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Milarska SE, Androsiuk P, Paukszto Ł, Jastrzębski JP, Maździarz M, Larson KW, Giełwanowska I. Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis. Sci Rep 2023; 13:18774. [PMID: 37907682 PMCID: PMC10618263 DOI: 10.1038/s41598-023-46017-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.
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Affiliation(s)
- Sylwia E Milarska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Keith W Larson
- Climate Impacts Research Centre, Umeå University, 90187, Umeå, Sweden
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Su W, Liang R. The complete chloroplast genome of a fast-growing tree Lophostemon confertus (Myrtaceae). Mitochondrial DNA B Resour 2023; 8:26-29. [PMID: 36620314 PMCID: PMC9815246 DOI: 10.1080/23802359.2022.2158691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Lophostemon confertus (Myrtaceae), a fast-growing ornamental tree, is widely cultivated in tropical and subtropical regions. To determine its phylogenetic position within Myrtaceae, here we report its complete chloroplast (cp) genome, which is 160,297 bp long and contains two inverted repeats (IRs) of 26,490 bp each, separated by a small single-copy region of 18,826 bp and a large single-copy region of 88,491 bp. The cp genome contains 123 genes, including 73 unique protein-coding genes (six duplicated in the IR regions), 29 unique tRNA genes (seven duplicated in the IR regions), and four unique rRNA genes (all located in the IR regions). Phylogenetic analysis of 18 species of Myrtaceae showed that L. confertus is sister to Xanthostemon chrysanthus. The complete cp genome of L. confertus provides a valuable genetic resource for further phylogenetic studies.
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Affiliation(s)
- Wenhang Su
- Department of Art and Design, Guangxi Vocational & Technical College, Nanning, Guangxi, China
| | - Rifan Liang
- Department of Art and Design, Guangxi Vocational & Technical College, Nanning, Guangxi, China,CONTACT Rifan Liang Department of Art and DesignGuangxi, Vocational & Technical College, No. 19, Mingyang Avenue, Jiangnan District, Nanning530226, Guangxi Zhuang Autonomous Region, China
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Kuang Q, Sheng W. The entire chloroplast genome sequence of Asparagus setaceus (Kunth) Jessop: Genome structure, gene composition, and phylogenetic analysis in Asparagaceae. Open Life Sci 2022; 17:1541-1554. [PMID: 36474705 PMCID: PMC9684740 DOI: 10.1515/biol-2022-0497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 09/08/2024] Open
Abstract
Asparagus setaceus (Kunth) Jessop is a horticultural plant of the genus Asparagus. Herein, the whole chloroplast (cp) genome of A. setaceus was sequenced with PacBio and Illumina sequencing systems. The cp genome shows a characteristic quadripartite structure with 158,076 bp. In total, 135 genes were annotated, containing 89 protein-coding, 38 tRNA, and 8 rRNA genes. Contrast with the previous cp genome of A. setaceus registered in NCBI, we identified 7 single-nucleotide polymorphisms and 15 indels, mostly situated in noncoding areas. Meanwhile, 36 repeat structures and 260 simple sequence repeats were marked out. A bias for A/T-ending codons was shown in this cp genome. Furthermore, we predicted 78 RNA-editing sites in 29 genes, which were all for C-to-U transitions. And it was also proven that positive selection was exerted on the rpoC1 gene of A. setaceus with the K a/K s data. Meanwhile, a conservative gene order and highly similar sequences of protein-coding genes were revealed within Asparagus species. Phylogenetic tree analysis indicated that A. setaceus was a sister to Asparagus cochinchinensis. Taken together, our released genome provided valuable information for the gene composition, genetics comparison, and the phylogeny studies of A. setaceus.
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Affiliation(s)
- Quan Kuang
- Department of Biological Technology, Nanchang Normal University, Nanchang, 330032, Jiangxi, China
| | - Wentao Sheng
- Department of Biological Technology, Nanchang Normal University, Nanchang, 330032, Jiangxi, China
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Niu Y, Luo Y, Wang C, Xu Q, Liao W. The chloroplast genome of Rosa rugosa × Rosa sertata (Rosaceae): genome structure and comparative analysis. Genet Mol Biol 2022; 45:e20210319. [PMID: 36205728 PMCID: PMC9540792 DOI: 10.1590/1678-4685-gmb-2021-0319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/15/2022] [Indexed: 11/04/2022] Open
Abstract
Rosa rugosa × Rosa sertata, which belongs to the family
Rosaceae, is one of the native oil-bearing roses in China. Most research has
focused on its essential oil components and medicinal values. However, there
have been few studies about its chloroplast genome. In this study, the whole
chloroplast genome of R. rugosa × R. sertata was sequenced,
analyzed, and compared to other genus Rosa species. The
chloroplast genome of R. rugosa × R. sertata is a circular
structure and 157,120 bp in length. The large single copy and small single copy
is 86,173 bp and 18,743 bp in size, respectively, and the inverted repeats are
26,102 bp in size. The GC content of the whole genome is 37.96%, while those of
regions of LSC, SSC, and IR are 35.20%, 31.18%, and 42.73%, respectively. There
are 130 different genes annotated in this chloroplast genome, including 84
protein coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene.
Phylogenetic analysis of 19 species revealed that R. rugosa × R.
sertata belong to the Sect. Cinnamomeae. Overall,
this study, providing genomic resources of R. rugosa × R.
sertata, will be beneficial for species identification and
biological research.
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Affiliation(s)
- Yuan Niu
- Gansu Agricultural University, College of Horticulture, Lanzhou,
China. ,Lanzhou Agro-technical research and Popularization Center, Lanzhou,
China
| | - Yanyan Luo
- Gansu Agricultural University, College of Horticulture, Lanzhou,
China.
| | - Chunlei Wang
- Gansu Agricultural University, College of Horticulture, Lanzhou,
China.
| | - Qiong Xu
- Lanzhou Agro-technical research and Popularization Center, Lanzhou,
China
| | - Weibiao Liao
- Gansu Agricultural University, College of Horticulture, Lanzhou,
China.
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Chen C, Xia X, Peng J, Wang D. Comparative Analyses of Six Complete Chloroplast Genomes from the Genus Cupressus and Juniperus (Cupressaceae). Gene 2022; 837:146696. [PMID: 35738448 DOI: 10.1016/j.gene.2022.146696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/05/2022] [Accepted: 06/17/2022] [Indexed: 11/26/2022]
Abstract
Cupressaceae is a conifer family distributed around the world. Cupressus and Juniperus are the main genera of the Cupressaceae family and have important medicinal value. This leads to confusion between Cupressus and Juniperus due to similar morphologies. Here, the complete cp genomes of two Cupressus (C. duclouxiana and C. funebri) and four Juniperus (J. chinensis, J. gaussenii J. pingii and J. procumbens) were sequenced. The results revealed that the length of the cp genomes ranged from 126,996 bp to 129,959 bp, with 119 genes comprising 82 protein-coding genes, 33 transfer RNAs and 4 ribosomal RNAs. All chloroplast genomes of Cupressus and Juniperus lost whole IR regions, which is consistent with gymnosperm cp genome studies. In addition, the number of SSRs per species ranged from 54 to 73 and was dominated by mononucleotide repeats. In the six cp genomes of Cupressus and Juniperus, five highly divergent regions, including accD, accD-rpl2, ycf1, ycf2 and rrn23-rrn4.5, can be used as DNA barcodes of interspecific relationships and potential genetic markers. We compared the gene selection pressures (C. chengiana as reference species), and 6 genes underwent positive selection, the majority of which were related to photosynthesis. Phylogenetic results showed that the monophyly of Cupressus and Juniperus supported most bootstrap support. Cupressus funebris and J. chinensis were resolved to be early diverging species within Cupressus and Juniperus, and the two genera were sister groups to each other. This research revealed a new understanding of the structural pluralism and phylogenetic relationships of Cupressaceae cp genomes. These results will facilitate comprehension of the complexity and diversity of conifer cp genomes. SIGNIFICANCE:: Phylogenetic relationships among Cupressus, Juniperus, and their closest relatives are controversial, and generic delimitations have been in flux for the past decade. To address relationships and attempt to produce a more robust classification, we sequenced 6 new plastid genomes (plastomes) from the two variously described genera in this complex (Cupressus and Juniperus) and compared them with additional plastomes from diverse members of Cupressaceae. Our study corroborated the accD of Cupressophytes have a tendency to expand in size and strongly supported a sister relationship between Cupressus and Juniperus. The disparity in these results could be traced to the facts that the chloroplast genome is uniparentally inherited, also the usage of the whole chloroplast genome for this research is of a better advantage compared to usage of selected genes or portion of the plastome. The complete CP genomic data will provide useful information for studying genetic diversity and species identification, which is important for the overarching goal of biodiversity conservation.
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Affiliation(s)
- Can Chen
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
| | - Xi Xia
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
| | - Jingyu Peng
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
| | - Dawei Wang
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
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Balbinott N, Rodrigues NF, Guzman FL, Turchetto-Zolet AC, Margis R. Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies. Genet Mol Biol 2022; 45:e20210191. [PMID: 35088818 PMCID: PMC8796035 DOI: 10.1590/1678-4685-gmb-2021-0191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/20/2021] [Indexed: 05/05/2023] Open
Abstract
Myrtaceae is a large and species-rich family of woody eudicots, with prevalent
distribution in the Southern Hemisphere. Classification and taxonomy of species
belonging to this family is quite challenging, sometimes with difficulty in
species identification and producing phylogenies with low support for species
relationships. Most of the current knowledge comes from few molecular markers,
such as plastid genes and intergenic regions, which can be difficult to handle
and produce conflicting results. Based on plastid protein-coding sequences and
nuclear markers, we present a topology for the phylogenetic relationships among
Myrtaceae tribes. Our phylogenetic estimate offers a contrasting topology over
previous analysis with fewer markers. Plastome phylogeny groups the tribes
Syzygieae and Eucalypteae and individual chloroplast genes produce divergent
topologies, especially among species within Myrteae tribe, but also in regard to
the grouping of Syzygieae and Eucalypteae. Results are consistent and
reproducible with both nuclear and organellar datasets. It confronts previous
data about the deep nodes of Myrtaceae phylogeny.
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Affiliation(s)
- Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
| | | | - Frank Lino Guzman
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Innovación Agraria, Perú
| | | | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
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Complete chloroplast genome sequence of Sinojackia microcarpa (Styracaceae): comparative and phylogenetic analysis. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00913-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Wang ZF, Cao HL. The complete mitochondrial genome sequence of Aquilaria sinensis. Mitochondrial DNA B Resour 2021; 6:381-383. [PMID: 33628874 PMCID: PMC7889115 DOI: 10.1080/23802359.2020.1869609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/19/2020] [Indexed: 11/19/2022] Open
Abstract
Aquilaria sinensis, endemic to China, is an economically important evergreen tree species and a source of agarwood. Due to the high market demand for agarwood, this species is heavily overexploited in the wild and is now listed as an endangered species. Although its nuclear and chloroplast genomes have been previously reported, little is known about its mitochondrial genome. Using the paired-end short reads generated by the Illumina sequencing platform, we assembled and herein report the mitochondrial genome of A. sinensis for future phylogenetic, evolutionary, and preservative studies. The length of the A. sinensis mitochondrial genome was found to be 341,829 bp and the GC content was 45.01%. A total of 32 protein-coding genes, 19 tRNA genes, and three rRNA genes were annotated. The phylogenetic tree indicated that A. sinensis is most closely genetically related to Vigna radiata.
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Affiliation(s)
- Zheng-Feng Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Hong-Lin Cao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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Liang D, Zhu L, He Y, Xiong X. Characterization of the complete chloroplast genome of Melaleuca cajuputi subsp. cumingiana (Myrtaceae). Mitochondrial DNA B Resour 2021; 6:462-464. [PMID: 33628889 PMCID: PMC7889186 DOI: 10.1080/23802359.2020.1871438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Plants in the genus Melaleuca have been widely used as traditional medicine mainly because of their broad spectrum antimicrobial activity. In this study, we reported the complete chloroplast genome of Melaleuca cajuputi subsp. cumingiana. The chloroplast genome of this species is 158,855 bp in length, including a pair of inverted repeat regions (IRs) (26,727 bp) that is divided by a large single-copy (LSC) area (87,338 bp) and a small single-copy (SSC) area (18,063 bp). The circular chloroplast genome of M. cajuputi subsp. cumingiana contains 135 unique genes, composing of 87 protein-coding genes, 40 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicates that M. cajuputi subsp. cumingiana was clustered with species in the tribe Melaleuceae. This complete chloroplast genome of M. cajuputi subsp. cumingiana will provide a powerful tool to accelerate breeding, biotechnological and phylogenetic study.
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Affiliation(s)
- Danhui Liang
- The No. 15 Middle School of Yueyang City, Yueyang, China
| | - Liming Zhu
- The No. 15 Middle School of Yueyang City, Yueyang, China
| | - Yuyu He
- The No. 15 Middle School of Yueyang City, Yueyang, China
| | - Xin Xiong
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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