous aphids of the family Aphididae has previously been shown to reflect a capacity to overproduce this essential amino acid (C.-Y. Lai, L. Baumann, and P. Baumann, Proc. Natl. Acad. Sci. USA 91:3819–3823, 1994). This involved amplification of the genes for the first enzyme in the pathway, anthranilate synthase (TrpEG), on a low-copy-number plasmid. Here we report on the finding and molecular characterization of TrpEG-encoding plasmids in Buchnera from aphids of the distantly related family Pemphigidae. Buchnera fromTetraneura caerulescens contained a 3.0-kb plasmid (pBTc2) that carried a single copy of trpEG and resembledtrpEG plasmids of Buchnera from the Aphididae. The second plasmid (pBPs2), isolated from Buchnera ofPemphigus spyrothecae, contained a different replicon. It consisted of a putative origin of replication containing iterons and an open reading frame, designated repAC, which showed a high similarity to the gene encoding the replication initiation protein RepA of the RepA/C replicon from the broad-host-range IncA/C group of plasmids. The plasmid population was heterogeneous with respect to the number of tandem repeats of a 1.8-kb unit carryingrepAC1 , trpG, and remnants of trpE. The two principal forms consisted of either five or six copies of this repeat and a single-copy region carryingrepAC2 , the putative origin of replication, andtrpE. The unexpected finding of elements of the RepA/C replicon in previously characterized trpEG plasmids fromBuchnera of the Aphididae suggests that a replacement of replicons has occurred during the evolution of these plasmids, which may point to a common ancestry for all Buchnera trpEGamplifications.

Download Full-text

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

PeerJ ◽

10.7717/peerj.9552 ◽

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.

Download Full-text

Plastome Diversity and Phylogenomic Relationships in Asteraceae

10.20944/preprints202111.0167.v1 ◽

2021 ◽

Author(s):

Joan Pere Pascual-Díaz ◽

Sònia Garcia ◽

Daniel Vitales

Keyword(s):

Ribosomal Rna ◽

Evolutionary Rate ◽

Plastid Dna ◽

Single Copy ◽

Phylogenomic Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Plastid Genomes ◽

The Family ◽

Rna Genes

Plastid genomes are in general highly conserved given their slow evolutionary rate, thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridisation, both processes usually complicating systematic inferences. In this study, we have generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity, and repeat composition of these sequences. By comparing the whole plastome sequences obtained, we confirmed the double inversion located in the long single copy region, for most of the species analysed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also show that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae -as well as in the sister family Calyceraceae - are lacking the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, are overall consistent with the general consensus for the family’s phylogeny, while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

Download Full-text