Comparative Chloroplast Genome Analysis of Rhubarb Botanical Origins and the Development of Specific Identification Markers

Rhubarb is an important ingredient in traditional Chinese medicine known as Rhei radix et rhizome. However, this common name refers to three different botanical species with different pharmacological effects. To facilitate the genetic identification of these three species for their more precise application in Chinese medicine we here want to provide chloroplast sequences with specific identification sites that are easy to amplify. We therefore sequenced the complete chloroplast genomes of all three species and then screened those for suitable sequences describing the three species. The length of the three chloroplast genomes ranged from 161,053 bp to 161,541 bp, with a total of 131 encoded genes including 31 tRNA, eight rRNA and 92 protein-coding sequences. The simple repeat sequence analysis indicated the differences existed in these species, phylogenetic analyses showed the chloroplast genome can be used as an ultra-barcode to distinguish the three botanical species of rhubarb, the variation of the non-coding regions is higher than that of the protein coding regions, and the variations in single-copy region are higher than that in inverted repeat. Twenty-one specific primer pairs were designed and eight specific identification sites were experimentally confirmed that can be used as special DNA barcodes for the identification of the three species based on the highly variable regions. This study provides a molecular basis for precise medicinal plant selection, and supplies the groundwork for the next investigation of the closely related Rheum species comparing and correctly identification on these important medicinal species.

Download Full-text

Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽

10.3390/f12060744 ◽

2021 ◽

Vol 12 (6) ◽

pp. 744

Author(s):

Yunyan Zhang ◽

Yongjing Tian ◽

David Y. P. Tng ◽

Jingbo Zhou ◽

Yuntian Zhang ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Eastern China ◽

Chloroplast Microsatellites ◽

Endangered Tree ◽

Protein Coding ◽

Intergenic Spacers ◽

Chloroplast Genomes ◽

Phylogenetic Implications ◽

Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

Download Full-text

Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽

10.1186/s12864-021-07394-8 ◽

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.

Download Full-text

Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

Plants ◽

10.3390/plants9091116 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1116 ◽

Cited By ~ 1

Author(s):

Xue-Li Zhao ◽

Zhang-Ming Zhu

Keyword(s):

Phylogenetic Analyses ◽

Evolutionary Process ◽

Rrna Genes ◽

Trna Genes ◽

Sister Relationship ◽

Protein Coding ◽

Variable Regions ◽

Chloroplast Genomes ◽

Distinct Genus ◽

Relationship Of

Taxonomic and phylogenetic relationships of Christia, Urariopsis, Uraria and related genera within the tribe Desmodieae (Fabaceae: Papilionoideae) have long been controversial. Here, we report the complete chloroplast (cp) genomes of Christia vespertilionis and Urariopsis brevissima and perform comparative and phylogenetic analyses with Uraria lagopodioides and other relatives in the Desmodieae. The cp genomes of C. vespertilionis and U. brevissima are 149,656 and 149,930 bp long, with 128 unique genes (83 protein-coding genes, 37 tRNA genes and 8 rRNA genes), respectively. Comparative analyses revealed 95-129 simple sequence repeats (SSRs) and eleven highly variable regions (trnK-rbcL, rbcL-atpB, ndhJ-trnF, trnL-trnT, psbD-rpoB, accD-cemA, petA-psbL, psbE-petL, rps11-rps19, ndhF-ccsA, and rps15-ycf1) among six Desmodieae species. Phylogenetic analyses clearly resolved two subtribes (Desmodiinae and Lespedezinae) of Desmodieae as monophyletic, and the newly reported C. vespertilionis and U. brevissima clustered in subtribe Desmodiinae. A sister relationship of C. vespertilionis to U. lagopodioides was supported. Evidence was presented to support the treatment of Urariopsis as a distinct genus rather than in synonymy with Uraria. The results provide valuable information for further studies on species delimitation, phylogenetics, population genetics, and the evolutionary process of speciation in the Desmodieae.

Download Full-text

Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

10.21203/rs.3.rs-58796/v3 ◽

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.

Download Full-text

The complete chloroplast genome sequence of strawberry (Fragaria × ananassaDuch.) and comparison with related species of Rosaceae

PeerJ ◽

10.7717/peerj.3919 ◽

2017 ◽

Vol 5 ◽

pp. e3919 ◽

Cited By ~ 27

Author(s):

Hui Cheng ◽

Jinfeng Li ◽

Hong Zhang ◽

Binhua Cai ◽

Zhihong Gao ◽

...

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Rrna Genes ◽

Trna Genes ◽

Illumina Hiseq ◽

Complete Chloroplast Genome ◽

Coding Regions ◽

Chloroplast Genomes

Compared with other members of the family Rosaceae, the chloroplast genomes ofFragariaspecies exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing ofFragariaspecies is needed. In this study, we sequenced the complete chloroplast genome ofF. × ananassa‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination ofde novoassembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of theF. × ananassa‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallestFragariachloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content inFragaria, particularly among three octoploid strawberries which wereF. × ananassa‘Benihoppe’,F.chiloensis(GP33) andF.virginiana(O477). However, when the sequences of the coding and non-coding regions ofF. × ananassa‘Benihoppe’ were compared in detail with those ofF.chiloensis(GP33) andF.virginiana(O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK,trnS-trnG,atpF-atpH,trnC-petN,trnT-psbDandtrnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genusFragaria.

Download Full-text

Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae

Plants ◽

10.3390/plants9060737 ◽

2020 ◽

Vol 9 (6) ◽

pp. 737 ◽

Cited By ~ 2

Author(s):

Abdullah ◽

Claudia L. Henriquez ◽

Furrukh Mehmood ◽

Iram Shahzadi ◽

Zain Ali ◽

...

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Trna Genes ◽

Protein Coding ◽

Chloroplast Genomes ◽

History Of ◽

And Bisexual ◽

Contraction And Expansion

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

Download Full-text

Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

10.21203/rs.3.rs-58796/v1 ◽

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.

Download Full-text

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 ◽

10.1371/journal.pone.0242591 ◽

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.

Download Full-text

Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Forests ◽

10.3390/f12070861 ◽

2021 ◽

Vol 12 (7) ◽

pp. 861

Author(s):

Huijuan Zhou ◽

Xiaoxiao Gao ◽

Keith Woeste ◽

Peng Zhao ◽

Shuoxin Zhang

Keyword(s):

Comparative Analysis ◽

Phylogenetic Analyses ◽

Single Copy ◽

Nucleotide Substitutions ◽

Protein Coding ◽

Variable Regions ◽

Chloroplast Genomes ◽

Cp Genome ◽

Species Hybrids ◽

Rna Genes

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.

Download Full-text

Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae)

Genes ◽

10.3390/genes10010023 ◽

2019 ◽

Vol 10 (1) ◽

pp. 23 ◽

Cited By ~ 22

Author(s):

Ji-Hyeon Jeon ◽

Seung-Chul Kim

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Rosa Multiflora ◽

Protein Coding ◽

Short Branch ◽

Chloroplast Genomes ◽

Genome Wide ◽

Branch Lengths ◽

Genome Wide Data

Species belonging to Rosa section Synstylae (Rosaceae) are mainly distributed in East Asia, and represent recently diverged lineages within the genus. Over decades, inferring phylogenetic relationships within section Synstylae have been exceptional challenges, due to short branch lengths and low support values. Of approximately 36 species in the section Synstylae, Rosa multiflora, Rosa luciae and Rosa maximowicziana are widely distributed in the Sino-Japanese floristic region. In this study, we assembled chloroplast genomes of these three species to compare the genomic features within section Synstylae, and to compare with other infrageneric groups. We found that three Rosa sect. Synstylae species had lost infA genes with pseudogenization, and they were almost identical to each other. Two protein-coding gene regions (ndhF and ycf1) and five non-coding regions (5’matK-trnK, psbI-trnS-trnG, rps16-trnG, rpoB-trnC, and rps4-trnT) were identified as being highly informative markers. Within three section Synstylae chloroplast genomes, 85 simple sequence repeat (SSR) motifs were detected, of which at least 13 motifs were identified to be effective markers. The phylogenetic relationships of R. multiflora, R. luciae and R. maximowicziana could not be resolved, even with chloroplast genome-wide data. This study reveals the chloroplast genomic data of Rosa sect. Synstylae, and it provides valuable markers for DNA barcoding and phylogenetic analyses for further studies.

Download Full-text