scholarly journals Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiahui Sun ◽  
Yiheng Wang ◽  
Thomas Avery Garran ◽  
Ping Qiao ◽  
Mengli Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Heart Diseases ◽  
Plant Conservation ◽  
Intraspecific Diversity ◽  
Nucleotide Polymorphisms ◽  
Chloroplast Genomes ◽  
Leonurus Cardiaca ◽  
Rna Genes

Leonurus cardiaca has a long history of use in western herbal medicine and is applied for the treatment of gynaecological conditions, anxiety, and heart diseases. Because of its botanical relationship to the primary Chinese species, L. japonicus, and extensive medical indications that go beyond the traditional indications for the Chinese species, it is a promising medicinal resource. Therefore, the features of genetic diversity and variability in the species have been prioritized. To explore these issues, we sequenced the chloroplast genomes of 22 accessions of L. cardiaca from different geographical locations worldwide using high-throughput sequencing. The results indicate that L. cardiaca has a typical quadripartite structure and range from 1,51,236 bp to 1,51,831 bp in size, forming eight haplotypes. The genomes all contain 114 distinct genes, including 80 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Comparative analysis showed abundant diversity of single nucleotide polymorphisms (SNPs), indels, simple sequence repeats (SSRs) in 22 accessions. Codon usage showed highly similar results for L. cardiaca species. The phylogenetic and network analysis indicated 22 accessions forming four clades that were partly related to the geographical distribution. In summary, our study highlights the advantage of chloroplast genome with large data sets in intraspecific diversity evaluation and provides a new tool to facilitate medicinal plant conservation and domestication.

scholarly journals Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

scholarly journals Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

2021 ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background: Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing.Results: The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42-47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions: Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

scholarly journals Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

2020 ◽  
Author(s):  
yiheng wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In this study, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42-47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

scholarly journals Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

2020 ◽  
Author(s):  
yiheng wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background：Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing.Results: The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42-47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions: Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

scholarly journals Identification of DNA molecular markers by comparison of Pinus densiflora and Pinus sylvestris chloroplast genomes

2018 ◽  
Author(s):  
Sang-Chul Kim ◽  
Jei-Wan Lee ◽  
Seung-Hoon Baek ◽  
Ji-Young Ahn ◽  
Kyung-Nak Hong
Keyword(s):  
Molecular Markers ◽  
Pinus Sylvestris ◽  
Chloroplast Genome ◽  
Pinus Densiflora ◽  
Gene Annotation ◽  
Polymorphism Analysis ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Morphological Examination ◽  
Chloroplast Genomes

Background: Identifying and characterizing genetic variation can clarify the molecular basis of biological phenomena in plants. In particular, related or morphologically similar species can be distinguished by molecular markers. Pinus densiflora Siebold & Zucc. is a species that is distributed in the Korean peninsula, the Japanese archipelago, and China's Shandong and Manchu Provinces and has long been harvested for timber. However, it is difficult to distinguish P. densiflora from Pinus sylvestris L. both morphologically and phylogenetically. The complete chloroplast genome of P. densiflora has not yet been reported. In this study, we sequenced the P. densiflora chloroplast genome in order to identify the molecular markers that can be used to distinguish this species from P. sylvestris. Methods: Genomic DNA was extracted from P. densiflora samples obtained from the clone bank of the National Forest Seed Variety Center and was sequenced on an Ion Torrent platform. Filtered sequences were assembled with P. sylvestris sequences used as a reference and gene annotation was performed. The chloroplast genome sequences of the two species were aligned and the number and location of forward, reverse, complement and palindromic matches were determined. Single nucleotide polymorphisms (SNPs) and insertion/deletion mutations (Indels) were identified and analyzed by PCR. Results: The P. densiflora chloroplast genome consisted of circular double-stranded DNA with 119,835 bp compared to 119,758 bp for P. sylvestris. Between the two Pinus chloroplast genomes, we identified 73 SNPs and 171 Indels; two gene regions with amplification products ≤ 300 bp (rpoC1 and trnM-trnV) were validated as molecular markers. Discussion: PCR restriction fragment length polymorphism analysis revealed differences between P. sylvestris and P. densiflora at the molecular level. These differences can be used to distinguish between these two species, which is not possible by microscopy-based morphological examination.

scholarly journals Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya)

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Junling Cao ◽  
Dan Jiang ◽  
Zhenyu Zhao ◽  
Subo Yuan ◽  
Yujun Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complete Chloroplast Genome ◽  
Genomic Resources ◽  
Chinese Yam ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence ◽  
Simple Sequence

Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs). Seventy simple sequence repeats (SSRs) were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

scholarly journals Identification of DNA molecular markers by comparison of Pinus densiflora and Pinus sylvestris chloroplast genomes

2018 ◽  
Author(s):  
Sang-Chul Kim ◽  
Jei-Wan Lee ◽  
Seung-Hoon Baek ◽  
Ji-Young Ahn ◽  
Kyung-Nak Hong
Keyword(s):  
Molecular Markers ◽  
Pinus Sylvestris ◽  
Chloroplast Genome ◽  
Pinus Densiflora ◽  
Gene Annotation ◽  
Polymorphism Analysis ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Morphological Examination ◽  
Chloroplast Genomes

Background: Identifying and characterizing genetic variation can clarify the molecular basis of biological phenomena in plants. In particular, related or morphologically similar species can be distinguished by molecular markers. Pinus densiflora Siebold & Zucc. is a species that is distributed in the Korean peninsula, the Japanese archipelago, and China's Shandong and Manchu Provinces and has long been harvested for timber. However, it is difficult to distinguish P. densiflora from Pinus sylvestris L. both morphologically and phylogenetically. The complete chloroplast genome of P. densiflora has not yet been reported. In this study, we sequenced the P. densiflora chloroplast genome in order to identify the molecular markers that can be used to distinguish this species from P. sylvestris. Methods: Genomic DNA was extracted from P. densiflora samples obtained from the clone bank of the National Forest Seed Variety Center and was sequenced on an Ion Torrent platform. Filtered sequences were assembled with P. sylvestris sequences used as a reference and gene annotation was performed. The chloroplast genome sequences of the two species were aligned and the number and location of forward, reverse, complement and palindromic matches were determined. Single nucleotide polymorphisms (SNPs) and insertion/deletion mutations (Indels) were identified and analyzed by PCR. Results: The P. densiflora chloroplast genome consisted of circular double-stranded DNA with 119,835 bp compared to 119,758 bp for P. sylvestris. Between the two Pinus chloroplast genomes, we identified 73 SNPs and 171 Indels; two gene regions with amplification products ≤ 300 bp (rpoC1 and trnM-trnV) were validated as molecular markers. Discussion: PCR restriction fragment length polymorphism analysis revealed differences between P. sylvestris and P. densiflora at the molecular level. These differences can be used to distinguish between these two species, which is not possible by microscopy-based morphological examination.

scholarly journals Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8210
Author(s):  
Xueqing Zhao ◽  
Ming Yan ◽  
Yu Ding ◽  
Yan Huo ◽  
Zhaohe Yuan
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
High Throughput Sequencing ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Single Copy ◽  
Future Research ◽  
Sequencing Data ◽  
Complete Chloroplast Genome ◽  
Rna Genes

Background Sweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear. Methods In this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively. Results The complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.

scholarly journals Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6244 ◽  
Author(s):  
Simon Pfanzelt ◽  
Dirk C. Albach ◽  
K. Bernhard von Hagen
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Single Copy ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Nucleotide Polymorphisms ◽  
Sequence Comparisons ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence

Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.

scholarly journals Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

2019 ◽  
Author(s):  
Satsuki Tsuji ◽  
Atsushi Maruyama ◽  
Masaki Miya ◽  
Masayuki Ushio ◽  
Hirotoshi Sato ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Water Sample ◽  
Sanger Sequencing ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Dna Analysis ◽  
Environmental Dna ◽  
Intraspecific Diversity ◽  
Survey Method ◽  
Intraspecific Genetic Diversity

AbstractEnvironmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high-throughput sequencing, denoising was performed using two of the most widely used denoising packages, UNOISE3 and DADA2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (UNOISE3) and 41 (DADA2) haplotypes were detected by eDNA analysis. When DADA2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. This study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large-scale capture-based conventional methods, suggesting that it could become a more efficient survey method for investigating intraspecific genetic diversity in the field.

Sign in / Sign up

Export Citation Format

Share Document