ABSTRACT
Bassia scoparia, an annual potherb belonging to the family Amaranthaceae, has been widely used in traditional Chinese and Japanese medicine for over 2000 years. Herein, we presented its complete chloroplast. The chloroplast genome sequence was 151,278 bp in length with a 36.6% content of GC. The genome showed the typical quadripartite structure, comprising a pair of inverted repeat (IR) regions (24,353 bp) separated by a large single-copy (LSC) region (84,067 bp) and a small single-copy (SSC) region (18,505 bp). This chloroplast genome harbored 133 predicted genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that B. scoparia was closely related to B. littorea. This newly sequenced chloroplast genome not only enhances our understanding of the genome of Bassia but also provides valuable insights for the evolutionary study of the family Amaranthaceae.
ABSTRACT
Olea dioica Roxb, 1820 is a very important ethnomedicinal tree because of its medicinal properties and it belongs to the Oleaceae family. It is mainly distributed in evergreen and semi-evergreen forests. However, the chloroplast genome of O. dioica has not yet been reported. In this study, the chloroplast genome sequence of O. dioica was sequenced using next-generation sequencing technologies. The complete chloroplast genome of O. dioica was 155,138 bp in length (GenBank accession no. PP048999), comprising a large single-copy (LSC) region of 86,048 bp, a small single-copy (SSC) region of 17,816 bp, and two inverted repeat (IR) regions 25,637 bp each. The overall GC content was 37.8%. The complete chloroplast genome of O. dioica contains 131 complete genes, which are 88 protein-coding genes, 35 transfer RNA genes, and eight ribosomal RNA genes. A maximum-likelihood (ML) tree of O. dioica and 14 other species in the family Oleaceae suggested that O. dioica showed a close relationship with Olea brachiata.
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Hydrocotyle vulgaris is a perennial wetland clonal plant in the Araliaceae family, which was introduced to China as an ornamental plant in the 1990s. Although H. vulgaris is now considered a potential invasiveness species in China, it also plays a significant role in the remediation of water pollution. Here, we reported its complete chloroplast genome and analyzed the basic characteristics. The chloroplast genome was 153,165 bp in length, including a pair of inverted repeat (IR) regions of 25,072 bp separated by a large single-copy (LSC) region of 84,291 bp and a small single-copy (SSC) region of 18,730 bp. The H. vulgaris chloroplast genome contained 132 predicted genes, and its overall GC content was 37.60%. Phylogenetic analysis revealed that H. vulgaris was closely related to H. verticillata. The H. vulgaris chloroplast genome presented in this study will lay a foundation for further genetic and genomic studies of the genus Hydrocotyle.
ABSTRACT
Calystegia hederacea Wall. in Roxb. 1824 is a perennial herbaceous vine in the family Convolvulaceae and has several biological effects. Herein, we reported the first complete chloroplast genome of C. hederacea. The chloroplast genome sequence was 152,057 bp in length, comparing a large single-copy (LSC) region of 87,891 bp, a small single-copy (SSC) region of 19,866 bp, and a pair of inverted repeat (IR) regions of 22,150 bp. This sequenced chloroplast genome contained 126 predicted genes, including 81 protein-coding genes, 37 tRNA genes, and eight rRNA genes, and the total GC content of the chloroplast genome was 37.79%. Phylogenetic analysis revealed that C. hederacea was closely related to C. soldanella. The chloroplast genome presented in this study will enrich the genome information of the genus Calystegia and provide deeper insights into the evolution study of the family Convolvulaceae.
ABSTRACT
Eremurus zoae Vved. 1971 is a perennial herbaceous plant in the family Asphodelaceae and an endemic species of the Kyrgyz Republic; however, its complete chloroplast genome sequence has not been reported. Here, we investigated the complete chloroplast (cp) genome of E. zoae using next-generation sequencing. The cp genome was 153,744 bp long, with a large single copy (84,020 bp), a small single copy (16,766 bp), and a pair of inverted repeats (26,479 bp). The genome encodes 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that the genus Eremurus forms a monophyletic group and E. zoae is closely related to E. chinensis. This study provides a molecular foundation for future phylogenetic studies of Eremurus.
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Plumbago zeylanica L. 1753 is a medicinally-important herb in family Plumbaginaceae. In this study, we assembled and reported the complete chloroplast genome of P. zeylanica. The plastome of P. zeylanica was 169,178 bp, including a large single-copy region of 92,135 bp, a small single-copy region (SSC) of 13,455 bp and a pair of inverted repeat regions (IRs) of 31,794 bp. It contained 124 genes, including 79 protein-coding genes, 37 tRNA genes and eight rRNA genes. Phylogenetic analysis showed that P. zeylanica formed a close relationship with P. auriculata in Plumbago. The first complete chloroplast genome report of P. zeylanica providing an opportunity to explore the genetic diversity, and would be also helpful in the species identification and conservation.
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Lycium qingshuiheense is a typical drought and salt-alkali-tolerant plant, which has been added to the new species of Lycium in recent years. Here, we first sequenced the complete chloroplast genome of L. qingshuiheense to investigate its evolutionary relationship within the family Solanaceae. Results suggested that the circular complete chloroplast genome of L. qingshuiheense was 154,945 bp in length, including a large single-copy (LSC) of 85,930 bp, a small single-copy (SSC) of 18,203 bp, and two inverted repeats (IRs) of 25,406 bp. The GC content accounts for 37.90% and annotated 131 genes, including 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. A neighbor-joining phylogenetic tree revealed that L. qingshuiheense was a sister species to L. ruthenicum. Our study provides a new insight into the systematic evolution of Lycium in the Solanaceae family.
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Tragopogon dubius Scopoli is native to Europe and western Asia and is considered an invasive plant in China. In this study, the complete chloroplast genome of T. dubius was obtained using high-throughput next-generation sequencing technology. The whole chloroplast genome was 153,017 bp long with a GC content of 38% and comprised 130 genes (86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes). Phylogenetic analysis based on the concatenated chloroplast protein-coding sequences showed that T. dubius is most closely related to Tragopogon pratensis. This study provides valuable genetic data for further phylogenetic analysis and molecular identification of species in the genus Tragopogon.
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Myricaria wardii Marquand 1929, endemic to the Tibet Plateau, is a perennial shrub with important medicinal and ecological values. In this study, the complete chloroplast (cp) genome of M. wardii was assembled, and the phylogenetic tree was reconstructed to evaluate the phylogenetic location of the species. The results showed that the cp genome size of the M. wardii was 155,299 bp, which contained a pair of inverted repeat (IR) regions (26,150 bp), a large single copy (LSC) region (84,715 bp), and a small single copy (SSC) region (18,284 bp). The total GC content of the cp genome was 36.30%. A total of 128 genes were annotated, consisting of 83 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The phylogenetic analysis showed that M. wardii was closely related to M. prostrata. This study provides useful information for the conservation of this species and the phylogenetic analysis of Tamaricaceae.
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Pulsatilla chinensis f. alba D. K. Zang 1993 is a forma of Pulsatilla chinensis (Bge.) Regel, the root of P. chinensis is traditional Chinese medicine called Pulsatillae radix. The biggest difference between P. chinensis f. alba and P. chinensis is that P. chinensis f. alba sepals is white. The complete chloroplast genome of P. chinensis f. alba was sequenced using the Illumina NovaSeq platform for the first time. The lengths of the genome, large single-copy (LSC), small single-copy (SSC), two inverted repeats (IRs), and GC content were 163,654 bp, 82,355 bp, 19,069 bp, 31,115 bp, and 37.2%, respectively. It had 134 genes, including 90 protein-coding genes, 36 tRNA genes, and eight rRNA genes. The maximum-likelihood tree indicated that P. chinensis f. alba had a closer relationship with P. chinensis. This study would provide a theoretical basis for the further study of Pulsatilla plants genetics phylogenetic research.
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Philodendron hederaceum (Jacq.) Schott 1829, a species of the Araceae family, is a foliage plant of ornamental value. The complete chloroplast genome sequence of Philodendron hederaceum was obtained by the de novo assembly of NovaSeq 6000 (Illumina Co., San Diego, CA) paired-end short reads and Oxford Nanopore long reads. The complete chloroplast genome of P. hederaceum was 168,609 bp in length, with a large single-copy (LSC) region of 94,393 bp, a small single-copy (SSC) region of 25,774 bp, and a pair of identical inverted repeat regions (IRs) of 24,221 bp. The genome contained a total of 129 genes, including 85 protein-coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis of P. hederaceum with 19 related species and two outgroup species revealed the closest taxonomical relationship with Philodendron lanceolatum in the Araceae family.
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Phlomoides kirghisorum Adylov, Kamelin & Makhmedov 1987 is one of the poorly studied narrow endemics of Fergana Valley, one of Central Asia's most densely human-populated regions. In this study, we sequenced, assembled, and characterized the complete plastome of P. kirghisorum by using high-throughput Illumina reads. The complete chloroplast genome consisted of 151,324 bp, including a large single-copy (LSC) region (82,775 bp), a small single-copy (SSC) region (17,357 bp), and two inverted repeat regions (25,596 bp each). In the chloroplast genome of P. kirghisorum, 133 genes were detected, comprising 88 protein-encoding genes, eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. The phylogenetic analysis indicated that the genetic relationship between P. kirghisorum and P. alpina was very close. This study provides basic information to explore the molecular evolution of the Phlomoides genus and the Lamiaceae family.
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Pinus tabuliformis var. henryi (Mast.) C.T.Kuan 1983 is an endemic and rare subtropical pine, mainly distributed in central China. In this study, we sequenced the complete chloroplast (cp) genome of P. tabuliformis var. henryi and reported it for the first time. The cp genome was 119,634 base pairs (bp) in total length, including two inverted repeats (IRs, 495 bp), separated by a large single-copy region (LSC, 65,600 bp) and a small single-copy region (SSC, 53,044 bp). There are 114 different genes in the cp genome of P. tabuliformis var. henryi, including 74 protein-coding genes, 36 transfer RNA genes, and four ribosomal RNA genes. The overall GC content of the cp genome was 38.5%. Our phylogenetic analysis of P. tabuliformis var. henryi demonstrated that it was closely related to P. tabuliformis and could be used to identify and analyze its genetic diversity, which was expected to provide new data for taxonomic and phylogenetic studies of Pinus.
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Cyperus malaccensis Lam is a perennial herbaceous plant that is distributed over a large area along the southern coast of China. Some plants of the Cyperaceae family are highly similar morphologically, which makes them difficult to classify and identify. In this study, the complete chloroplast genome of C. malaccensis was sequenced and assembled. The chloroplast genome is 186,098 bp long with a 33.18% content of GC. The structure of chloroplast genome includes a quadripartite structure that is composed of a pair of inverted repeats (IRs) of 37,434 bp, a small single copy (SSC) region of 10,296 bp, and a large single copy (LSC) region of 100,934 bp. The genome contains 141 genes, including 94 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. A phylogenetic analysis showed that C. malaccensis is the most closely related to the congeneric species C. rotundus. These results enrich the genetic resources of the Cyperaceae and provide a molecular basis for further study on the phylogeny of this family.
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Asterothamnus centraliasiaticus Novopokr., a species of perennial deciduous semi-shrub within the family Asteraceae, has excellent medical, economic, ecological and genetic value. In this study, the chloroplast genome of A. centraliasiaticus was first assembled using Illumina HiSeq2500 sequences. The results indicate that the complete cp genome of A. centraliasiaticus is 152,205 bp in length, and comprises a pair of inverted repeat (IR) regions of 25,031 bp each, a large single-copy (LSC) region of 83,956 bp and a small single-copy (SSC) region of 18,187 bp. The GC content of A. centraliasiaticus is 37.3%. A total of 130 genes were successfully annotated containing 85 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The maximum likelihood (ML) phylogenetic analysis based on the complete chloroplast genome data highly supported that A. centraliasiaticus was close to Aster lavandulifolius. These results will provide significant genetic information for the germplasm protection and reasonable development.
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Justicia procumbens L. is a traditional medicinal plant that is widely distributed in China. However, little is known about the genetic diversity and evolution of this genus, and no genomic studies have been carried out on J. procumbens previously. In this study, we aimed to assemble and annotate the first complete chloroplast genome (cpDNA) of J. procumbens and compare it with all previously published cpDNAs within the tribe Justicieae. Genome structure and comparative and phylogenetic analyses were performed. The 150,454 bp-long J. procumbens cpDNA has a circular and quadripartite structure consisting of a large single copy, a small single copy, and two inverted repeat regions. It contains 133 genes, of which 88 are protein-coding genes, 37 are tRNA genes, and eight are rRNA genes. Twenty-four simple sequence repeats (SSRs) and 81 repeat sequences were identified. Comparative analyses with other Justicieae species revealed that the non-coding regions of J. procumbens cpDNA showed greater variation than did the coding regions. Moreover, phylogenetic analysis based on 14 cpDNA sequences from Justicieae species showed that J. procumbens and J. flava were most closely related. This study provides valuable genetic information to support further research on the genetic diversity and evolutionary development of the tribe Justicieae.
Subject(s)
Genome, Chloroplast , Justicia , Phylogeny , Justicia/genetics , Genomics , Repetitive Sequences, Nucleic AcidABSTRACT
Elaeagnus 'viridis', an artificial hybrid of E. macrophylla (â) Thunb. (1784) × E. pungens (â) Thunb. (1784), is known for its economic and ecological value. In this study, we sequenced and assembled the whole chloroplast (cp) genome of E. 'viridis'. The results showed that its cp genome was 152,284 bp long, showing a typical quadripartite structure and containing a large single-copy region (LSC, 82,299 bp), a small single-copy region (SSC, 18,239 bp), and a pair of inverted repeats (IRs, 51,746 bp). The cp genome contains 132 genes, including 86 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 66 common PCGs revealed that E. 'viridis' is most closely related to its maternal parent E. pungens. The chloroplast genomic information reported in this study will shed some useful light for further genetic studies in the genus Elaeagnus.
ABSTRACT
BACKGROUND: Justicia L. is the largest genus in Acanthaceae Juss. and widely distributed in tropical and subtropical regions of the world. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies were mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp.) genomes of 12 Asian plants and combined with the previously published cp. genome of Justicia leptostachya Hemsl. for further comparative genomics and phylogenetic analyses. RESULTS: All the cp. genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739 bp, including a large single copy (LSC, 81,434-83,676 bp), a small single copy (SSC, 16,833-17,507 bp) and two inverted repeats (IR, 24,947-25,549 bp). GC contents range from 38.1 to 38.4%. All the plastomes contain 114 genes, including 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa C. B. Clarke is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for the genus Justicia. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with the morphology evolution. CONCLUSION: Our study not only elucidates basic features of Justicia whole plastomes, but also sheds light on interspecific relationships of Asian Justicia plants for the first time.
Subject(s)
Acanthaceae , Genome, Chloroplast , Genome, Plastid , Justicia , Justicia/genetics , Acanthaceae/genetics , Phylogeny , Genome, Chloroplast/genetics , GenomicsABSTRACT
Adonis pseudoamurensis W.T. Wang 1980 is an important traditional medicinal plant used for the treatment of cardiac diseases. The complete chloroplast (cp) genome of Adonis pseudoamurensis is reported for the first time in this study. The circular cp genome is 156,917 bp in length, consisting of a large single-copy region (86,262 bp), a small single-copy region (18,067 bp), and two inverted repeat regions (26,294 bp). The genome encodes 129 genes, comprising 84 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis showed that A. pseudoamurensis is closely related to A. amurensis.
ABSTRACT
Aster altaicus Willd. is an important medicinal plant and can also be used as a forage grass. To better understand the diversity and phylogeny between A. altaicus and other Aster species, we sequenced and annotated the complete chloroplast genome of A. altaicus by using the Illumina Hiseq 2500 platform. This complete chloroplast genome is 152,473 bp long and the GC content is 37.3% presented a negative AT-skew (-0.002) and a positive GC-skew (0.003). The genome contains a large single-copy region (LSC) of 84,235 bp, a small single-copy region (SSC) of 18,212 bp, which separated by a pair of inverted repeat regions (IRA and IRB) of 25,013 bp. Moreover, 129 genes were found in the chloroplast of A. altaicus, including 85 protein-coding genes (PCGs), 36 transfer RNA genes (tRNAs), 8 ribosomal RNA unit genes (rRNAs). Phylogenetic analysis showed that A. altaicus was more closely related to A. altaicus and A. altaicus var. uchiyamae. This study lays the foundation for further studies on the evolution and phylogeny of Aster.
