“…The program GetOrganelle produced two distinct chloroplast genome assemblies, both of 155,895 bp. This corresponds well to the 155,871 bp size of the first published chloroplast genome of D. stramonium and to the 155,884 bp size from a pair of more recently published D. stramonium chloroplast assemblies [ 61 , 62 ]. Following annotation with GeSeq, we noticed that our two assemblies differed from one another only in the orientation of their small single-copy region, but otherwise displayed the typical quadripartite structure of most angiosperm plastid genomes (Fig.…”
Section: Resultssupporting
confidence: 81%
“…Independent pairwise alignments of the small single-copy region and of the large single-copy region with both flanking inverted-region regions from our two genomes show no further polymorphisms. Because the assemblies from the more recent study by De la Cruz et al have not been released, we aligned the complete sequence of the original assembly from the earlier Yang et al publication to our assembly and observed a 99.97% identity [ 61 , 62 ]. Fig.…”
Background
Datura stramonium (Jimsonweed) is a medicinally and pharmaceutically important plant in the nightshade family (Solanaceae) known for its production of various toxic, hallucinogenic, and therapeutic tropane alkaloids. Recently, we published a tissue-culture based transformation protocol for D. stramonium that enables more thorough functional genomics studies of this plant. However, the tissue culture process can lead to undesirable phenotypic and genomic consequences independent of the transgene used. Here, we have assembled and annotated a draft genome of D. stramonium with a focus on tropane alkaloid biosynthetic genes. We then use mRNA sequencing and genome resequencing of transformants to characterize changes following tissue culture.
Results
Our draft assembly conforms to the expected 2 gigabasepair haploid genome size of this plant and achieved a BUSCO score of 94.7% complete, single-copy genes. The repetitive content of the genome is 61%, with Gypsy-type retrotransposons accounting for half of this. Our gene annotation estimates the number of protein-coding genes at 52,149 and shows evidence of duplications in two key alkaloid biosynthetic genes, tropinone reductase I and hyoscyamine 6 β-hydroxylase. Following tissue culture, we detected only 186 differentially expressed genes, but were unable to correlate these changes in expression with either polymorphisms from resequencing or positional effects of transposons.
Conclusions
We have assembled, annotated, and characterized the first draft genome for this important model plant species. Using this resource, we show duplications of genes leading to the synthesis of the medicinally important alkaloid, scopolamine. Our results also demonstrate that following tissue culture, mutation rates of transformed plants are quite high (1.16 × 10− 3 mutations per site), but do not have a drastic impact on gene expression.
“…The program GetOrganelle produced two distinct chloroplast genome assemblies, both of 155,895 bp. This corresponds well to the 155,871 bp size of the first published chloroplast genome of D. stramonium and to the 155,884 bp size from a pair of more recently published D. stramonium chloroplast assemblies [ 61 , 62 ]. Following annotation with GeSeq, we noticed that our two assemblies differed from one another only in the orientation of their small single-copy region, but otherwise displayed the typical quadripartite structure of most angiosperm plastid genomes (Fig.…”
Section: Resultssupporting
confidence: 81%
“…Independent pairwise alignments of the small single-copy region and of the large single-copy region with both flanking inverted-region regions from our two genomes show no further polymorphisms. Because the assemblies from the more recent study by De la Cruz et al have not been released, we aligned the complete sequence of the original assembly from the earlier Yang et al publication to our assembly and observed a 99.97% identity [ 61 , 62 ]. Fig.…”
Background
Datura stramonium (Jimsonweed) is a medicinally and pharmaceutically important plant in the nightshade family (Solanaceae) known for its production of various toxic, hallucinogenic, and therapeutic tropane alkaloids. Recently, we published a tissue-culture based transformation protocol for D. stramonium that enables more thorough functional genomics studies of this plant. However, the tissue culture process can lead to undesirable phenotypic and genomic consequences independent of the transgene used. Here, we have assembled and annotated a draft genome of D. stramonium with a focus on tropane alkaloid biosynthetic genes. We then use mRNA sequencing and genome resequencing of transformants to characterize changes following tissue culture.
Results
Our draft assembly conforms to the expected 2 gigabasepair haploid genome size of this plant and achieved a BUSCO score of 94.7% complete, single-copy genes. The repetitive content of the genome is 61%, with Gypsy-type retrotransposons accounting for half of this. Our gene annotation estimates the number of protein-coding genes at 52,149 and shows evidence of duplications in two key alkaloid biosynthetic genes, tropinone reductase I and hyoscyamine 6 β-hydroxylase. Following tissue culture, we detected only 186 differentially expressed genes, but were unable to correlate these changes in expression with either polymorphisms from resequencing or positional effects of transposons.
Conclusions
We have assembled, annotated, and characterized the first draft genome for this important model plant species. Using this resource, we show duplications of genes leading to the synthesis of the medicinally important alkaloid, scopolamine. Our results also demonstrate that following tissue culture, mutation rates of transformed plants are quite high (1.16 × 10− 3 mutations per site), but do not have a drastic impact on gene expression.
“…In our study, 35 repeat sequences were detected in PMA cp genome, which was five fewer than the number of repeats detected in the cp genome of PIX. The lengths of most repeats in the two species (77.1% in PMA and 77.5% in PIX) were between 30 and 39 bp, a finding consistent with that of most other Physaleae cp genomes [50,58]. Interestingly, most of the repeats in the cp genomes of the two species were distributed in the LSC region, whereas the number of repeats distributed in the PCG was more than that in the IGS and tRNA.…”
Physalis macrophysa (PMA) and Physalis ixocarpa (PIX) have significant economic, medicinal, and ornamental value and are often used in the fields of edible fruits, medicinal herbs, and ornamental plants. In the present study, we obtained the complete chloroplast (cp) genome sequences of PMA and PIX, compared to the cp genome sequences of 10 Physalis species, and constructed the phylogenetic tree among the tribe Physaleae. The results showed that the cp genomes of PMA and PIX consisted of a large single copy (LSC) region (87,115 bp and 87,103 bp, respectively), a small single copy (SSC) region (18,412 bp and 18,420 bp, respectively), and a pair of same-length inverted-repeat (IRa and IRb) regions (25,604 bp and 25,674 bp, respectively). The two species contained 132 genes, including 87 encoding proteins, eight encoding ribosomal RNAs (rRNAs), and 37 encoding transfer RNAs (tRNAs), which indicated that the two species have strong similarities with respect to genome structure and gene content. PMA and PIX contained repeat sequences (35 and 40, respectively) and simple-sequence repeats (SSRs) (61 and 60, respectively). Nine regions with considerable nucleotide divergence were found, most of which were located in the LSC and SSC regions. The gene selective pressure analysis indicated that eight genes were affected by positive selection, the Ka/Ks values of which were greater than one. Our phylogenetic results indicated that PMA and PIX had the closest genetic relationship and are closely adjacent to Physalis philadelphica (PPH) in the subtribe Physalinae. Our analysis of the cp genomes in both Physalis species will be beneficial for further research into species identification, phylogeny, evolution, and the potential for germplasm resource exploitation in Physalis.
“…The size of the P. angulata var. villosa plastome (156,898 bp) was comparable to that of other sequenced plastomes of members of the Solanaceae, being longer than those of Datura stramonium [ 46 ], Solanum brevicaule [ 47 ] and Withania somnifera [ 48 ], but shorter than those of Iochroma ellipticum (GenBank accession: KU323367), P. pubescens [ 45 ] and Eriolarynx fasciculata (GenBank accession: KU306938). The GC content of the P. angulata var.…”
Physalis angulata var. villosa, rich in withanolides, has been used as a traditional Chinese medicine for many years. To date, few extensive molecular studies of this plant have been conducted. In the present study, the plastome of P. angulata var. villosa was sequenced, characterized and compared with that of other Physalis species, and a phylogenetic analysis was conducted in the family Solanaceae. The plastome of P. angulata var. villosa was 156,898 bp in length with a GC content of 37.52%, and exhibited a quadripartite structure typical of land plants, consisting of a large single-copy (LSC, 87,108 bp) region, a small single-copy (SSC, 18,462 bp) region and a pair of inverted repeats (IR: IRA and IRB, 25,664 bp each). The plastome contained 131 genes, of which 114 were unique and 17 were duplicated in IR regions. The genome consisted of 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. A total of 38 long, repeat sequences of three types were identified in the plastome, of which forward repeats had the highest frequency. Simple sequence repeats (SSRs) analysis revealed a total of 57 SSRs, of which the T mononucleotide constituted the majority, with most of SSRs being located in the intergenic spacer regions. Comparative genomic analysis among nine Physalis species revealed that the single-copy regions were less conserved than the pair of inverted repeats, with most of the variation being found in the intergenic spacer regions rather than in the coding regions. Phylogenetic analysis indicated a close relationship between Physalis and Withania. In addition, Iochroma, Dunalia, Saracha and Eriolarynx were paraphyletic, and clustered together in the phylogenetic tree. Our study published the first sequence and assembly of the plastome of P. angulata var. villosa, reported its basic resources for evolutionary studies and provided an important tool for evaluating the phylogenetic relationship within the family Solanaceae.
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