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 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 Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qiu-jie Li ◽  
Na Su ◽  
Ling Zhang ◽  
Ru-chang Tong ◽  
Xiao-hui Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Medicinal Value ◽  
Cp Genome

AbstractPulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.

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 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 The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

2021 ◽  
Vol 51 (3) ◽  
pp. 326-331
Author(s):  
Sung-Dug OH ◽  
Seong-Kon LEE ◽  
Doh-Won YUN ◽  
Hyeon-Jin SUN ◽  
Hong-Gyu KANG ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Single Copy ◽  
Phylogenetic Position ◽  
Nucleotide Polymorphisms ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Intraspecific Variations

The complete chloroplast genome of Zoysia macrostachya Franch. & Sav. isolated in Korea is 135,902 bp long (GC ratio is 38.4%) and has four subregions; 81,546 bp of large single-copy (36.3%) and 12,586 bp of small single-copy (32.7%) regions are separated by 20,885 bp of inverted repeat (44.1%) regions, including 130 genes (83 protein-coding genes, eight rRNAs, and 39 tRNAs). Thirty-nine single nucleotide polymorphisms and 11 insertions and deletion (INDEL) regions were identified from two Z. macrostachya chloroplast genomes, the smallest among other Zoysia species. Phylogenetic trees show that two Z. macrostachya chloroplast genomes are clustered into a single clade. However, we found some incongruency with regard to the phylogenetic position of the Z. macrostachya clade. Our chloroplast genome provides insights into intraspecific variations and species delimitation issues pertaining to the Zoysia species.

scholarly journals The complete chloroplast genome of Glycyrrhiza uralensis Fisch. isolated in Korea (Fabaceae)

2021 ◽  
Vol 51 (4) ◽  
pp. 353-362
Author(s):  
Mi-Hee KIM ◽  
Suhyeon PARK ◽  
Junho LEE ◽  
Jinwook BAEK ◽  
Jongsun PARK ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Trees ◽  
Glycyrrhiza Uralensis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Glycyrrhiza Uralensis Fisch ◽  
Insertion And Deletion ◽  
Chloroplast Genomes ◽  
Intraspecific Variations

The chloroplast genome of Glycyrrhiza uralensis Fisch was sequenced to investigate intraspecific variations on the chloroplast genome. Its length is 127,689 bp long (34.3% GC ratio) with atypical structure of chloroplast genome, which is congruent to those of Glycyrrhiza genus. It includes 110 genes (76 protein-coding genes, four rRNAs, and 30 tRNAs). Intronic region of ndhA presented the highest nucleotide diversity based on the six G. uralenesis chloroplast genomes. A total of 150 single nucleotide polymorphisms and 10 insertion and deletion (INDEL) regions were identified from the six G. uralensis chloroplast genomes. Phylogenetic trees show that the six chloroplast genomes of G. uralensis formed the two clades, requiring additional studies to understand it.

scholarly journals Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242591
Author(s):  
Jie Li ◽  
Guang-ying Ye ◽  
Hai-lin Liu ◽  
Zai-hua Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Intergenic Spacer ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Protein Coding ◽  
Important Species ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Mutational Hotspots

Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A. moschatus, A. manihot and A. sagittifolius, and compared with A. esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A. esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A. moschatus and A. manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus, such as start-psbA, atpB-rbcL, petD-exon2-rpoA, clpP-intron1 and clpP-exon2.These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus. Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus.

scholarly journals The Complete Chloroplast Genome Sequence of Four Plant Species, Their SSR Identification and Phylogenetic Analysis

2021 ◽  
Author(s):  
Yueyi Zhu ◽  
Xianwen Zhang ◽  
Guopeng Li ◽  
Jiqian Xiang ◽  
Jinghua Su ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Markers ◽  
Chloroplast Genome ◽  
Simple Sequence Repeats ◽  
Genetic Information ◽  
Phylogenetic Trees ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence ◽  
Simple Sequence

The chloroplast genome is conservative and stable, which can be employed to resolve genotypes. Currently, published nuclear sequences and molecular markers failed to differentiate the species from taxa robustly, including Machilus leptophylla, Hanceola exserta, Rubus bambusarum, and Rubus henryi. In this study, the four chloroplast genomes were characterized, and then their simple sequence repeats (SSRs) and phylogenetic positions were analyzed. The results demonstrated the four chloroplast genomes consisted of 152.624 kb, 153.296kb, 156.309 kb, and 158.953 kb in length, involving 124, 130, 129, and 131 genes, respectively. Moreover, the chloroplast genomes contained typical four regions. Six classes of SSR were identified from the four chloroplast genomes, in which mononucleotide was the class with the most members. The types of the repeats were various within individual classes of SSR. Phylogenetic trees indicated that M. leptophylla was clustered with M. yunnanensis, and H. exserta was confirmed under family Ocimeae. Additionally, R. bambusarum and R. henryi were clustered together, whereas they did not belong to the same species due to the differing SSR features. This research would provide evidence for resolving the species and contributed new genetic information for further study.

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.

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