Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus Dalbergia (Fabacaeae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood

Abstract The genus Dalbergia contains more than 120 species several of which are trees that produce traditional medicines and extremely high value timber commonly referred to as rosewood. Due to the rarity of these species in the wild, the high value of the timber, and a growing international illicit trade CITES has listed the entire genus in appendix II and the species D. nigra in appendix I because it is considered threatened with extinction. Given this and the fact that species or even genus level determination is nearly impossible from cut timber alternative molecular methods are needed to identify and track intercepted rosewood. In order to improve molecular identification of rosewood, we sequenced and assembled eight chloroplast genomes including D. nigra as well as conducted comparative analyses with all other available chloroplast genomes in Dalbergia and closely related lineages. From these analyses numerous repeats including simple sequence repeats (SSR) and conserved nucleotide polymorphisms unique to subclades within the genus were detected. From phylogenetic analysis using the CDS of 77 coding genes the groups Siam rosewood and scented rosewood based mainly on wood characteristics were supported as monophyletic. In addition, several instances of paraphyly and polyphyly resulting from mismatch between taxonomic determinations and phylogenetic tree topology were identified. Ultimately, the highly variable regions in the chloroplast genomes will provide useful plastid markers for further studies regarding the identification, phylogeny, and population genetics of Dalbergia species including those frequently intercepted in illegal trade.

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

Scientific Reports ◽

10.1038/s41598-020-76699-7 ◽

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.

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Generation of Chloroplast Molecular Markers to Differentiate Sophora toromiro and Its Hybrids as a First Approach to Its Reintroduction in Rapa Nui (Easter Island)

Plants ◽

10.3390/plants10020342 ◽

2021 ◽

Vol 10 (2) ◽

pp. 342

Author(s):

Ignacio Pezoa ◽

Javier Villacreses ◽

Miguel Rubilar ◽

Carolina Pizarro ◽

María Jesús Galleguillos ◽

...

Keyword(s):

De Novo ◽

Nucleotide Polymorphisms ◽

Rapa Nui ◽

Single Nucleotide ◽

Chloroplast Genomes ◽

In The Wild ◽

Ssr Loci ◽

Hybrid Lines ◽

First Time ◽

Private Collections

Sophora toromiro is an endemic tree of Rapa Nui with religious and cultural relevance that despite being extinct in the wild, still persists in botanical gardens and private collections around the world. The authenticity of some toromiro trees has been questioned because the similarities among hybrid lines leads to misclassification of the species. The conservation program of toromiro has the objective of its reinsertion into Rapa Nui, but it requires the exact genotyping and certification of the selected plants in order to efficiently reintroduce the species. In this study, we present for the first time the complete chloroplast genome of S. toromiro and four other Sophora specimens, which were sequenced de-novo and assembled after mapping the raw reads to a chloroplast database. The length of the chloroplast genomes ranges from 154,239 to 154,473 bp. A total of 130–143 simple sequence repeats (SSR) loci and 577 single nucleotide polymorphisms (SNPs) were identified.

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

BioMed Research International ◽

10.1155/2018/6293847 ◽

2018 ◽

Vol 2018 ◽

pp. 1-11 ◽

Cited By ~ 15

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.

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The Complete Chloroplast Genome Sequences of Eight Fagopyrum Species: Insights Into Genome Evolution and Phylogenetic Relationships

Frontiers in Plant Science ◽

10.3389/fpls.2021.799904 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yu Fan ◽

Ya’nan Jin ◽

Mengqi Ding ◽

Yu Tang ◽

Jianping Cheng ◽

...

Keyword(s):

Light Adaptation ◽

Gc Content ◽

Taxonomic Status ◽

Evolutionary Analysis ◽

Variable Regions ◽

Complete Chloroplast Genome ◽

Complex Phenotypes ◽

Chloroplast Genomes ◽

Flower Type ◽

Simple Sequence

Buckwheat (Fagopyrum genus, Polygonaceae), is an annual or perennial, herbaceous or semi-shrub dicotyledonous plant. There are mainly three cultivated buckwheat species, common buckwheat (Fagopyrum esculentum) is widely cultivated in Asia, Europe, and America, while Tartary buckwheat (F. tataricum) and F. cymosum (also known as F. dibotrys) are mainly cultivated in China. The genus Fagopyrum is taxonomically confusing due to the complex phenotypes of different Fagopyrum species. In this study, the chloroplast (cp) genomes of three Fagopyrum species, F. longistylum, F. leptopodum, F. urophyllum, were sequenced, and five published cp genomes of Fagopyrum were retrieved for comparative analyses. We determined the sequence differentiation, repeated sequences of the cp genomes, and the phylogeny of Fagopyrum species. The eight cp genomes ranged, gene number, gene order, and GC content were presented. Most of variations of Fagopyrum species cp genomes existed in the LSC and SSC regions. Among eight Fagopyrum chloroplast genomes, six variable regions (ndhF-rpl32, trnS-trnG, trnC, trnE-trnT, psbD, and trnV) were detected as promising DNA barcodes. In addition, a total of 66 different SSR (simple sequence repeats) types were found in the eight Fagopyrum species, ranging from 8 to 16 bp. Interestingly, many SSRs showed significant differences especially in some photosystem genes, which provided valuable information for understanding the differences in light adaptation among different Fagopyrum species. Genus Fagopyrum has shown a typical branch that is distinguished from the Rumex, Rheum, and Reynoutria, which supports the unique taxonomic status in Fagopyrum among the Polygonaceae. In addition, phylogenetic analysis based on the cp genomes strongly supported the division of eight Fagopyrum species into two independent evolutionary directions, suggesting that the separation of cymosum group and urophyllum group may be earlier than the flower type differentiation in Fagopyrum plants. The results of the chloroplast-based phylogenetic tree were further supported by the matK and Internal Transcribed Spacer (ITS) sequences of 17 Fagopyrum species, which may help to further anchor the taxonomic status of other members in the urophyllum group in Fagopyrum. This study provides valuable information and high-quality cp genomes for identifying species and evolutionary analysis for future Fagopyrum research.

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Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

Plants ◽

10.3390/plants9020286 ◽

2020 ◽

Vol 9 (2) ◽

pp. 286 ◽

Cited By ~ 4

Author(s):

Dong-Mei Li ◽

Gen-Fa Zhu ◽

Ye-Chun Xu ◽

Yuan-Jun Ye ◽

Jin-Mei Liu

Keyword(s):

Species Identification ◽

Phylogenetic Relationships ◽

Single Copy ◽

Nucleotide Polymorphisms ◽

Comparative Analyses ◽

Alpinia Oxyphylla ◽

Phylogenetic Studies ◽

Chloroplast Genomes ◽

The Family ◽

Medicinal Properties

Alpinia katsumadai (A. katsumadai), Alpinia oxyphylla (A. oxyphylla) and Alpinia pumila (A. pumila), which belong to the family Zingiberaceae, exhibit multiple medicinal properties. The chloroplast genome of a non-model plant provides valuable information for species identification and phylogenetic analysis. Here, we sequenced three complete chloroplast genomes of A. katsumadai, A. oxyphylla sampled from Guangdong and A. pumila, and analyzed the published chloroplast genomes of Alpinia zerumbet (A. zerumbet) and A. oxyphylla sampled from Hainan to retrieve useful chloroplast molecular resources for Alpinia. The five Alpinia chloroplast genomes possessed typical quadripartite structures comprising of a large single copy (LSC, 87,248–87,667 bp), a small single copy (SSC, 15,306–18,295 bp) and a pair of inverted repeats (IR, 26,917–29,707 bp). They had similar gene contents, gene orders and GC contents, but were slightly different in the numbers of small sequence repeats (SSRs) and long repeats. Interestingly, fifteen highly divergent regions (rpl36, ycf1, rps15, rpl22, infA, psbT-psbN, accD-psaI, petD-rpoA, psaC-ndhE, ccsA-ndhD, ndhF-rpl32, rps11-rpl36, infA-rps8, psbC-psbZ, and rpl32-ccsA), which could be suitable for species identification and phylogenetic studies, were detected in the Alpinia chloroplast genomes. Comparative analyses among the five chloroplast genomes indicated that 1891 mutational events, including 304 single nucleotide polymorphisms (SNPs) and 118 insertion/deletions (indels) between A. pumila and A. katsumadai, 367 SNPs and 122 indels between A. pumila and A. oxyphylla sampled from Guangdong, 331 SNPs and 115 indels between A. pumila and A. zerumbet, 371 SNPs and 120 indels between A. pumila and A. oxyphylla sampled from Hainan, and 20 SNPs and 23 indels between the two accessions of A. oxyphylla, were accurately located. Additionally, phylogenetic relationships based on SNP matrix among 28 whole chloroplast genomes showed that Alpinia was a sister branch to Amomum in the family Zingiberaceae, and that the five Alpinia accessions were divided into three groups, one including A. pumila, another including A. zerumbet and A. katsumadai, and the other including two accessions of A. oxyphylla. In conclusion, the complete chloroplast genomes of the three medicinal Alpinia species in this study provided valuable genomic resources for further phylogeny and species identification in the family Zingiberaceae.

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Complete Chloroplast Genome Sequences of Three Aroideae Species (Araceae): Lights into Selective Pressure, Marker Development and Phylogenetic Relationships

10.21203/rs.3.rs-602156/v1 ◽

2021 ◽

Author(s):

Bicong Li ◽

Tao Liu ◽

Asjad Ali ◽

Yao Xiao ◽

Nan Shan ◽

...

Keyword(s):

Dna Barcodes ◽

Protein Coding ◽

Variable Regions ◽

Complete Chloroplast Genome ◽

Protein Coding Genes ◽

Chloroplast Genomes ◽

Xanthosoma Sagittifolium ◽

Close Relationship ◽

Relationship Of ◽

First Time

Abstract Background : Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are taxonomically perplexing due to shared interspecific morphological traits and variation.Result : This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily.Conclusion : These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.

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Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats

Genome ◽

10.1139/g97-014 ◽

1997 ◽

Vol 40 (1) ◽

pp. 104-110 ◽

Cited By ~ 52

Author(s):

J. Provan ◽

G. Corbett ◽

W. Powell ◽

J. W. McNicol

Keyword(s):

Simple Sequence Repeats ◽

Wild Rice ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Cultivated Rice ◽

Chloroplast Markers ◽

Chloroplast Genomes ◽

In The Wild ◽

Wild Accessions ◽

Simple Sequence

Short mononucleotide repeats analogous to nuclear microsatellites or simple sequence repeats (SSRs) have been identified in chloroplast genomes. Primers flanking mononucleotide repeats in the fully sequenced rice chloroplast genome have been used in conjunction with PCR to amplify genomic DNA from 42 wild rice accessions. The amplification products exhibited length polymorphism, which allowed the levels of chloroplast variability detected to be quantified. Seven primer pairs that amplified products from different regions of the rice chloroplast were used, five of which also amplified polymorphic products in cultivated rice (Oryza sativa). Diversity values ranged from 0.5224 ± 0.0845 (SE) to 0.8298 ± 0.0085 in the wild accessions, which was higher than that detected in the O. sativa accessions. Both intra- and inter-specific polymorphism was detected, and the extent of chloroplast genomic differentiation based on chloroplast simple sequence repeat (cpSSR) assays was quantified using the RST statistic. Primers designed to amplify cpSSRs in O. sativa can also be used to generate polymorphic chloroplast markers in related taxa. The potential of using cpSSR to trace the origin of rice polyploid species is discussed.Key words: rice, chloroplast, simple sequence repeat, microsatellites.

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Development of Molecular Markers for Predicting Radish (Raphanus sativus) Flesh Color Based on Polymorphisms in the RsTT8 Gene

Plants ◽

10.3390/plants10071386 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1386

Author(s):

Soyun Kim ◽

Keunho Yun ◽

Han Yong Park ◽

Ju Young Ahn ◽

Ju Yeon Yang ◽

...

Keyword(s):

Molecular Markers ◽

Raphanus Sativus ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cosmetic Industry ◽

Natural Colorants ◽

Health Promoting ◽

Primer Sets ◽

Red Radish ◽

Simple Sequence

Red radish (Raphanus sativus L.) cultivars are a rich source of health-promoting anthocyanins and are considered a potential source of natural colorants used in the cosmetic industry. However, the development of red radish cultivars via conventional breeding is very difficult, given the unusual inheritance of the anthocyanin accumulation trait in radishes. Therefore, molecular markers linked with radish color are needed to facilitate radish breeding. Here, we characterized the RsTT8 gene isolated from four radish genotypes with different skin and flesh colors. Sequence analysis of RsTT8 revealed a large number of polymorphisms, including insertion/deletions (InDels), single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs), between the red-fleshed and white-fleshed radish cultivars. To develop molecular markers on the basis of these polymorphisms for discriminating between radish genotypes with different colored flesh tissues, we designed four primer sets specific to the RsTT8 promoter, InDel, SSR, and WD40/acidic domain (WD/AD), and tested these primers on a diverse collection of radish lines. Except for the SSR-specific primer set, all primer sets successfully discriminated between red-fleshed and white-fleshed radish lines. Thus, we developed three molecular markers that can be efficiently used for breeding red-fleshed radish cultivars.

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Comparative analyses of the complete chloroplast genomes of nymphoides and menyanthes species (menyanthaceae)

Aquatic Botany ◽

10.1016/j.aquabot.2019.05.001 ◽

2019 ◽

Vol 156 ◽

pp. 73-81 ◽

Cited By ~ 1

Author(s):

Ann W. Njuguna ◽

Zhi-Zhong Li ◽

Josphat K. Saina ◽

Justus M. Munywoki ◽

Andrew W. Gichira ◽

...

Keyword(s):

Comparative Analyses ◽

Chloroplast Genomes

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A systematic comparison of eight new plastome sequences from Ipomoea L

PeerJ ◽

10.7717/peerj.6563 ◽

2019 ◽

Vol 7 ◽

pp. e6563

Author(s):

Jianying Sun ◽

Xiaofeng Dong ◽

Qinghe Cao ◽

Tao Xu ◽

Mingku Zhu ◽

...

Keyword(s):

Comparative Analysis ◽

Next Generation Sequencing ◽

Chloroplast Genome ◽

Dna Sequences ◽

Repetitive Sequences ◽

Single Copy ◽

Next Generation ◽

Variable Regions ◽

Chloroplast Genomes ◽

Generation Sequencing

Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.

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