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

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.

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Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships

Molecules ◽

10.3390/molecules23092165 ◽

2018 ◽

Vol 23 (9) ◽

pp. 2165 ◽

Cited By ~ 3

Author(s):

Xiao Zhang ◽

Tao Zhou ◽

Jia Yang ◽

Jingjing Sun ◽

Miaomiao Ju ◽

...

Keyword(s):

Chloroplast Genome ◽

Sequence Divergence ◽

Economic Plant ◽

Genome Sequences ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Phylogenetic Studies ◽

Chloroplast Genomes ◽

Representative Species ◽

Translation Initiation Codon

Cucurbitaceae is the fourth most important economic plant family with creeping herbaceous species mainly distributed in tropical and subtropical regions. Here, we described and compared the complete chloroplast genome sequences of ten representative species from Cucurbitaceae. The lengths of the ten complete chloroplast genomes ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), and they shared the most common genomic features. 618 repeats of three categories and 813 microsatellites were found. Sequence divergence analysis showed that the coding and IR regions were highly conserved. Three protein-coding genes (accD, clpP, and matK) were under selection and their coding proteins often have functions in chloroplast protein synthesis, gene transcription, energy transformation, and plant development. An unconventional translation initiation codon of psbL gene was found and provided evidence for RNA editing. Applying BI and ML methods, phylogenetic analysis strongly supported the position of Gomphogyne, Hemsleya, and Gynostemma as the relatively original lineage in Cucurbitaceae. This study suggested that the complete chloroplast genome sequences were useful for phylogenetic studies. It would also determine potential molecular markers and candidate DNA barcodes for coming studies and enrich the valuable complete chloroplast genome resources of Cucurbitaceae.

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The complete chloroplast genome sequence of American elm (Ulmus americana) and comparative genomics of related species

10.1101/2020.01.27.920181 ◽

2020 ◽

Author(s):

Aziz Ebrahimi ◽

Jennifer D. Antonides ◽

Cornelia C. Pinchot ◽

James M. Slavicek ◽

Charles E. Flower ◽

...

Keyword(s):

Chloroplast Genome ◽

Natural Populations ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Ulmus Americana ◽

Important Species ◽

Complete Chloroplast Genome ◽

American Elm ◽

Chloroplast Genomes

ABSTRACTAmerican elm, Ulmus americana L., was cultivated widely in USA and Canada as a landscape tree, but the genome of this important species is poorly characterized. For the first time, we describe the sequencing and assembly of the chloroplast genomes of two American elm genotypes (RV16 and Am57845). The complete chloroplast genome of U. americana ranged from 158,935-158,993 bp. The genome contains 127 genes, including 85 protein-coding genes, 34 tRNA genes and 8 rRNA genes. Between the two American elm chloroplasts we sequenced, we identified 240 sequence variants (SNPs and indels). To evaluate the phylogeny of American elm, we compared the chloroplast genomes of two American elms along with seven Asian elm species and twelve other chloroplast genomes available through the NCBI database. As expected, Ulmus was closely related to Morus and Cannabis, as all three genera are assigned to the Urticales. Comparison of American elm with Asian elms revealed that trnH was absent from the chloroplast of American elm but not most Asian elms; conversely, petB, petD, psbL, trnK, and rps16 are present in the American elm but absent from all Asian elms. The complete chloroplast genome of U. americana will provide useful genetic resources for characterizing the genetic diversity of U. americana and potentially help to conserve natural populations of American elm.

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Complete chloroplast genomes of Impatiens cyanantha and Impatiens monticola: Insights into genome structures, mutational hotspots, comparative and phylogenetic analysis with its congeneric species

PLoS ONE ◽

10.1371/journal.pone.0248182 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0248182

Author(s):

Chao Luo ◽

Yang Li ◽

Roshani Budhathoki ◽

Jiyuan Shi ◽

Huseyin Yer ◽

...

Keyword(s):

Sister Relationship ◽

Protein Coding ◽

Important Species ◽

Phylogenetic Studies ◽

Chloroplast Genomes ◽

Mutational Hotspots ◽

Identification Of Species ◽

The Comparative Study ◽

Rna Genes ◽

Different Altitudes

Impatiens L., the largest genus in the family Balsaminaceae with approximately 1000 species, is a controversial and complex genus that includes many economically important species well known for medicinal and ornamental values. However, there is limited knowledge of molecular phylogeny and chloroplast genomics, and uncertainties still exist at a taxonomic level. In this study, we have assembled four chloroplast genomics specimens of Impatiens cyanantha and Impatiens monticola, which are found at the different altitudes of Guizhou and Yunnan in China, and compared them with previously published three wild Balsaminaceae species (Impatiens piufanensis, Impatiens glandlifera, and Hydrocera triflora). The complete chloroplast genome sequences ranged from 152,236 bp (I. piufanensis) to 154,189 bp (H. triflora) and encoded 115 total distinct genes, of which 81 were protein-coding, 30 were distinct transfer RNA genes(tRNA), and 4 were ribosomal RNA genes (rRNA). A comparative analysis of I. cyanantha (Guizhou) vs. I. cyanantha (Yunnan) and I. monticola (Guizhou) vs. I. monticola (Yunnan) revealed minor changes in lengths; however, similar gene contents, gene orders, and GC contents existed among them. Interestingly, highly coding and non-coding genes, and regions matK, psbK, atpH-atpI, trnC-trnT, petN, psbM, atpE, rbcL, accD, psaL, rps3-rps19, ndhG-ndhA,rpl16, rpoB, ndhB, ndhF, ycf1, and ndhH were found, which could be suitable for identification of species and phylogenetic studies. During the comparison between I. cyanantha (Guizhou) and I. cyanantha (Yunnan), we observed that the rps4, ycf2, ndhF, ycf1, and rpoC2 genes underwent positive selection. Meanwhile, in the comparative study of I. monticola (Guizhou) vs. I. monticola (Yunnan), The accD and ycf1 genes were positively selected. Additionally, phylogenetic relationships based on maximum likelihood (ML) and Bayesian inference (BI) among whole chloroplast genomes showed that a sister relationship with I. monticola (Guizhou) and I. monticola (Yunnan) formed a clade with I.piufanensis proving their close connection. Besides, I.cyanantha (Guizhou) and I. cyanantha (Yunnan) formed a clade with I. glandlifera. Along with the findings and the results, the current study might provide valuable significant genomic resources for systematics and evolution of the genus impatiens in different altitudes of regions.

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Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis

Molecules ◽

10.3390/molecules24030474 ◽

2019 ◽

Vol 24 (3) ◽

pp. 474 ◽

Cited By ~ 13

Author(s):

Dong-Mei Li ◽

Chao-Yi Zhao ◽

Xiao-Fei Liu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Species Identification ◽

Single Copy ◽

Rrna Genes ◽

Genome Sequences ◽

Variable Regions ◽

Complete Chloroplast Genome ◽

Kaempferia Galanga ◽

Chloroplast Genomes

Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.

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Complete chloroplast genome sequence of Adenophora racemosa (Campanulaceae): Comparative analysis with congeneric species

PLoS ONE ◽

10.1371/journal.pone.0248788 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248788

Author(s):

Kyung-Ah Kim ◽

Kyeong-Sik Cheon

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Illumina Miseq ◽

Congeneric Species ◽

Protein Coding ◽

Important Species ◽

Protein Coding Genes ◽

Chloroplast Genomes ◽

Miseq Platform ◽

Chloroplast Genome Sequence

Adenophora racemosa, belonging to the Campanulaceae, is an important species because it is endemic to Korea. The goal of this study was to assemble and annotate the chloroplast genome of A. racemosa and compare it with published chloroplast genomes of congeneric species. The chloroplast genome was reconstructed using de novo assembly of paired-end reads generated by the Illumina MiSeq platform. The chloroplast genome size of A. racemosa was 169,344 bp. In total, 112 unique genes (78 protein-coding genes, 30 tRNAs, and 4 rRNAs) were identified. A Maximum likelihood (ML) tree based on 76 protein-coding genes divided the five Adenophora species into two clades, showing that A. racemosa is more closely related to Adenophora stricta than to Adenophora divaricata. The gene order and contents of the LSC region of A. racemosa were identical to those of A. divaricata and A. stricta, but the structure of the SSC and IRs was unique due to IR contraction. Nucleotide diversity (Pi) >0.05 was found in eleven regions among the three Adenophora species not included in sect. Remotiflorae and in six regions between two species (A. racemosa and A. stricta).

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

Korean Journal of Plant Taxonomy ◽

10.11110/kjpt.2021.51.3.326 ◽

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.

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Complete chloroplast genome sequences of five Bruguiera species (Rhizophoraceae): comparative analysis and phylogenetic relationships

PeerJ ◽

10.7717/peerj.12268 ◽

2021 ◽

Vol 9 ◽

pp. e12268

Author(s):

Panthita Ruang-areerate ◽

Wasitthee Kongkachana ◽

Chaiwat Naktang ◽

Chutima Sonthirod ◽

Nattapol Narong ◽

...

Keyword(s):

Comparative Analysis ◽

Chloroplast Genome ◽

Genetic Relationships ◽

Strong Support ◽

Rrna Genes ◽

Genome Sequences ◽

Mangrove Species ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes

Bruguiera is a genus of true mangroves that are mostly distributed in the Indo-West Pacific region. However, the number of published whole chloroplast genome sequences of Bruguiera species are limited. Here, the complete chloroplast sequences of five Bruguiera species were sequenced and assembled using Illumina data. The chloroplast genomes of B. gymnorhiza, B. hainesii, B. cylindrica, B. parviflora and B. sexangula were assembled into 161,195, 164,295, 164,297, 163,228 and 164,170 bp, respectively. All chloroplast genomes contain 37 tRNA and eight rRNA genes, with either 84 or 85 protein-coding genes. A comparative analysis of these genomes revealed high similarity in gene structure, gene order and boundary position of the LSC, SSC and two IR regions. Interestingly, B. gymnorhiza lost a rpl32 gene in the SSC region. In addition, a ndhF gene in B. parviflora straddles both the SSC and IRB boundary regions. These genes reveal differences in chloroplast evolution among Bruguiera species. Repeats and SSRs in the chloroplast genome sequences were found to be highly conserved between B. cylindrica and B. hainesii as well as B. gymnorhiza and B. sexangula indicating close genetic relationships based on maternal inheritance. Notably, B. hainesii, which is considered a hybrid between B. gymnorhiza and B. cylindrica, appears to have inherited the chloroplast from B. cylindrica. Investigating the effects of selection events on shared protein-coding genes showed a positive selection in rps7 and rpl36 genes in all species compared to land-plant species. A phylogenetic analysis, based on 59 conserved chloroplast protein-coding genes, showed strong support that all Bruguiera species are in the clade Rhizophoraceae. This study provides valuable genetic information for the study of evolutionary relationships and population genetics in Bruguiera and other mangrove species.

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

Molecules ◽

10.3390/molecules23112811 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2811 ◽

Cited By ~ 8

Author(s):

Yuxin Zhou ◽

Jing Nie ◽

Ling Xiao ◽

Zhigang Hu ◽

Bo Wang

Keyword(s):

Chinese Medicine ◽

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Genetic Identification ◽

Protein Coding ◽

Variable Regions ◽

Specific Identification ◽

Coding Regions ◽

Botanical Species ◽

Chloroplast Genomes

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.

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

Korean Journal of Plant Taxonomy ◽

10.11110/kjpt.2021.51.4.353 ◽

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.

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A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains

PeerJ ◽

10.7717/peerj.9448 ◽

2020 ◽

Vol 8 ◽

pp. e9448

Author(s):

Swati Tyagi ◽

Jae-A Jung ◽

Jung Sun Kim ◽

So Youn Won

Keyword(s):

Phylogenetic Analysis ◽

De Novo ◽

Evolutionary Relationship ◽

Gc Content ◽

Rrna Genes ◽

Trna Genes ◽

Nucleotide Polymorphisms ◽

Coding Regions ◽

Chloroplast Genomes ◽

Chrysanthemum Boreale

Background Chrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology. Methods The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe. Results The sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531) and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species.

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