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Zhou YR, Li Y, Yang LH, Kozlowski G, Yi LT, Liu MH, Zheng SS, Song YG. The adaptive evolution of Quercus section Ilex using the chloroplast genomes of two threatened species. Sci Rep 2024; 14:20577. [PMID: 39232239 PMCID: PMC11375091 DOI: 10.1038/s41598-024-71838-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024] Open
Abstract
Chloroplast (cp) genome sequences have been extensively used for phylogenetic and evolutionary analyses, as many have been sequenced in recent years. Identification of Quercus is challenging because many species overlap phenotypically owing to interspecific hybridization, introgression, and incomplete lineage sorting. Therefore, we wanted to gain a better understanding of this genus at the level of the maternally inherited chloroplast genome. Here, we sequenced, assembled, and annotated the cp genomes of the threatened Quercus marlipoensis (160,995 bp) and Q. kingiana (161,167 bp), and mined these genomes for repeat sequences and codon usage bias. Comparative genomic analyses, phylogenomics, and selection pressure analysis were also performed in these two threatened species along with other species of Quercus. We found that the guanine and cytosine content of the two cp genomes were similar. All 131 annotated genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes, had the same order in the two species. A strong A/T bias was detected in the base composition of simple sequence repeats. Among the 59 synonymous codons, the codon usage pattern of the cp genomes in these two species was more inclined toward the A/U ending. Comparative genomic analyses indicated that the cp genomes of Quercus section Ilex are highly conserved. We detected eight highly variable regions that could be used as molecular markers for species identification. The cp genome structure was consistent and different within and among the sections of Quercus. The phylogenetic analysis showed that section Ilex was not monophyletic and was divided into two groups, which were respectively nested with section Cerris and section Cyclobalanopsis. The two threatened species sequenced in this study were grouped into the section Cyclobalanopsis. In conclusion, the analyses of cp genomes of Q. marlipoensis and Q. kingiana promote further study of the taxonomy, phylogeny and evolution of these two threatened species and Quercus.
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Affiliation(s)
- Yu-Ren Zhou
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yu Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Liang-Hai Yang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Biology and Botanic Garden, University of Fribourg, 1700, Fribourg, Switzerland
- Natural History Museum Fribourg, 1700, Fribourg, Switzerland
| | - Li-Ta Yi
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Mei-Hua Liu
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
| | - Si-Si Zheng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Yi-Gang Song
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
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Wen J, Wu BC, Li HM, Zhou W, Song CF. Plastome structure and phylogenetic relationships of genus Hydrocotyle (apiales): provide insights into the plastome evolution of Hydrocotyle. BMC PLANT BIOLOGY 2024; 24:778. [PMID: 39148054 PMCID: PMC11325595 DOI: 10.1186/s12870-024-05483-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused on separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, the genetic basis of its adaptive evolution remains poorly understood. To investigate the phylogeny and evolution of the genus, we selected ten representative species covering two of three diversity distribution centers and exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify the structural character of Hydrocotyle plastomes. Positive selection analyses were implemented to assess the evolution of the genus. Phylogenetic inferences with protein-coding sequences (CDS) of Hydrocotyle and 17 related species were also performed. RESULTS Plastomes within Hydrocotyle were generally conservative in structure, gene order, and size. A total of 14 regions (rps16-trnK, trnQ-rps16, atpI-atpH, trnC-petN-psbM, ycf3-trnS, accD-psaI-ycf4, petA-psbJ, rps12-rpl20, rpl16 intron, rps3-rpl16 intron, rps9-rpl22, ndhF-rpl32, ndhA intron, and ycf1a) were recognized as hotspot regions within the genus, which suggested to be promising DNA barcodes for global phylogenetic analysis of Hydrocotyle. The ycf15 gene was suggested to be a protein-coding gene for Hydrocotyle species, and it could be used as a DNA barcode to identify Hydrocotyle. In phylogenetic analysis, three monophyletic clades (Clade I, II, III) were identified with evidence of rapid radiation speciation within Clade I. The selective pressure analysis detected that six CDS genes (ycf1b, matK, atpF, accD, rps14, and psbB) of Hydrocotyle species were under positive selection. Within the genus, the last four genes were conservative, suggesting a relation to the unique evolution of the genus in Apiales. Seven genes (atpE, matK, psbH, ycf1a, ycf1b, rpoA, and ycf2) were detected to be under some degree of positive selection in different taxa within the genus Hydrocotyle, indicating their role in the adaptive evolution of species. CONCLUSIONS Our study offers new insights into the phylogeny and adaptive evolution of Hydrocotyle. The plastome sequences could significantly enhance phylogenetic resolution and provide genomic resources and potential DNA markers useful for future studies of the genus.
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Affiliation(s)
- Jun Wen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Bao-Cheng Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Hui-Min Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Wei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Chun-Feng Song
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China.
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Choi YR, Kim SC, Kim TH, Ha YH, Kim HJ. Complete chloroplast genome of Asarum chungbuensis (C.S. Yook & J.G. Kim) B.U. Oh 2005 (Aristolochiaceae), a Korean endemic species. Mitochondrial DNA B Resour 2024; 9:1005-1009. [PMID: 39113748 PMCID: PMC11305027 DOI: 10.1080/23802359.2024.2387262] [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: 03/13/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Asarum chungbuensis, a species endemic to Korea, has a limited distribution across the Korean Peninsula and is used in traditional medicine. Despite its importance, the genome structure, genetic composition, and phylogenetic relationships based on its chloroplast genome have not been documented. In this study, the complete chloroplast genome of A. chungbuensis was newly assembled. The chloroplast genome is 190,179 base pairs (bp) long, and the overall GC content (%) of the plastid was 36.8%. The chloroplast genome size of A. chungbuensis is longer than that of the normal chloroplast genome (160 kb) because of an inverted small single-copy (SSC) duplication that incorporates the SSC into an inverted repeat (IR) region. By extension, this duplication event causes this chloroplast genome to lack an SSC, unlike other formal structures. The chloroplast genome, with a tripartite structure, consisted of a single-copy region of 93,351 bp with a 34.6% GC content and two IR regions, each with a length of 48,414 bp and a 38.8% GC content. Additionally, it was found to have 113 genes, including 79 PCG genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis revealed that A. chungbuensis was grouped with A. heterotropoides var. seoulense, which diverged from the clade comprising A. koreanum and A. patens. The newly sequenced A. chungbuensis chloroplast genome could provide valuable genomic information for determining unique genome structures, especially for the assessment of genetic diversity, phylogenetic relationships, species conservation, and biogeographic studies of the genus Asarum.
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Affiliation(s)
- Ye-Rim Choi
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Republic of Korea
| | - Sang-Chul Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Republic of Korea
| | - Tae-Hee Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Republic of Korea
| | - Young-Ho Ha
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Republic of Korea
| | - Hyuk-Jin Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Republic of Korea
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Qin J, Ma Y, Liu Y, Wang Y. Phylogenomic analysis and dynamic evolution of chloroplast genomes of Clematis nannophylla. Sci Rep 2024; 14:15109. [PMID: 38956388 PMCID: PMC11220099 DOI: 10.1038/s41598-024-65154-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Clematis nannophylla is a perennial shrub of Clematis with ecological, ornamental, and medicinal value, distributed in the arid and semi-arid areas of northwest China. This study successfully determined the chloroplast (cp) genome of C. nannophylla, reconstructing a phylogenetic tree of Clematis. This cp genome is 159,801 bp in length and has a typical tetrad structure, including a large single-copy, a small single-copy, and a pair of reverse repeats (IRa and IRb). It contains 133 unique genes, including 89 protein-coding, 36 tRNA, and 8 rRNA genes. Additionally, 66 simple repeat sequences, 50 dispersed repeats, and 24 tandem repeats were found; many of the dispersed and tandem repeats were between 20-30 bp and 10-20 bp, respectively, and the abundant repeats were located in the large single copy region. The cp genome was relatively conserved, especially in the IR region, where no inversion or rearrangement was observed, further revealing that the coding regions were more conserved than the noncoding regions. Phylogenetic analysis showed that C. nannophylla is more closely related to C. fruticosa and C. songorica. Our analysis provides reference data for molecular marker development, phylogenetic analysis, population studies, and cp genome processes to better utilise C. nannophylla.
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Affiliation(s)
- Jinping Qin
- College of Animal Husbandry and Veterinary Science, Qinghai University, Xining, 810016, Qinghai, China
| | - Yushou Ma
- College of Animal Husbandry and Veterinary Science, Qinghai University, Xining, 810016, Qinghai, China
| | - Ying Liu
- College of Animal Husbandry and Veterinary Science, Qinghai University, Xining, 810016, Qinghai, China.
| | - Yanlong Wang
- College of Animal Husbandry and Veterinary Science, Qinghai University, Xining, 810016, Qinghai, China.
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Li S, Tian C, Hu H, Yang Y, Ma H, Liu Q, Liu L, Li Z, Wu Z. Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species. Genes (Basel) 2024; 15:815. [PMID: 38927750 PMCID: PMC11202509 DOI: 10.3390/genes15060815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Bromus (Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced Bromus ciliatus, Bromus benekenii, Bromus riparius, and Bromus rubens chloroplast genomes and compared them with four previously described species. The genome sizes of Bromus species ranged from 136,934 bp (Bromus vulgaris) to 137,189 bp (Bromus ciliates, Bromus biebersteinii), with a typical quadripartite structure. The studied species had 129 genes, consisting of 83 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The highest GC content was found in the inverted repeat (IR) region (43.85-44.15%), followed by the large single-copy (LSC) region (36.25-36.65%) and the small single-copy (SSC) region (32.21-32.46%). There were 33 high-frequency codons, with those ending in A/U accounting for 90.91%. A total of 350 simple sequence repeats (SSRs) were identified, with single-nucleotide repeats being the most common (61.43%). A total of 228 forward and 141 palindromic repeats were identified. No reverse or complementary repeats were detected. The sequence identities of all sequences were very similar, especially with respect to the protein-coding and inverted repeat regions. Seven highly variable regions were detected, which could be used for molecular marker development. The constructed phylogenetic tree indicates that Bromus is a monophyletic taxon closely related to Triticum. This comparative analysis of the chloroplast genome of Bromus provides a scientific basis for species identification and phylogenetic studies.
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Affiliation(s)
- Shichao Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Pratacultural College, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunyu Tian
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Haihong Hu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Yanting Yang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Huiling Ma
- Pratacultural College, Gansu Agricultural University, Lanzhou 730070, China
| | - Qian Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Lemeng Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
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Hu X, Liu Y, Chen J, Su X. The complete chloroplast genome of Oxytropis ochrocephala Bunge 1874 (Fabaceae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:641-646. [PMID: 38770145 PMCID: PMC11104710 DOI: 10.1080/23802359.2024.2350626] [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] [Received: 02/20/2024] [Accepted: 04/28/2024] [Indexed: 05/22/2024] Open
Abstract
This study presents the first-ever complete chloroplast (cp) genome sequence of Oxytropis ochrocephala Bunge 1874, a member of the Fabaceae family. The cp genome spans 126,996 base pairs and includes 109 genes, comprising 76 protein-coding genes, 29 tRNA genes, and four rRNA genes. Notably, the genome lacks an inverted repeat (IR) region. Additionally, we constructed phylogenetic trees for 34 species within Trib. Galegeae, employing both maximum likelihood (ML) and Bayesian inference (BI) methods. These analyses robustly support the monophyly of the Oxytropis species, evidenced by high bootstrap values (BP = 100) and posterior probabilities (PP = 1). Within this clade, O. ochrocephala exhibits a sister relationship with other Oxytropis species. Our findings provide valuable insights into the genetic makeup and evolutionary relationships of O. ochrocephala within the Galegeae tribe.
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Affiliation(s)
- XiaYu Hu
- School of Life Sciences, Qinghai Normal University, Xining, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, China
| | - YuPing Liu
- School of Life Sciences, Qinghai Normal University, Xining, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
| | - JinYuan Chen
- School of Life Sciences, Qinghai Normal University, Xining, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
| | - Xu Su
- School of Life Sciences, Qinghai Normal University, Xining, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
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Jost M, Wanke S. A comparative analysis of plastome evolution in autotrophic Piperales. AMERICAN JOURNAL OF BOTANY 2024; 111:e16300. [PMID: 38469876 DOI: 10.1002/ajb2.16300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
PREMISE Many plastomes of autotrophic Piperales have been reported to date, describing a variety of differences. Most studies focused only on a few species or a single genus, and extensive, comparative analyses have not been done. Here, we reviewed publicly available plastome reconstructions for autotrophic Piperales, reanalyzed publicly available raw data, and provided new sequence data for all previously missing genera. Comparative plastome genomics of >100 autotrophic Piperales were performed. METHODS We performed de novo assemblies to reconstruct the plastomes of newly generated sequence data. We used Sanger sequencing and read mapping to verify the assemblies and to bridge assembly gaps. Furthermore, we reconstructed the phylogenetic relationships as a foundation for comparative plastome genomics. RESULTS We identified a plethora of assembly and annotation issues in published plastome data, which, if unattended, will lead to an artificial increase of diversity. We were able to detect patterns of missing and incorrect feature annotation and determined that the inverted repeat (IR) boundaries were the major source for erroneous assembly. Accounting for the aforementioned issues, we discovered relatively stable junctions of the IRs and the small single-copy region (SSC), whereas the majority of plastome variations among Piperales stems from fluctuations of the boundaries of the IR and the large single-copy (LSC) region. CONCLUSIONS This study of all available plastomes of autotrophic Piperales, expanded by new data for previously missing genera, highlights the IR-LSC junctions as a potential marker for discrimination of various taxonomic levels. Our data indicates a pseudogene-like status for cemA and ycf15 in various Piperales. Based on a review of published data, we conclude that incorrect IR-SSC boundary identification is the major source for erroneous plastome assembly. We propose a gold standard for assembly and annotation of high-quality plastomes based on de novo assembly methods and appropriate references for gene annotation.
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Affiliation(s)
- Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Botanik und Molekulare Evolutionsforschung, Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Biodiversität, Goethe-Universität, Frankfurt am Main, Germany
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Wang LL, Li Y, Zheng SS, Kozlowski G, Xu J, Song YG. Complete Chloroplast Genomes of Four Oaks from the Section Cyclobalanopsis Improve the Phylogenetic Analysis and Understanding of Evolutionary Processes in the Genus Quercus. Genes (Basel) 2024; 15:230. [PMID: 38397219 PMCID: PMC10888318 DOI: 10.3390/genes15020230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Quercus is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four Quercus section Cyclobalanopsis species (Q. poilanei, Q. helferiana, Q. camusiae, and Q. semiserrata) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus Quercus. These four chloroplast genomes ranged from 160,784 bp (Q. poilanei) to 161,632 bp (Q. camusiae) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other Quercus species. We identified seven regions with relatively high variability (rps16, ndhk, accD, ycf1, psbZ-trnG-GCC, rbcL-accD, and rpl32-trnL-UAG) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within Quercus. Our phylogenetic tree supported the idea that the genus Quercus forms two well-differentiated lineages (corresponding to the subgenera Quercus and Cerris). Of the three sections in the subgenus Cerris, the section Ilex was split into two clusters, each nested in the other two sections. Moreover, Q. camusiae and Q. semiserrata detected in this study diverged first in the section Cyclobalanopsis and mixed with Q. engleriana in the section Ilex. In particular, 11 protein coding genes (atpF, ndhA, ndhD, ndhF, ndhK, petB, petD, rbcL, rpl22, ycf1, and ycf3) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of Quercus, which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus.
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Affiliation(s)
- Ling-Ling Wang
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai 201418, China;
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| | - Yu Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| | - Si-Si Zheng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
- Department of Biology and Botanic Garden, University of Fribourg, 1700 Fribourg, Switzerland
- Natural History Museum Fribourg, 1700 Fribourg, Switzerland
| | - Jin Xu
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai 201418, China;
| | - Yi-Gang Song
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
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Li MF, Xiao T, Zhang YH. The complete chloroplast genome of Hedychium flavum Roxb., an ornamental, edible and medicinal plant. Mitochondrial DNA B Resour 2023; 8:1253-1257. [PMID: 38026495 PMCID: PMC10653761 DOI: 10.1080/23802359.2023.2281029] [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: 05/17/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Hedychium flavum Roxb. 1820 is a perennial herb mainly distributed in China, India, Myanmar and Thailand with ornamental, edible and medicinal value. It is extensively cultivated as a source of aromatic essential oils, ornamental plant, food flavorings and vegetables, and folk medicine. In this study, we sequence the complete chloroplast genome of H. flavum by de novo assembly. The assembled genome has a typical quadripartite circular structure with 163,909 bp in length, containing a large single-copy region (LSC, 88,589 bp), a small single-copy region (SSC, 15,762 bp), and two inverted repeat regions (IRs, 29,779 bp). The cp genome contains 133 genes, including 87 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on the complete cp genome shows a close affinity of H. flavum and H. neocarneum with 100% bootstrap support. This study will provide useful genetic resource for further phylogenetic analysis of the genus Hedychium and Zingiberaceae.
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Affiliation(s)
- Mei-Fei Li
- School of Life Science, Yunnan Normal University, Kunming, China
| | - Tao Xiao
- School of Life Science, Yunnan Normal University, Kunming, China
| | - Yong-Hong Zhang
- School of Life Science, Yunnan Normal University, Kunming, China
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Yao ST, Lu YB, Zhang ZJ, Li C, Wang PF, Qin XM. The complete chloroplast genome of Chloranthus nervosus Collett ex Hemsl. 1890 (Chloranthaceae). Mitochondrial DNA B Resour 2023; 8:1224-1228. [PMID: 38026494 PMCID: PMC10653614 DOI: 10.1080/23802359.2023.2278818] [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: 08/09/2023] [Accepted: 10/29/2023] [Indexed: 12/01/2023] Open
Abstract
In this study, we sequenced and assembled the complete chloroplast genome of Chloranthus nervosus Collett ex Hemsl. 1890. The total length of the complete chloroplast sequence was found to be 158,002 bp. It consisted of a large single-copy (LSC) region of 87,127 bp, a small single-copy (SSC) region of 18,541 bp, and a pair of inverted repeat (IR) regions, each with a length of 26,167 bp. The overall GC content of the complete chloroplast genome was 38.9%, with the LSC region, SSC region, and IR regions exhibiting GC contents of 37.4%, 34.1%, and 43.1%, respectively. The annotation of the chloroplast genome revealed a total of 131 genes, comprising 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis revealed that the seven sampled species of Chloranthus were divided into two clades. Within the clade characterized by long filamentous anther connectives, C. nervosus showed the closest relation to C. japonicus. These findings validated the previous preliminary results on the phylogenetic relationships of the seven species of Chloranthus with strong support.
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Affiliation(s)
- Shu-Ting Yao
- College of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Yong-Bin Lu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Zhan-Jiang Zhang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plant, Nanning, China
| | - Cui Li
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plant, Nanning, China
| | - Peng-Fei Wang
- Technology Center, China Tobacco Henan Industrial Co., Ltd., Zhengzhou, China
| | - Xin-Mei Qin
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
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11
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Chen X, Li B, Zhang X. Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis. Sci Rep 2023; 13:18731. [PMID: 37907468 PMCID: PMC10618267 DOI: 10.1038/s41598-023-45421-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.
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Affiliation(s)
- Xiaoli Chen
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Buyu Li
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Xuemei Zhang
- College of Life Sciences, China West Normal University, Nanchong, 637009, China.
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12
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Yang Z, Ferguson DK, Yang Y. New insights into the plastome evolution of Lauraceae using herbariomics. BMC PLANT BIOLOGY 2023; 23:387. [PMID: 37563571 PMCID: PMC10413609 DOI: 10.1186/s12870-023-04396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND The family Lauraceae possesses ca. 50 genera and 2,500-3,000 species that are distributed in the pantropics. Only half of the genera of the family were represented in previously published plastome phylogenies because of the difficulty of obtaining research materials. Plastomes of Hypodaphnideae and the Mezilaurus group, two lineages with unusual phylogenetic positions, have not been previously reported and thus limit our full understanding on the plastome evolution of the family. Herbariomics, promoted by next generation sequencing technology, can make full use of herbarium specimens, and provides opportunities to fill the sampling gap. RESULTS In this study, we sequenced five new plastomes (including four genera which are reported for the first time, viz. Chlorocardium, Hypodaphnis, Licaria and Sextonia) from herbarium specimens using genome skimming to conduct a comprehensive analysis of plastome evolution of Lauraceae as a means of sampling representatives of all major clades of the family. We identified and recognized six types of plastomes and revealed that at least two independent loss events at the IR-LSC boundary and an independent expansion of SSC occurred in the plastome evolution of the family. Hypodaphnis possesses the ancestral type of Lauraceae with trnI-CAU, rpl23 and rpl2 duplicated in the IR regions (Type-I). The Mezilaurus group shares the same plastome structure with the core Lauraceae group in the loss of trnI-CAU, rpl23 and rpl2 in the IRa region (Type-III). Two new types were identified in the Ocotea group: (1) the insertion of trnI-CAU between trnL-UAG and ccsA in the SSC region of Licaria capitata and Ocotea bracteosa (Type-IV), and (2) trnI-CAU and pseudogenizated rpl23 inserted in the same region of Nectandra angustifolia (Type-V). Our phylogeny suggests that Lauraceae are divided into nine major clades largely in accordance with the plastome types. The Hypodaphnideae are the earliest diverged lineage supported by both robust phylogeny and the ancestral plastome type. The monophyletic Mezilaurus group is sister to the core Lauraceae. CONCLUSIONS By using herbariomics, we built a more complete picture of plastome evolution and phylogeny of the family, thus providing a convincing case for further use of herbariomics in phylogenetic studies of the Lauraceae.
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Affiliation(s)
- Zhi Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing, 210037, China
| | | | - Yong Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing, 210037, China.
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Mkala EM, Jost M, Dong X, Mwachala G, Musili PM, Wanke S, Hu GW, Wang QF. Phylogenetic and comparative analyses of Hydnora abyssinica plastomes provide evidence for hidden diversity within Hydnoraceae. BMC Ecol Evol 2023; 23:34. [PMID: 37464315 PMCID: PMC10353213 DOI: 10.1186/s12862-023-02142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND To date, plastid genomes have been published for all but two holoparasitic angiosperm families. However, only a single or a few plastomes represent most of these families. Of the approximately 40 genera of holoparasitic angiosperms, a complete plastid genome sequence is available for only about half. In addition, less than 15 species are currently represented with more than one published plastid genome, most of which belong to the Orobanchaceae. Therefore, a significant portion of the holoparasitic plant plastome diversity remains unexplored. This limited information could hinder potential evolutionary pattern recognition as well as the exploration of inter- and intra-species plastid genome diversity in the most extreme holoparasitic angiosperms. RESULTS Here, we report the first plastomes of Kenyan Hydnora abyssinica accessions. The plastomes have a typical quadripartite structure and encode 24 unique genes. Phylogenetic tree reconstruction recovers the Kenyan accessions as monophyletic and together in a clade with the Namibian H. abyssinica accession and the recently published H. arabica from Oman. Hydnora abyssinica as a whole however is recovered as non-monophyletic, with H. arabica nested within. This result is supported by distinct structural plastome synapomorphies as well as pairwise distance estimates that reveal hidden diversity within the Hydnora species in Africa. CONCLUSION We propose to increase efforts to sample widespread holoparasitic species for their plastid genomes, as is the case with H. abyssinica, which is widely distributed in Africa. Morphological reinvestigation and further molecular data are needed to fully investigate the diversity of H. abyssinica along the entire range of distribution, as well as the diversity of currently synonymized taxa.
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Affiliation(s)
- Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
- University of Chinese Academy of Sciences, Beijing, CN-100049, China
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
- University of Chinese Academy of Sciences, Beijing, CN-100049, China
| | - Geoffrey Mwachala
- East African Herbarium, National Museums of Kenya, P. O. Box 451660-0100, Nairobi, Kenya
| | - Paul Mutuku Musili
- East African Herbarium, National Museums of Kenya, P. O. Box 451660-0100, Nairobi, Kenya
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China.
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
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14
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Kim YK, Jo S, Cheon SH, Hong JR, Kim KJ. Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae). Int J Mol Sci 2023; 24:11448. [PMID: 37511216 PMCID: PMC10380568 DOI: 10.3390/ijms241411448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.
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Affiliation(s)
- Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sangjin Jo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ja-Ram Hong
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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15
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Xia Q, Zhang H, Lv D, El-Kassaby YA, Li W. Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes. BMC Genomics 2023; 24:346. [PMID: 37349702 DOI: 10.1186/s12864-023-09439-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Pinus is the largest genus of Pinaceae and the most primitive group of modern genera. Pines have become the focus of many molecular evolution studies because of their wide use and ecological significance. However, due to the lack of complete chloroplast genome data, the evolutionary relationship and classification of pines are still controversial. With the development of new generation sequencing technology, sequence data of pines are becoming abundant. Here, we systematically analyzed and summarized the chloroplast genomes of 33 published pine species. RESULTS Generally, pines chloroplast genome structure showed strong conservation and high similarity. The chloroplast genome length ranged from 114,082 to 121,530 bp with similar positions and arrangements of all genes, while the GC content ranged from 38.45 to 39.00%. Reverse repeats showed a shrinking evolutionary trend, with IRa/IRb length ranging from 267 to 495 bp. A total of 3,205 microsatellite sequences and 5,436 repeats were detected in the studied species chloroplasts. Additionally, two hypervariable regions were assessed, providing potential molecular markers for future phylogenetic studies and population genetics. Through the phylogenetic analysis of complete chloroplast genomes, we offered novel opinions on the genus traditional evolutionary theory and classification. CONCLUSION We compared and analyzed the chloroplast genomes of 33 pine species, verified the traditional evolutionary theory and classification, and reclassified some controversial species classification. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.
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Affiliation(s)
- Qijing Xia
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongbin Zhang
- Gansu Province Academy of Qilian Water Resource Conservation Forests Research Institute, Zhangye, 734031, China
| | - Dong Lv
- Gansu Province Academy of Qilian Water Resource Conservation Forests Research Institute, Zhangye, 734031, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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16
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Xu Q, Li Z, Wu N, Yang J, Yuan L, Zhao T, Sima Y, Xu T. Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants. Genes (Basel) 2023; 14:1262. [PMID: 37372442 DOI: 10.3390/genes14061262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The genus Houpoea belongs to the family Magnoliaceae, and the species in this genus have important medicinal values. However, the investigation of the correlation between the evolution of the genus and its phylogeny has been severely hampered by the unknown range of species within the genus and the paucity of research on its chloroplast genome. Thus, we selected three species of Houpoea: Houpoea officinalis var officinalis (OO), Houpoea officinalis var. biloba (OB), and Houpoea rostrata (R). With lengths of 160,153 bp (OO), 160,011 bp (OB), and 160,070 bp (R), respectively, the whole chloroplast genomes (CPGs) of these three Houpoea plants were acquired via Illumina sequencing technology, and the findings were annotated and evaluated. These three chloroplast genomes were revealed by the annotation findings to be typical tetrads. A total of 131, 132, and 120 different genes were annotated. The CPGs of the three species had 52, 47, and 56 repeat sequences, which were primarily found in the ycf2 gene. A useful tool for identifying species is the approximately 170 simple sequence repeats (SSRs) that have been found. The border area of the reverse repetition region (IR) was studied, and it was shown that across the three Houpoea plants, it is highly conservative, with only changes between H. rostrata and the other two plants observed. Numerous highly variable areas (rps3-rps19, rpl32-trnL, ycf1, ccsA, etc.) have the potential to serve as the barcode label for Houpoea, according to an examination of mVISTA and nucleotide diversity (Pi). Phylogenetic relation indicates that Houpoea is a monophyletic taxon, and its genus range and systematic position are consistent with the Magnoliaceae system of Sima Yongkang-Lu Shugang, including five species and varieties of H. officinalis var. officinalis, H. rostrata, H. officinalis var. biloba, Houpoea obovate, and Houpoea tripetala, which evolved and differentiated from the ancestors of Houpoea to the present Houpoea in the above order. This study provides valuable information on the genus Houpoea, enriches the CPG information on Houpoea genus, and provides genetic resources for the further classification of and phylogenetic research on Houpoea.
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Affiliation(s)
- Qinbin Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Zhuoran Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Nannan Wu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Jing Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Lang Yuan
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Tongxing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yongkang Sima
- Kunming Arboretum, Yunnan Academy of Forestry & Grassland Science, Kunming 650201, China
| | - Tao Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
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17
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Shen Z, Ding X, Cheng J, Wu F, Yin H, Wang M. Phylogenetic studies of magnoliids: Advances and perspectives. FRONTIERS IN PLANT SCIENCE 2023; 13:1100302. [PMID: 36726671 PMCID: PMC9885158 DOI: 10.3389/fpls.2022.1100302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Magnoliids are the largest flowering plant clades outside of the eudicots and monocots, which are distributed worldwide and have high economic, ornamental and ecological values. Eudicots, monocots and magnoliids are the three major clades of Mesangiospermae, and their phylogenetic relationship is one of the most interesting issues. In recent years, with the continuous accumulation of genomic information, the evolutionary status of magnoliids has become a hot spot in plant phylogenetic research. Although great efforts have been made to study the evolution of magnoliids using molecular data from several representative species such as nuclear genome, plastid genome, mitochondrial genome, and transcriptome, the results of current studies on the phylogenetic status of magnoliids are inconsistent. Here, we systematically describe the current understanding of the molecular research on magnoliid phylogeny and review the differences in the evolutionary state of magnoliids. Understanding the research approaches and limitations of magnoliid phylogeny can guide research strategies to further improve the study of the phylogenetic evolution of magnoliids.
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Affiliation(s)
- Zhiguo Shen
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Xin Ding
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Jianming Cheng
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Fangfang Wu
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Hengfu Yin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Minyan Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
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18
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Gaikwad AB, Kaila T, Maurya A, Kumari R, Rangan P, Wankhede DP, Bhat KV. The chloroplast genome of black pepper ( Piper nigrum L.) and its comparative analysis with related Piper species. FRONTIERS IN PLANT SCIENCE 2023; 13:1095781. [PMID: 36714762 PMCID: PMC9878596 DOI: 10.3389/fpls.2022.1095781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Piper nigrum, also known as black pepper, is an economically and ecologically important crop of the genus Piper. It has been titled as the king of spices due to its wide consumption throughout the world. In the present investigation, the chloroplast genome of P. nigrum has been assembled from a whole genome sequence by integrating the short and long reads generated through Illumina and PacBio platforms, respectively. The chloroplast genome was observed to be 161,522 bp in size, having a quadripartite structure with a large single copy (LSC) region of 89,153 bp and a small single copy (SSC) region of 18,255 bp separated by a copy of inverted repeats (IRs), each 27,057 bp in length. Taking into consideration all the duplicated genes, a total of 131 genes were observed, which included 81 protein-coding genes, 37 tRNAs, 4 rRNAs, and 1 pseudogene. Individually, the LSC region consisted of 83 genes, the SSC region had 13 genes, and 18 genes were present in each IR region. Additionally, 216 SSRs were detected and 11 of these were validated through amplification in 12 species of Piper. The features of the chloroplast genome have been compared with those of the genus Piper. Our results provide useful insights into evolutionary and molecular studies of black pepper which will contribute to its further genetic improvement and breeding.
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Affiliation(s)
- Ambika Baldev Gaikwad
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Tanvi Kaila
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - Avantika Maurya
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ratna Kumari
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Parimalan Rangan
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dhammaprakash Pandhari Wankhede
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - K. V. Bhat
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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19
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Yu X, Song YR, Zhao ZN. The complete chloroplast genome of Elsholtzia fruticosa (D. Don) Rehd. (Labiatae), an ornamental plant with high medicinal value. Mitochondrial DNA B Resour 2023; 8:336-341. [PMID: 36876144 PMCID: PMC9980026 DOI: 10.1080/23802359.2023.2183069] [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: 03/05/2023] Open
Abstract
Elsholtzia fruticosa is an ornamental plant with high medicinal value. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of the species. The complete cp sequence is 151,550 bp, including the large single-copy (LSC) region of 82,778 bp, the small single-copy (SSC) region of 17,492 bp, and a pair of invert repeats (IRs) regions of 25,640 bp. It encodes 132 unique genes in total, including 87 protein-coding genes, 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). The comparative analysis of complete cp genomes showed that the genomic structure and gene order of E. fruticosa cps were conserved. The sequences of rps15, rps19, ycf1, ycf3, ycf15, psbL, psaI, trnG-UCC, trnS-GCU, trnR-UCU, trnL-UAG, trnP-UG, and trnL-UAA serve as hotspots for developing the DNA barcoding of Elsholtzia species. There are 49 SSR loci in the cp genome of E. fruticosa, among which the repeat numbers of mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotides SSR are 37, 9, 3, 0, and 0, respectively. A total of 50 repeats were detected, including 15 forward repeats, seven reverse repeats, 26 palindromic repeats, and two complementary repeats. Phylogenetic analysis based on the complete cp genome and protein-coding DNA sequences of 26 plants indicates that E. fruticosa has a dose relationship with E. splendens and E. byeonsanensis.
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Affiliation(s)
- Xiao Yu
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, China
| | - Yu-Ru Song
- School of Forestry, Southwest Forestry University, Kunming, China
| | - Zhen-Ning Zhao
- School of Forestry, Southwest Forestry University, Kunming, China
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Wang Y, Xie Y, Jin J, Li J, Qiu X, Tong Y, Li Z, Zhang Z, Lai W. Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae. PeerJ 2023; 11:e15322. [PMID: 37187516 PMCID: PMC10178313 DOI: 10.7717/peerj.15322] [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] [Received: 10/13/2022] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Background Elaeocarpaceae is a vital family in tropical and subtropical forests. Compared with the important position of Elaeocarpaceae species in forest ecosystem and the concern of medicinal value, the most research on Elaeocarpaceae are classification and taxonomy. Molecular systematics has corrected the morphological misjudgment, and it belongs to Oxalidales. Phylogenetic and divergence time estimates of Elaeocarpaceae is mostly constructed by using chloroplast gene fragments. At present, although there are reports on the chloroplast structure of Elaeocarpaceae, a comprehensive analysis of the chloroplast structure of Elaeocarpaceae is lacking. Methods To understand the variation in chloroplast sequence size and structure in Elaeocarpaceae, the chloroplast genomes of nine species were sequenced using the Illumina HiSeq 2500 platform and further assembled and annotated with Elaeocarpus japonicus and Sloanea sinensis (family Elaeocarpaceae) as references. A phylogenomic tree was constructed based on the complete chloroplast genomes of the 11 species representing five genera of Elaeocarpaceae. Chloroplast genome characteristics were examined by using Circoletto and IRscope software. Results The results revealed the following: (a) The 11 sequenced chloroplast genomes ranged in size from 157,546 to 159,400 bp. (b) The chloroplast genomes of Elaeocarpus, Sloanea, Crinodendron and Vallea lacked the rpl32 gene in the small single-copy (SSC) region. The large single-copy (LSC) region of the chloroplast genomes lacked the ndhK gene in Elaeocarpus, Vallea stipularis, and Aristotelia fruticosa. The LSC region of the chloroplast genomes lacked the infA gene in genus Elaeocarpus and Crinodendron patagua. (c) Through inverted repeat (IR) expansion and contraction analysis, a significant difference was found between the LSC/IRB and IRA/LSC boundaries among these species. Rps3 was detected in the neighboring regions of the LSC and IRb regions in Elaeocarpus. (d) Phylogenomic analysis revealed that the genus Elaeocarpus is closely related to Crinodendron patagua on an independent branch and Aristotelia fruticosa is closely related to Vallea stipularis, forming a clade with the genus Sloanea. Structural comparisons showed that Elaeocarpaceae diverged at 60 Mya, the genus Elaeocarpus diverged 53 Mya and that the genus Sloanea diverged 0.44 Mya. These results provide new insight into the evolution of the Elaeocarpaceae.
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Affiliation(s)
- Yihui Wang
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- School of Landscape Architecture, Beijing Forestry University, Beijing, P.R. China
| | - Yifei Xie
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China
| | - Jiayi Jin
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
| | - Jinyue Li
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna, P.R. China
| | - Xiangdong Qiu
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
| | - Yang Tong
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
| | - Zhongyang Li
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China
| | - Zhixiang Zhang
- School of Ecology and Nature conservation, Beijing Forestry University, Beijing, P.R. China
| | - Wenling Lai
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China
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Kang JS, Kim BY, Yoo KO. The complete plastid genome sequence of Chloranthus fortunei (A. Gray) Solms-Laub. in Chloranthaceae. Mitochondrial DNA B Resour 2022; 7:1829-1833. [PMID: 36325282 PMCID: PMC9621198 DOI: 10.1080/23802359.2022.2132840] [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] [Indexed: 11/14/2022] Open
Abstract
Chloranthus fortunei (A. Gray) Solms-Laub. is a perennial herb in a basal angiosperm family Chloranthaceae. Here, we reported the complete plastid genome of C. fortunei using Illumina short-read data. The total genome size was 157,063 bp in length, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The gene content and order were consistent with previously reported Chloranthus plastid genomes. The overall GC content of the C. fortunei plastid genome was 39.0%. In the phylogenetic result, genus Chloranthus was monophyletic and divided into two subclades: C. japonicus+C. angustifolius+C. fortunei, and C. henryi+C. spicatus+C. erectus. Our phylogenetic result was consistent with previous phylogenetic studies, and was supported by a previously proposed infrageneric classification of the genus Chloranthus.
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Affiliation(s)
- Jong-Soo Kang
- Department of Biological Sciences, Kangwon National University, Chuncheon, South Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Ki-Oug Yoo
- Department of Biological Sciences, Kangwon National University, Chuncheon, South Korea,CONTACT Ki-Oug Yoo Department of Biological Sciences, Kangwon National University, Chuncheon, Gangwon-do, South Korea
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22
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Xie H, Zhang L, Zhang C, Chang H, Xi Z, Xu X. Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species. BMC Genomics 2022; 23:716. [PMID: 36261795 PMCID: PMC9583488 DOI: 10.1186/s12864-022-08934-6] [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: 04/06/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus Gynopodium contains eight species, but six of these species are threatened. No studies to date have characterized the characteristics of the chloroplast genomes (CPGs) within subgenus Gynopodium species. In this study, we compared the structure of CPGs, identified the mutational hotspots and resolved the phylogenetic relationship of subgenus Gynopodium. RESULTS The CPGs of six subgenus Gynopodium species ranged in size from 160,027 bp to 160,114 bp. A total of 131 genes were identified, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. We detected neither major expansions or contractions in the inverted repeat region, nor rearrangements or insertions in the CPGs of six subgenus Gynopodium species. A total of 300 large repeat sequences (forward, reverse, and palindrome repeats), 847 simple sequence repeats, and five highly variable regions were identified. One gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG, and ccsA-ndhD) were identified as mutational hotspots by their high nucleotide diversity (Pi) values (≥ 0.004), which were useful for species discrimination. Maximum likelihood and Bayesian inference trees were concordant and indicated that Magnoliaceae consisted of two genera Liriodendron and Magnolia. Six species of subgenus Gynopodium clustered as a monophyletic clade, forming a sister clade with subgenus Yulania (BS = 100%, PP = 1.00). Due to the non-monophyly of subgenus Magnolia, subgenus Gynopodium should be treated as a section of Magnolia. Within section Gynopodium, M. sinica diverged first (posterior probability = 1, bootstrap = 100), followed by M. nitida, M. kachirachirai and M. lotungensis. M. omeiensis was sister to M. yunnanensis (posterior probability = 0.97, bootstrap = 50). CONCLUSION The CPGs and characteristics information provided by our study could be useful in species identification, conservation genetics and resolving phylogenetic relationships of Magnoliaceae species.
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Affiliation(s)
- Huanhuan Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People's Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan, 750021, China
| | - Cheng Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Hong Chang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Xiaoting Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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23
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Li J, Fan R, Xu J, Hu L, Su F, Hao C. Comparative analysis of the chloroplast genomes of eight Piper species and insights into the utilization of structural variation in phylogenetic analysis. Front Genet 2022; 13:925252. [PMID: 36246585 PMCID: PMC9556897 DOI: 10.3389/fgene.2022.925252] [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] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
With more than 2000 species, Piper is regarded as having high medicinal, cosmetic, and edible value. There also remain some taxonomic and evolutionary uncertainties about the genus. This study performed chloroplast genome sequencing of eight poorly studied Piper species and a comparative analysis with black pepper (Piper nigrum). All examined species were highly similar in gene content, with 79 protein-coding genes, 24 tRNAs, and four rRNAs. They also harbored significant structural differences: The number of SSRs ranged from 63 to 87, over 10,000 SNPs were detected, and over 1,000 indels were found. The spatial distribution of structural differences was uneven, with the IR and LSC being relatively more conserved and the SSC region highly variable. Such structural variations of the chloroplast genome can help in evaluating the phylogenetic relationships between species, deciding some hard-to-distinguish evolutionary relationships, or eliminating improper markers. The SSC region may be evolving at high speed, and some species showed a high degree of sequence variation in the SSC region, which seriously affected marker sequence detection. Conversely, CDS sequences tended to lack variation, and some CDSs can serve as ideal markers for phylogenetic reconstruction. All told, this study provides an effective strategy for selecting chloroplast markers, analyzing difficult-to-distinguish phylogenetic relationships and avoiding the taxonomic errors caused by high degree of sequence variations.
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Affiliation(s)
- Jing Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Jintao Xu
- Yangtze Normal University, Chongqing, China
| | - Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Fan Su
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
- *Correspondence: Chaoyun Hao,
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Yan L, Wang H, Huang X, Li Y, Yue Y, Wang Z, Tang S. Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution. Front Genet 2022; 13:925726. [PMID: 35873491 PMCID: PMC9305825 DOI: 10.3389/fgene.2022.925726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/17/2022] [Indexed: 11/26/2022] Open
Abstract
Tilia is a complex genus in the family Malvaceae that has high ecological and economical values. Owing to the lack of sufficient distinguishable morphological and molecular characteristics, interspecific relationships in this genus are not clear. Chloroplast (cp) genomes are small, meanwhile most angiosperms usually undergo matrilineal inheritance. Consequently, they can be used in molecular systematics and phylogenetic analyses. Here, we sequenced and assembled cp genomes from T. endochrysea, T. tomentosa, T. miqueliana, T. americana and T. cordata, and compared them with those of seven previously reported Tilia species. Similar gene contents, gene orders and GC contents existed among the 12 cp genomes, which ranged from 162,564 to 162,855 bp and encoded 113 unique genes. Abundant simple sequence repeats (119–127) and dispersed repeats (97–135) were detected in Tilia cp genomes. In total, 11 hypervariable regions were identified that could be suitable for species identification and phylogenetic studies. A phylogenetic analysis of Malvaceae based on 5 hypervariable genes (matK + ndhF + rpoB + rpoC2+ycf1) revealed that all eight subfamilies were monophyletic groups. Additionally, the genus Tilia was divided into three groups on the basis of all 521 molecular variation loci. The current study provides valuable insights into the genomic evolution of the genus Tilia.
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Affiliation(s)
- Linjun Yan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Huanli Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Xi Huang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Yingchao Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuanhao Yue
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Zhongwei Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Shijie Tang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
- *Correspondence: Shijie Tang,
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25
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Jost M, Naumann J, Bolin JF, Martel C, Rocamundi N, Cocucci AA, Lupton D, Neinhuis C, Wanke S. Structural plastome evolution in holoparasitic Hydnoraceae with special focus on inverted and direct repeats. Genome Biol Evol 2022; 14:6602284. [PMID: 35660863 PMCID: PMC9168662 DOI: 10.1093/gbe/evac077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Plastome condensation during adaptation to a heterotrophic lifestyle is generally well understood and lineage-independent models have been derived. However, understanding the evolutionary trajectories of comparatively old heterotrophic lineages, that are on the cusp of a minimal plastomes, is essential to complement and expand current knowledge. We study Hydnoraceae, one of the oldest and least investigated parasitic angiosperm lineages. Plastome comparative genomics, using seven out of eight known species of the genus Hydnora and three species of Prosopanche, reveal a high degree of structural similarity and shared gene content; contrasted by striking dissimilarities with respect to repeat content (inverted and direct repeats). We identified varying IR content and positions, likely resulting from multiple, independent evolutionary events and a direct repeat gain in Prosopanche. Considering different evolutionary trajectories and based on a fully resolved and supported species-level phylogenetic hypothesis, we describe three possible, distinct models to explain the Hydnoraceae plastome states. For comparative purposes we also report the first plastid genomes for the closely related autotrophic genera Lactoris (Lactoridaceae) and Thottea (Aristolochiaceae).
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Affiliation(s)
- Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Germany
| | - Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Germany
| | | | - Carlos Martel
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.,Instituto de Ciencias Ómicas y Biotecnología Aplicada, Pontificia Universidad Católica del Perú, Peru
| | - Nicolás Rocamundi
- Laboratorio de Ecología Evolutiva y Biología Floral, IMBIV, CONICET and Universidad Nacional de Córdoba, Argentina
| | - Andrea A Cocucci
- Laboratorio de Ecología Evolutiva y Biología Floral, IMBIV, CONICET and Universidad Nacional de Córdoba, Argentina
| | - Darach Lupton
- Oman Botanic Garden, Sultanate of Oman.,National Botanic Gardens, Glasnevin, Ireland
| | | | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Germany.,Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Fan X, Wang W, Wagutu GK, Li W, Li X, Chen Y. Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships. BMC PLANT BIOLOGY 2022; 22:230. [PMID: 35513783 PMCID: PMC9069798 DOI: 10.1186/s12870-022-03608-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 04/19/2022] [Indexed: 05/06/2023]
Abstract
BACKGROUND Trapa L. is a floating-leaved aquatic plant with important economic and ecological values. However, the species identification and phylogenetic relationship within Trapa are still controversial, which necessitates the need for plastid genome information of Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences, comparative analyses of chloroplast genomes were performed on the 15 Trapa species/taxa for the first time. RESULTS The Trapa chloroplast genomes exhibited typical quadripartite structures with lengths from 155,453 to 155,559 bp. The gene orders and contents within Trapa were conservative, but several changes were found in the microstructure. The intron loss of rpl2, also detected in Lythraceae, was found in all Trapa species/taxa, suggesting close genetic relationship between Lythraceae and Trapaceae. Notably, two small-seed species (T. incisa and T. maximowiczii) showed the smallest genome size with 155,453 and 155,477 bp, respectively. Each cp genome contained the same 130 genes consisting of 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Trapa species/taxa showed 37 (T. incisa and T. maximowiczii) to 41 (T. sibirica) long repeats, including forward, palindromic, reversed and complementary repeats. There were 110 (T. quadrispinosa) to 123 (T. incisa and T. maximowiczii) SSR (simple sequence repeat) loci in Trapa chloroplast genomes. Comparative analyses revealed that two hotspot regions (atpA-atpF and rps2-rpoC2) in Trapa chloroplast genomes could be served as potential molecular markers. Three phylogenetic analyses (ML, MP and BI) consistently showed that there were two clusters within Trapa, including large- and small-seed species/taxa, respectively; for the large-seed Trapa, they clustered according to their geographical origin and tubercle morphology on the surface of seeds. CONCLUSION In summary, we have acquired the sequences of 13 Trapa chloroplast genomes, and performed the comparative analyses within Trapa for the first time. The results have helped us better identify the Trapa species/taxa and deepen the understanding of genetic basis and phylogenetic relationship of Trapa, which will facilitate the effective management and utilization of the important genetic resources in the future.
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Affiliation(s)
- Xiangrong Fan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- College of Science, Tibet University, Lhasa, 850000, People's Republic of China
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, 850000, People's Republic of China
| | - Wuchao Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Godfrey K Wagutu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Wei Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Xiuling Li
- College of Life Science, Linyi University, Linyi, 276000, People's Republic of China.
| | - Yuanyuan Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
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Samigullin T, Logacheva M, Terentieva E, Degtjareva G, Pimenov M, Valiejo-Roman C. Plastid Phylogenomic Analysis of Tordylieae Tribe (Apiaceae, Apioideae). PLANTS (BASEL, SWITZERLAND) 2022; 11:709. [PMID: 35270181 PMCID: PMC8912408 DOI: 10.3390/plants11050709] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
Abstract
Based on the nrDNA ITS sequence data, the Tordylieae tribe is recognized as monophyletic with three major lineages: the subtribe Tordyliinae, the Cymbocarpum clade, and the Lefebvrea clade. Recent phylogenomic investigations showed incongruence between the nuclear and plastid genome evolution in the tribe. To assess phylogenetic relations and structure evolution of plastomes in Tordylieae, we generated eleven complete plastome sequences using the genome skimming approach and compared them with the available data from this tribe and close relatives. Newly assembled plastomes had lengths ranging from 141,148 to 150,103 base pairs and contained 122-127 genes, including 79-82 protein-coding genes, 35-37 tRNAs, and 8 rRNAs. We observed substantial differences in the inverted repeat length and gene content, accompanied by a complex picture of multiple JLA and JLB shifts. In concatenated phylogenetic analyses, Tordylieae plastomes formed at least three not closely related lineages with plastomes of the Lefebvrea clade as a sister group to plastomes from the Selineae tribe. The newly obtained data have increased our knowledge on the range of plastome variability in Apiaceae.
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Affiliation(s)
- Tahir Samigullin
- Department of Evolutionary Biochemistry, A. N. Belozersky Research Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory 1–40, 119992 Moscow, Russia; (M.L.); (C.V.-R.)
| | - Maria Logacheva
- Department of Evolutionary Biochemistry, A. N. Belozersky Research Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory 1–40, 119992 Moscow, Russia; (M.L.); (C.V.-R.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Elena Terentieva
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119992 Moscow, Russia; (E.T.); (G.D.); (M.P.)
| | - Galina Degtjareva
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119992 Moscow, Russia; (E.T.); (G.D.); (M.P.)
| | - Michael Pimenov
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119992 Moscow, Russia; (E.T.); (G.D.); (M.P.)
| | - Carmen Valiejo-Roman
- Department of Evolutionary Biochemistry, A. N. Belozersky Research Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory 1–40, 119992 Moscow, Russia; (M.L.); (C.V.-R.)
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28
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Ananda G, Norton S, Blomstedt C, Furtado A, Møller B, Gleadow R, Henry R. Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes. THE PLANT GENOME 2021; 14:e20123. [PMID: 34323394 DOI: 10.1002/tpg2.20123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is an important food crop with a diverse gene pool residing in its wild relatives. A total of 15 sorghum accessions from the unexploited wild gene pool of the Sorghum genus, representing the five subgenera, were sequenced, and the complete chloroplast genomes and 99 common single-copy concatenated nuclear genes were assembled. Annotation of the chloroplast genomes identified a total of 81 protein-coding genes, 38 tRNA, and four rRNA genes. The gene content and gene order among the species was identical. A total of 153 nonsynonymous amino acid changes in 40 genes were identified across the species. Phylogenetic analysis of both the whole chloroplast genome and nuclear genes revealed a similar topology with two distinct clades within the genus. The species within the subgenera Eusorghum, Chaetosorghum, and Heterosorghum clustered in one clade, whereas the species within the subgenera Parasorghum and Stiposorghum clustered in a second clade. However, the subgenera Parasorghum and Stiposorghum were not monophyletic, suggesting the need for further research to resolve the relationships within this group. The close relationship between the two monotypic subgenera Chaetosorghum and Heterosorghum suggests that species within these subgenera could be considered as one group. This analysis provides an improved understanding of the genetic relationships within the Sorghum genus and defines diversity in wild sorghum species that may be useful for crop improvement.
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Affiliation(s)
- Galaihalage Ananda
- Queensland Alliance for Agriculture and Food Innovation, The Univ. of Queensland, St Lucia, QLD, Australia
| | - Sally Norton
- Australian Grains Genebank, Agriculture Victoria, Horsham, VIC, Australia
| | - Cecilia Blomstedt
- School of Biological Sciences, Monash Univ., Clayton, VIC, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The Univ. of Queensland, St Lucia, QLD, Australia
| | - Birger Møller
- Plant Biochemistry Laboratory, Dep. of Plant and Environmental Sciences, Univ. of Copenhagen, Copenhagen, Denmark
| | - Roslyn Gleadow
- Queensland Alliance for Agriculture and Food Innovation, The Univ. of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, Monash Univ., Clayton, VIC, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, The Univ. of Queensland, St Lucia, QLD, Australia
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Yang C, Zhao Q, Wang Y, Zhao J, Qiao L, Wu B, Yan S, Zheng J, Zheng X. Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species. Front Genet 2021; 12:732432. [PMID: 34490050 PMCID: PMC8417831 DOI: 10.3389/fgene.2021.732432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022] Open
Abstract
The synonymous codons usage shows a characteristic pattern of preference in each organism. This codon usage bias is thought to have evolved for efficient protein synthesis. Synonymous codon usage was studied in genes of the hexaploid wheat Triticum aestivum (AABBDD) and its progenitor species, Triticum urartu (AA), Aegilops tauschii (DD), and Triticum turgidum (AABB). Triticum aestivum exhibited stronger usage bias for G/C-ending codons than did the three progenitor species, and this bias was especially higher compared to T. turgidum and Ae. tauschii. High GC content is a primary factor influencing codon usage in T. aestivum. Neutrality analysis showed a significant positive correlation (p<0.001) between GC12 and GC3 in the four species with regression line slopes near zero (0.16–0.20), suggesting that the effect of mutation on codon usage was only 16–20%. The GC3s values of genes were associated with gene length and distribution density within chromosomes. tRNA abundance data indicated that codon preference corresponded to the relative abundance of isoaccepting tRNAs in the four species. Both mutation and selection have affected synonymous codon usage in hexaploid wheat and its progenitor species. GO enrichment showed that GC biased genes were commonly enriched in physiological processes such as photosynthesis and response to acid chemical. In some certain gene families with important functions, the codon usage of small parts of genes has changed during the evolution process of T. aestivum.
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Affiliation(s)
- Chenkang Yang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Qi Zhao
- School of Life Science, Shanxi University, Taiyuan, China
| | - Ying Wang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Jiajia Zhao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ling Qiao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Suxian Yan
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jun Zheng
- School of Life Science, Shanxi University, Taiyuan, China.,State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Xingwei Zheng
- School of Life Science, Shanxi University, Taiyuan, China.,State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
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30
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Zhang L, Hu X, Liu M. Complete chloroplast genome sequences of the medicinal plant Piper hancei. Mitochondrial DNA B Resour 2021; 6:2775-2776. [PMID: 34471701 PMCID: PMC8405093 DOI: 10.1080/23802359.2021.1967217] [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: 04/29/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Chloroplast genome sequences have been used in phylogenetic and population genetics studies. Here, we assembled the chloroplast genome of Piper hancei Maxim. that is a traditional Chinese medicine. The genome length was 161,476 bp and included a pair of inverted repeats of 27,058 bp, a large single-copy region of 89,144 bp and a small single-copy region of 18,216 bp. It contained 113 different genes, including 79 protein-coding genes, 30 transfer RNA (tRNA), and four ribosomal RNA genes. Moreover, we also identified 82 SSRs. The phylogenetic inference based on the whole chloroplast genome of 20 taxa showed P. hancei was sister to P. kadsura.
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Affiliation(s)
- Lvshui Zhang
- College of Landscape Architecture and Arts, Jiangxi Agricultural University, Nanchang, China
| | | | - Mu Liu
- College of Landscape Architecture and Arts, Jiangxi Agricultural University, Nanchang, China
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31
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Lee C, Ruhlman TA, Jansen RK. Unprecedented Intraindividual Structural Heteroplasmy in Eleocharis (Cyperaceae, Poales) Plastomes. Genome Biol Evol 2021; 12:641-655. [PMID: 32282915 PMCID: PMC7426004 DOI: 10.1093/gbe/evaa076] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2020] [Indexed: 12/13/2022] Open
Abstract
Plastid genomes (plastomes) of land plants have a conserved quadripartite structure in a gene-dense unit genome consisting of a large inverted repeat that separates two single copy regions. Recently, alternative plastome structures were suggested in Geraniaceae and in some conifers and Medicago the coexistence of inversion isomers has been noted. In this study, plastome sequences of two Cyperaceae, Eleocharis dulcis (water chestnut) and Eleocharis cellulosa (gulf coast spikerush), were completed. Unlike the conserved plastomes in basal groups of Poales, these Eleocharis plastomes have remarkably divergent features, including large plastome sizes, high rates of sequence rearrangements, low GC content and gene density, gene duplications and losses, and increased repetitive DNA sequences. A novel finding among these features was the unprecedented level of heteroplasmy with the presence of multiple plastome structural types within a single individual. Illumina paired-end assemblies combined with PacBio single-molecule real-time sequencing, long-range polymerase chain reaction, and Sanger sequencing data identified at least four different plastome structural types in both Eleocharis species. PacBio long read data suggested that one of the four E. dulcis plastome types predominates.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin.,Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
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32
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Simmonds SE, Smith JF, Davidson C, Buerki S. Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae). Mol Phylogenet Evol 2021; 163:107229. [PMID: 34129936 DOI: 10.1016/j.ympev.2021.107229] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 05/28/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
Biological radiations provide unique opportunities to understand the evolution of biodiversity. One such radiation is the pepper plant family Piperaceae, an early-diverging and mega-diverse lineage that could serve as a model to study the diversification of angiosperms. However, traditional genetic markers lack sufficient variation for such studies, and testing hypotheses on poorly resolved phylogenetic frameworks becomes challenging. Limited genomic data is available for Piperaceae, which contains two of the largest genera of angiosperms, Piper (>2100 species) and Peperomia (>1300 species). To address this gap, we used genome skimming to assemble and annotate whole plastomes (152-161kbp) and >5kbp nuclear ribosomal DNA region from representatives of Piper and Peperomia. We conducted phylogenetic and comparative genomic analyses to study plastome evolution and investigate the role of hybridization in this group. Plastome phylogenetic trees were well resolved and highly supported, with a hard incongruence observed between plastome and nuclear phylogenetic trees suggesting hybridization in Piper. While all plastomes of Piper and Peperomia had the same gene content and order, there were informative structural differences between them. First, ycf1 was more variable and longer in Piper than Peperomia, extending well into the small single copy region by thousands of base pairs. We also discovered previously unknown structural variation in 14 out of 25 Piper taxa, tandem duplication of the trnH-GUG gene resulting in an expanded large single copy region. Other early-diverging angiosperms have a duplicated trnH-GUG, but the specific rearrangement we found is unique to Piper and serves to refine knowledge of relationships among early-diverging angiosperms. Our study demonstrates that genome skimming is an efficient approach to produce plastome assemblies for comparative genomics and robust phylogenies of species-rich plant genera.
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Affiliation(s)
- Sara E Simmonds
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA
| | - James F Smith
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA
| | | | - Sven Buerki
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA.
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Jo S, Kim KJ. The complete plastome sequences of Pseudowintera colorata and Tasmannia lanceolata ( Winteraceae - Canellales). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:104-105. [PMID: 33537417 PMCID: PMC7832585 DOI: 10.1080/23802359.2020.1847620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
In this study, we report the complete plastome sequences of two Winteraceae taxa, Pseudowintera colorata (MT555077) and Tasmannia lanceolata (MT555078). Both plastomes show typical quadripartite structure. The plastome size of P. colorata is 161,675 bp, which consists of 89,583 bp large single-copy (LSC), 18,606 bp small single-copy (SSC), and 26,743 bp inverted repeat (IR) regions. The plastome size of T. lanceolata is 160,424 bp, which consist of 88,589 bp LSC, 18,351 bp SSC, and 26,742 bp IR regions. Both plastomes contain 113 genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. Sixteen genes contain one intron and two genes (clpP and ycf3) have two introns. Ninety-three and 89 simple sequence repeat (SSR) loci are scattered in the P. colorata and T. lanceolata plastomes, respectively. Our phylogenetic tree shows the relationship of (T. lanceolate (P. colorata,Drimys granadensis)) in the Winteraceae. The Canellales (incl. Winteraceae) are the sister group of Piperales.
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Affiliation(s)
- Sangjin Jo
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul, South Korea
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34
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Liu K, Wang R, Guo XX, Zhang XJ, Qu XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae). PLANTS 2021; 10:plants10010109. [PMID: 33419221 PMCID: PMC7825611 DOI: 10.3390/plants10010109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 11/24/2022]
Abstract
Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed. The length of these chloroplast genomes varied from 130,773 bp to 135,322 bp. These chloroplast genomes showed a typical quadripartite structure, including a large single-copy region (77,993–80,643 bp), a small single-copy region (12,410–12,668 bp), and a pair of inverted repeats region (19,394–21,074 bp). There were, in total, 129–133 genes annotated in the genome, including 83–87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Forward and palindromic repeats were the most common repeat types. In total, 10 hypervariable regions (rpl22, rpoA, ndhF, matK, trnG–UCC-trnT–GGU, ndhF–rpl32, ycf4–cemA, rpl32–trnL–UAG, trnG–GCC–trnfM–CAU, and ccsA–ndhD) were found, which can be used as candidate molecular markers for Eragrostideae. Phylogenomic studies concluded that Enneapogon diverged first, and Eragrostis including Harpachne is the sister to Uniola. Furthermore, Harpachne harpachnoides is considered as a species of Eragrostis based on morphological and molecular evidence. In addition, the interspecies relationships within Eragrostis are resolved based on complete chloroplast genomes. This study provides useful chloroplast genomic information for further phylogenetic analysis of Eragrostideae.
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Affiliation(s)
| | | | | | | | - Xiao-Jian Qu
- Correspondence: (X.-J.Q.); (S.-J.F.); Tel.: +86-0531-8618-0718 (S.-J.F.)
| | - Shou-Jin Fan
- Correspondence: (X.-J.Q.); (S.-J.F.); Tel.: +86-0531-8618-0718 (S.-J.F.)
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35
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Abstract
The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Robert K Jansen
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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36
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Chen N, Sha LN, Wang YL, Yin LJ, Zhang Y, Wang Y, Wu DD, Kang HY, Zhang HQ, Zhou YH, Sun GL, Fan X. Variation in Plastome Sizes Accompanied by Evolutionary History in Monogenomic Triticeae (Poaceae: Triticeae). FRONTIERS IN PLANT SCIENCE 2021; 12:741063. [PMID: 34966398 PMCID: PMC8710740 DOI: 10.3389/fpls.2021.741063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/02/2021] [Indexed: 05/17/2023]
Abstract
To investigate the pattern of chloroplast genome variation in Triticeae, we comprehensively analyzed the indels in protein-coding genes and intergenic sequence, gene loss/pseudonization, intron variation, expansion/contraction in inverted repeat regions, and the relationship between sequence characteristics and chloroplast genome size in 34 monogenomic Triticeae plants. Ancestral genome reconstruction suggests that major length variations occurred in four-stem branches of monogenomic Triticeae followed by independent changes in each genus. It was shown that the chloroplast genome sizes of monogenomic Triticeae were highly variable. The chloroplast genome of Pseudoroegneria, Dasypyrum, Lophopyrum, Thinopyrum, Eremopyrum, Agropyron, Australopyrum, and Henradia in Triticeae had evolved toward size reduction largely because of pseudogenes elimination events and length deletion fragments in intergenic. The Aegilops/Triticum complex, Taeniatherum, Secale, Crithopsis, Herteranthelium, and Hordeum in Triticeae had a larger chloroplast genome size. The large size variation in major lineages and their subclades are most likely consequences of adaptive processes since these variations were significantly correlated with divergence time and historical climatic changes. We also found that several intergenic regions, such as petN-trnC and psbE-petL containing unique genetic information, which can be used as important tools to identify the maternal relationship among Triticeae species. Our results contribute to the novel knowledge of plastid genome evolution in Triticeae.
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Affiliation(s)
- Ning Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yi-Ling Wang
- College of Life Science, Shanxi Normal University, Shanxi, China
| | - Ling-Juan Yin
- Lijiang Nationality Secondary Specialized School, Lijiang, China
| | - Yue Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Dan-Dan Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Gen-Lou Sun
- Saint Mary’s University, Halifax, NS, Canada
- *Correspondence: Gen-Lou Sun,
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Xing Fan,
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Zhu B, Feng Q, Yu J, Yu Y, Zhu X, Wang Y, Guo J, Hu X, Cai M. Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae). PLoS One 2020; 15:e0239823. [PMID: 32986773 PMCID: PMC7521677 DOI: 10.1371/journal.pone.0239823] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/14/2020] [Indexed: 11/19/2022] Open
Abstract
Houttuynia cordata (Saururaceae), an ancient and relic species, has been used as an important medicinal and edible plant in most parts of Asia. However, because of the lack of genome information and reliable molecular markers, studies on its population structure, or phylogenetic relationships with other related species are still rare. Here, we de novo assembled the complete chloroplast (cp) genome of H. cordata using the integration of the long PacBio and short Illumina reads. The cp genome of H. cordata showed a typical quadripartite cycle of 160,226 bp. This included a pair of inverted repeats (IRa and IRb) of 26,853 bp, separated by a large single-copy (LSC) region of 88,180 bp and a small single-copy (SSC) region of 18,340 bp. A total of 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes, were identified in this cp genome. Eighty-one genes were located on the LSC region, 13 genes were located on the SSC region, and 17 two-copy genes were located on the IR region. Additionally, 48 repeat sequences and 86 SSR loci, which can be used as genomic markers for population structure analysis, were also detected. Phylogenetic analysis using 21 cp genomes of the Piperales family demonstrated that H. cordata had a close relationship with the species within the Aristolochia genus. Moreover, the results of mVISTA analysis and comparisons of IR regions demonstrated that the cp genome of H. cordata was conserved with that of the Aristolochia species. Our results provide valuable information for analyzing the genetic diversity and population structure of H. cordata, which can contribute to further its genetic improvement and breeding.
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Affiliation(s)
- Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Qun Feng
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Jie Yu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Yu Yu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Xiaoxiang Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Yu Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Juan Guo
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Hangzhou, China
| | - Mengxian Cai
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
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The complete chloroplast genome of Magnolia polytepala: Comparative analyses offer implication for genetics and phylogeny of Yulania. Gene 2020; 736:144410. [PMID: 32007581 DOI: 10.1016/j.gene.2020.144410] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 11/22/2022]
Abstract
Magnoliaceae is a primitive taxon in the angiosperms, comprising approximately 240 species in 2-17 genera. Many of them have been widely cultivated due to their horticultural and medicinal value. However, there are uncertainties and controversies about the delimitation of the genera except Liriodendron L. in this family. The Yulania taxa is also the focus of dispute at the genus and section levels. In this study, we compared ten Yulania plastomes, including the newly sequenced M. polytepala. The plastome-wide comparative analysis demonstrated that 1) Yulania cp genomes were highly conserved, and the majority differences existed in IR regions with the loss/retention of trnV-GAC or ycf15 gene, 2) mutational hotspots with high levels of nucleotide diversity (Pi > 0.02) existed in both coding (rpoA, and ycf1) and no-coding (ccsA-ndhD, ndhE-ndhG, ndhF-rpl32, petA-psbJ, rpl32-trnL, rps3-rps19, and trnH-psbA) regions among the genus Yulania. Combined with other data from Magnoliaceae plastomes, our reconstructed molecular phylogenetic tree revealed that Yulania is monophyletic, separated from the genus Magnolia L. (=Magnolia subg. Magnolia L.), but seems a sister of Michelia L. Moreover, M. polytepala which belongs to the genus Yulania is most closely related to M. liliiflora. All these results indicated that plastome data may contribute to investigating taxonomy, population genetics and phylogeny of Yulania.
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Song E, Park S, Kim S. Primers for complete chloroplast genome sequencing in Magnolia. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11286. [PMID: 31572627 PMCID: PMC6764489 DOI: 10.1002/aps3.11286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 05/28/2019] [Indexed: 06/10/2023]
Abstract
PREMISE A new set of primers was developed for sequencing of whole chloroplast genomes of Magnolia species and gap-filling of unfinished genomes. METHODS AND RESULTS Two hundred and fifty primers were newly designed based on two previously reported chloroplast genomes from two different genera in Magnoliaceae. A total of 134 primer pairs, including the ones developed in this study and 18 previously reported ones, were enough to cover the entire chloroplast genome sequences in Magnoliaceae. Four species from different sections of Magnolia (M. dealbata, M. fraseri var. pyramidata, M. liliiflora, and M. odora) were used to show the general application of these primers to chloroplast genome sequencing in Magnolia. CONCLUSIONS Using the developed primers, four Magnolia chloroplast genomes were successfully assembled. These results show the utility of these primers across Magnolia and their potential use for phylogenetic studies, DNA barcoding, and population genetics in this group.
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Affiliation(s)
- Eunji Song
- Department of BiologySungshin UniversitySeoul01133Korea
| | - Suhyeon Park
- Department of BiologySungshin UniversitySeoul01133Korea
| | - Sangtae Kim
- Department of BiologySungshin UniversitySeoul01133Korea
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40
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Park J, Kim Y, Kwon W, Xi H, Kwon M. The complete chloroplast genome of tulip tree, Liriodendron tulifipera L. (Magnoliaceae): investigation of intra-species chloroplast variations. Mitochondrial DNA B Resour 2019; 4:2523-2524. [PMID: 33365610 PMCID: PMC7687633 DOI: 10.1080/23802359.2019.1598822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/13/2019] [Indexed: 11/03/2022] Open
Abstract
Liriodendron tulifipera L. belongs to Magnoliaceae which is one of the basal angiosperm families. To understand intra-species variations on chloroplast genome in Liriodendron genus, we presented complete chloroplast genome of L. tulifipera, which is 156,387 bp long and has four subregions: 85,606 bp of large single copy (LSC) and 18,778 bp of small single copy (SSC) regions are separated by 26,002 bp of inverted repeat (IR) regions including 129 genes (84 coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.0% and those in the LSC, SSC, and IR regions are 34.9%, 30.5%, and 42.8%, respectively. Twelve single nucleotide polymorphisms (SNPs) located in one region and one insertion and deletion are found between two L. tulifipera genomes. INDEL Phylogenetic trees show that two L. tulifipera chloroplasts are clustered together and are sister to Magnolia species.
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Affiliation(s)
- Jongsun Park
- InfoBoss Co., Ltd., Gangnam-gu, Seoul, Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd., Gangnam-gu, Seoul, Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Korea
| | - Woochan Kwon
- InfoBoss Co., Ltd., Gangnam-gu, Seoul, Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Korea
| | - Hong Xi
- InfoBoss Co., Ltd., Gangnam-gu, Seoul, Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Korea
| | - Mi Kwon
- InfoBoss Co., Ltd., Gangnam-gu, Seoul, Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Korea
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41
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Park J, Kim Y, Kwon M. The complete mitochondrial genome of tulip tree, Liriodendron tulipifera L. (Magnoliaceae): intra-species variations on mitochondrial genome. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Jongsun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Mi Kwon
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species. Int J Mol Sci 2019; 20:ijms20051045. [PMID: 30823362 PMCID: PMC6429227 DOI: 10.3390/ijms20051045] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 11/16/2022] Open
Abstract
Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes range from 159,308 bp to 160,520 bp in length and have a similar GC content of 38.5%–38.9%. A total number of 113 genes were identified, including 79 protein-coding genes, 30 tRNAs and four rRNAs. Although genomic structure and size were highly conserved, the IR-SC boundary regions were variable between these seven cp genomes. The trnH-GUG genes, are one of major differences between the plastomes of the two subgenera Siphisia and Aristolochia. We analyzed the features of nucleotide substitutions, distribution of repeat sequences and simple sequences repeats (SSRs), positive selections in the cp genomes, and identified 16 hotspot regions for genomes divergence that could be utilized as potential markers for phylogeny reconstruction. Phylogenetic relationships of the family Aristolochiaceae inferred from the 18 cp genome sequences were consistent and robust, using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis (BI) methods.
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Su HJ, Barkman TJ, Hao W, Jones SS, Naumann J, Skippington E, Wafula EK, Hu JM, Palmer JD, dePamphilis CW. Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proc Natl Acad Sci U S A 2019; 116:934-943. [PMID: 30598433 PMCID: PMC6338844 DOI: 10.1073/pnas.1816822116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in Balanophora consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.
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Affiliation(s)
- Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, 100 Taipei, Taiwan
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202
| | - Samuel S Jones
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
| | - Julia Naumann
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | | | - Eric K Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, 106 Taipei, Taiwan
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN 47405;
| | - Claude W dePamphilis
- Department of Biology, Pennsylvania State University, University Park, PA 16802;
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
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44
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Song E, Park S, Sun W, Kim S. Complete chloroplast genome sequence of Magnolia sinica (Y.W.Law) Noot. (magnoliaceae), A critically endangered species with extremely small populations in Magnoliaceae. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1546141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Eunji Song
- Department of Biology, Sungshin University, Seoul, Korea
| | - Suhyeon Park
- Department of Biology, Sungshin University, Seoul, Korea
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Sangtae Kim
- Department of Biology, Sungshin University, Seoul, Korea
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45
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Sathishkumar R, Kumar SR, Hema J, Baskar V. Green Biotechnology: A Brief Update on Plastid Genome Engineering. ADVANCES IN PLANT TRANSGENICS: METHODS AND APPLICATIONS 2019. [PMCID: PMC7120283 DOI: 10.1007/978-981-13-9624-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Plant genetic engineering has become an inevitable tool in the molecular breeding of crops. Significant progress has been made in the generation of novel plastid transformation vectors and optimized transformation protocols. There are several advantages of plastid genome engineering over conventional nuclear transformation. Some of the advantages include multigene engineering by expression of biosynthetic pathway genes as operons, extremely high-level expression of protein accumulation, lack of transgene silencing, etc. Transgene containment owing to maternal inheritance is another important advantage of plastid genome engineering. Chloroplast genome modification usually results in alteration of several thousand plastid genome copies in a cell. Several therapeutic proteins, edible vaccines, antimicrobial peptides, and industrially important enzymes have been successfully expressed in chloroplasts so far. Here, we critically recapitulate the latest developments in plastid genome engineering. Latest advancements in plastid genome sequencing are briefed. In addition, advancement of extending the toolbox for plastid engineering for selected applications in the area of molecular farming and production of industrially important enzyme is briefed.
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Affiliation(s)
- Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu India
| | | | - Jagadeesan Hema
- Department of Biotechnology, PSG College of Technology, Coimbatore, Tamil Nadu India
| | - Venkidasamy Baskar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu India
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46
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Song Y, Yu WB, Tan Y, Liu B, Yao X, Jin J, Padmanaba M, Yang JB, Corlett RT. Evolutionary Comparisons of the Chloroplast Genome in Lauraceae and Insights into Loss Events in the Magnoliids. Genome Biol Evol 2018; 9:2354-2364. [PMID: 28957463 PMCID: PMC5610729 DOI: 10.1093/gbe/evx180] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/01/2017] [Indexed: 12/15/2022] Open
Abstract
Available plastomes of the Lauraceae show similar structure and varied size, but there has been no systematic comparison across the family. In order to understand the variation in plastome size and structure in the Lauraceae and related families of magnoliids, we here compare 47 plastomes, 15 newly sequenced, from 27 representative genera. We reveal that the two shortest plastomes are in the parasitic Lauraceae genus Cassytha, with lengths of 114,623 (C. filiformis) and 114,963 bp (C. capillaris), and that they have lost NADH dehydrogenase (ndh) genes in the large single-copy region and one entire copy of the inverted repeat (IR) region. The plastomes of the core Lauraceae group, with lengths from 150,749 bp (Nectandra angustifolia) to 152,739 bp (Actinodaphne trichocarpa), have lost trnI-CAU, rpl23, rpl2, a fragment of ycf2, and their intergenic regions in IRb region, whereas the plastomes of the basal Lauraceae group, with lengths from 157,577 bp (Eusideroxylon zwageri) to 158,530 bp (Beilschmiedia tungfangensis), have lost rpl2 in IRa region. The plastomes of Calycanthus (Calycanthaceae, Laurales) have lost rpl2 in IRb region, but the plastome of Caryodaphnopsis henryi (Lauraceae) remain intact, as do those of the nonLaurales magnoliid genera Piper, Liriodendron, and Magnolia. On the basis of our phylogenetic analysis and structural comparisons, different loss events occurred in different lineages of the Laurales, and fragment loss events in the IR regions have largely driven the contraction of the plastome in the Lauraceae. These results provide new insights into the evolution of the Lauraceae as well as the magnoliids as a whole.
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Affiliation(s)
- Yu Song
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Yunhong Tan
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xin Yao
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jianjun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Michael Padmanaba
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Richard T Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
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47
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Su Y, Huang L, Wang Z, Wang T. Comparative chloroplast genomics between the invasive weed Mikania micrantha and its indigenous congener Mikania cordata: Structure variation, identification of highly divergent regions, divergence time estimation, and phylogenetic analysis. Mol Phylogenet Evol 2018; 126:181-195. [PMID: 29684597 DOI: 10.1016/j.ympev.2018.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/07/2018] [Accepted: 04/09/2018] [Indexed: 11/27/2022]
Abstract
Mikania micrantha and Mikania cordata are the only two species in genus Mikania (Asteraceae) in China. They share very similar morphological and life-history characteristics but occupy quite different habitats. Most importantly, they generate totally different ecological consequences. While M. micrantha has become an exotic invasive weed, M. cordata exists as an indigenous species with no harmful effects on native plants or habitats. As a continuous study of our previously reported M. micrantha chloroplast (cp) genome, in this study we have further sequenced the M. cordata cp genome to (1) conduct a comparative genome analysis to gain insights into the mechanism of invasiveness; (2) develop cp markers to examine the population genetic adaptation of M. micrantha; and (3) screen variable genome regions of phylogenetic utility. The M. cordata chloroplast genome is 151,984 bp in length and displays a typical quadripartite structure. The number and distribution of protein coding genes, tRNA genes, and rRNA genes of M. cordata are identical to those of M. micrantha. The main difference lays in that the pseudogenization of ndhF and a 118-bp palindromic repeat only arises in M. cordata. Fourteen highly divergent regions, 235 base substitutions, and 58 indels were identified between the two cp genomes. Phylogenetic inferences revealed a sister relationship between M. micrantha and M. cordata whose divergence was estimated to occur around 1.78 million years ago (MYA). Twelve cpSSR loci were detected to be polymorphic and adopted to survey the genetic adaptation of M. micrantha populations. No cpSSR loci were found to undergo selection. Our results build a foundation to examine the invasive mechanism of Mikania weed.
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Affiliation(s)
- Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Lu Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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48
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Manzanilla V, Kool A, Nguyen Nhat L, Nong Van H, Le Thi Thu H, de Boer HJ. Phylogenomics and barcoding of Panax: toward the identification of ginseng species. BMC Evol Biol 2018; 18:44. [PMID: 29614961 PMCID: PMC5883351 DOI: 10.1186/s12862-018-1160-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 03/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. RESULTS We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. CONCLUSIONS MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.
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Affiliation(s)
- V Manzanilla
- The Natural History Museum, University of Oslo, Oslo, Norway.
| | - A Kool
- The Natural History Museum, University of Oslo, Oslo, Norway
| | - L Nguyen Nhat
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Nong Van
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Le Thi Thu
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H J de Boer
- The Natural History Museum, University of Oslo, Oslo, Norway
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49
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Saina JK, Li ZZ, Gichira AW, Liao YY. The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree. Int J Mol Sci 2018; 19:E929. [PMID: 29561773 PMCID: PMC5979363 DOI: 10.3390/ijms19040929] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 12/17/2022] Open
Abstract
Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family.
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Affiliation(s)
- Josphat K Saina
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China.
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Andrew W Gichira
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Yi-Ying Liao
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China.
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50
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Song E, Park S, Park J, Kim S. The chloroplast genome sequence of Magnolia kobus DC. (Magnoliaceae). Mitochondrial DNA B Resour 2018; 3:342-343. [PMID: 33474163 PMCID: PMC7800189 DOI: 10.1080/23802359.2018.1450666] [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: 11/11/2022] Open
Abstract
As an endangered species, Magnolia kobus is distributed in Jeju island in Korea with only about 500–1000 individuals. In this study, we presented a complete chloroplast genome of M. kobus which is 159,443 bp and has four sub-regions: 87,484 bp of large single copy and 18,783 bp of small single copy regions are separated by 26,588 bp of inverted repeat regions including 113 genes (79 unique genes, four rRNAs and 30 tRNAs). Phylogenetic analysis using chloroplast genomes showed that M. kobus is a sister of M. insignis and M. laevifolia clade.
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Affiliation(s)
- Eunji Song
- Department of Biology, Sungshin University, Seoul, Korea
| | - Suhyeon Park
- Department of Biology, Sungshin University, Seoul, Korea
| | | | - Sangtae Kim
- Department of Biology, Sungshin University, Seoul, Korea
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