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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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Hu Q, Luo Y, Li Q, Deng Z, Liu J. The complete chloroplast genome sequence of Ampelopsis delavayana Planchon. ex Franch 1886 (Vitaceae). Mitochondrial DNA B Resour 2024; 9:777-781. [PMID: 38911520 PMCID: PMC11191827 DOI: 10.1080/23802359.2024.2364753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 05/31/2024] [Indexed: 06/25/2024] Open
Abstract
Ampelopsis delavayana Planchon. ex Franch 1886 is a plant with significant pharmacological effects and ornamental importance. This research unveiled the complete chloroplast (cp) genome sequence of A. delavayana. The study highlights that the cp genome of A. delavayana possesses a distinct tetrameric structure spanning 162,497 base pairs, comprising a small single-copy (SSC) region of 18,902 base pairs, a large single-copy (LSC) region of 90,441 base pairs, and two inverted-repeat regions (IRs), each 26,577 base pairs in length. The GC content of the SSC, LSC, and IR regions of the genome was 31.80%, 35.16%, and 42.82%, respectively, culminating in an overall GC content of 37.27%. The genome comprised 130 genes, which included eight rRNAs, 36 tRNAs, and 86 protein-coding genes. Through phylogenetic analysis utilizing the maximum-likelihood method, it was established that A. delavayana was closely related to Ampelopsis glandulosa var. brevipedunculata, positioning it as a sister species. This report not only provides a scientific reference for understanding the phylogeny of the family Vitaceae but also enriches our genetic information of Ampelopsis.
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Affiliation(s)
- Qun Hu
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, PR China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, PR China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture (Hubei Minzu University), Enshi, PR China
| | - Yongjian Luo
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, PR China
| | - Qing Li
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, PR China
| | - Zhijun Deng
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, PR China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture (Hubei Minzu University), Enshi, PR China
| | - Jun Liu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, PR China
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Zhang L, Meng Y, Wang D, He GH, Zhang JM, Wen J, Nie ZL. Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae). BMC Genomics 2024; 25:247. [PMID: 38443830 PMCID: PMC10916268 DOI: 10.1186/s12864-024-10149-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: 01/15/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Ampelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing a disjunct distribution worldwide across all the continents except Antarctica. There are numerous species from the tribe that are commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The tribe is usually recognized into three clades, i.e., Ampelopsis Michx., Nekemias Raf., and the Southern Hemisphere clade. However, the relationships of the three clades differ greatly between the nuclear and the plastid topologies. There has been limited exploration of the chloroplast phylogenetic relationships within Ampelopsideae, and studies on the chloroplast genome structure of this tribe are only available for a few individuals. In this study, we aimed to investigate the evolutionary characteristics of plastid genomes of the tribe, including their genome structure and evolutionary insights. RESULTS We sequenced, assembled, and annotated plastid genomes of 36 species from the tribe and related taxa in the family. Three main clades were recognized within Ampelopsideae, corresponding to Ampelopsis, Nekemias, and the Southern Hemisphere lineage, respectively, and all with 100% bootstrap supports. The genome sequences and content of the tribe are highly conserved. However, comparative analyses suggested that the plastomes of Nekemias demonstrate a contraction in the large single copy region and an expansion in the inverted repeat region, and possess a high number of forward and palindromic repeat sequences distinct from both Ampelopsis and the Southern Hemisphere taxa. CONCLUSIONS Our results highlighted plastome variations in genome length, expansion or contraction of the inverted repeat region, codon usage bias, and repeat sequences, are corresponding to the three lineages of the tribe, which probably faced with different environmental selection pressures and evolutionary history. This study provides valuable insights into understanding the evolutionary patterns of plastid genomes within the Ampelopsideae of Vitaceae.
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Affiliation(s)
- Lei Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Ying Meng
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Da Wang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Guan-Hao He
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun-Ming Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Ze-Long Nie
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China.
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Javaid N, Ramzan M, Jabeen S, Shah MN, Danish S, Hirad AH. Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan. BMC PLANT BIOLOGY 2023; 23:658. [PMID: 38124056 PMCID: PMC10731703 DOI: 10.1186/s12870-023-04670-5] [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: 07/07/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The Aizoaceae family's Sesuvium sesuvioides (Fenzl) Verdc is a medicinal species of the Cholistan desert, Pakistan. The purpose of this study was to determine the genomic features and phylogenetic position of the Sesuvium genus in the Aizoaceae family. We used the Illumina HiSeq2500 and paired-end sequencing to publish the complete chloroplast sequence of S. sesuvioides. RESULTS The 155,849 bp length cp genome sequence of S. sesuvioides has a 36.8% GC content. The Leucine codon has the greatest codon use (10.6%), 81 simple sequence repetitions of 19 kinds, and 79 oligonucleotide repeats. We investigated the phylogeny of the order Caryophyllales' 27 species from 23 families and 25 distinct genera. The maximum likelihood tree indicated Sesuvium as a monophyletic genus, and sister to Tetragonia. A comparison of S. sesuvioides, with Sesuvium portulacastrum, Mesembryanthemum crystallinum, Mesembryanthemum cordifolium, and Tetragonia tetragonoides was performed using the NCBI platform. In the comparative investigation of genomes, all five genera revealed comparable cp genome structure, gene number and composition. All five species lacked the rps15 gene and the rpl2 intron. In most comparisons with S. sesuvioides, transition substitutions (Ts) were more frequent than transversion substitutions (Tv), producing Ts/Tv ratios larger than one, and the Ka/Ks ratio was lower than one. We determined ten highly polymorphic regions, comprising rpl22, rpl32-trnL-UAG, trnD-GUC-trnY-GUA, trnE-UUC-trnT-GGU, trnK-UUU-rps16, trnM-CAU-atpE, trnH-GUG-psbA, psaJ-rpl33, rps4-trnT-UGU, and trnF-GAA-ndhJ. CONCLUSION The whole S. sesuvioides chloroplast will be examined as a resource for in-depth taxonomic research of the genus when more Sesuvium and Aizoaceae species are sequenced in the future. The chloroplast genomes of the Aizoaceae family are well preserved, with little alterations, indicating the family's monophyletic origin. This study's highly polymorphic regions could be utilized to build realistic and low-cost molecular markers for resolving taxonomic discrepancies, new species identification, and finding evolutionary links among Aizoaceae species. To properly comprehend the evolution of the Aizoaceae family, further species need to be sequenced.
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Affiliation(s)
- Nida Javaid
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan
| | - Musarrat Ramzan
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan.
| | - Shagufta Jabeen
- Government Associate College for Women Ahmedpur East, Bahawalpur, Punjab, Pakistan
| | - Muhammad Nadeem Shah
- Department of Agriculture, Government College University Lahore, Lahore, Punjab, Pakistan
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, Florida, USA
| | - Subhan Danish
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Punjab, Pakistan.
| | - Abdurahman Hajinur Hirad
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box.2455, Riyadh, 11451, Saudi Arabia
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Su Y, Zhang M, Guo Q, Wei M, Shi H, Wang T, Han Z, Liu H, Liu C, Huang J. Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes. BMC Genomics 2023; 24:465. [PMID: 37596543 PMCID: PMC10436401 DOI: 10.1186/s12864-023-09534-8] [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: 11/11/2022] [Accepted: 07/26/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Isatis tinctoria Linnaeus and Isatis indigotica Fortune are very inconsistent in their morphological characteristics, but the Flora of China treats them as the same species. In this work, a new technology that differs from conventional barcodes is developed to prove that they are different species and to clarify their classification. RESULTS AND METHODS I. indigotica was indistinguishable from I. tinctoria when using ITS2. CPGAVAS2 was used to construct the chloroplast genomes. MAFFT and DnaSP were used to calculate nucleotide polymorphism, the chloroplast genomes of the two have high diversity in the rpl32 ~ trnL-UAG short region. When using this region as a mini barcode, it was found that there are obvious differences in the base numbers of I. tinctoria and different ploidy I. indigotica were found, but diploid and tetraploid I. indigotica had the same number of bases. Moreover, the reconstruction of the maximum likelihood (ML) tree, utilizing the mini-barcode, demonstrated that I. tinctoria and both diploid and tetraploid I. indigotica are located on distinct branches. The genome size of tetraploid I. indigotica was approximately 643.773 MB, the heterozygosity rate was approximately 0.98%, and the repeat sequence content was approximately 90.43%. This species has a highly heterozygous, extremely repetitive genome. CONCLUSION A new method was established to differentiate between I. indigotica and I. tinctoria. Furthermore, this approach provides a reference and basis for the directional breeding of Isatis.
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Grants
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
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Affiliation(s)
- Yong Su
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Man Zhang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Qiaosheng Guo
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China.
| | - Min Wei
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China
| | - Hongzhuan Shi
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Tao Wang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Zhengzhou Han
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China
| | - Huihui Liu
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China
| | - Chang Liu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Jianmin Huang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
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Zecca G, Panzeri D, Grassi F. Detecting signals of adaptive evolution in grape plastomes with a focus on the Cretaceous-Palaeogene (K/Pg) transition. ANNALS OF BOTANY 2022; 130:965-980. [PMID: 36282948 PMCID: PMC9851337 DOI: 10.1093/aob/mcac128] [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: 07/15/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Although plastid genes are widely used in phylogenetic studies, signals of positive selection have been scarcely investigated in the grape family. The plastomes from 91 accessions of Vitaceae were examined to understand the extent to which positive selection is present and to identify which genes are involved. Moreover, the changes through time of genes under episodic positive selection were investigated and the hypothesis of an adaptive process following the Cretaceous-Palaeogene (K/Pg) transition about 66 million years ago was tested. METHODS Different codon-substitution models were used to assess pervasive and episodic positive selection events on 70 candidate plastid genes. Divergence times between lineages were estimated and stochastic character mapping analysis was used to simulate variation over time of the genes found to be under episodic positive selection. KEY RESULTS A total of 20 plastid genes (29 %) showed positive selection. Among them, 14 genes showed pervasive signatures of positive selection and nine genes showed episodic signatures of positive selection. In particular, four of the nine genes (psbK, rpl20, rpoB, rps11) exhibited a similar pattern showing an increase in the rate of variation close to the K/Pg transition. CONCLUSION Multiple analyses have shown that the grape family has experienced ancient and recent positive selection events and that the targeted genes are involved in essential functions such as photosynthesis, self-replication and metabolism. Our results are consistent with the idea that the K/Pg transition has favoured an increased rate of change in some genes. Intense environmental perturbations have influenced the rapid diversification of certain lineages, and new mutations arising on some plastid genes may have been fixed by natural selection over the course of many generations.
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Affiliation(s)
- Giovanni Zecca
- University of Milan-Bicocca, Department of Biotechnology and Bioscience, Piazza della Scienza 2, 20126, Milano, Italy
| | - Davide Panzeri
- University of Milan-Bicocca, Department of Biotechnology and Bioscience, Piazza della Scienza 2, 20126, Milano, Italy
| | - Fabrizio Grassi
- University of Milan-Bicocca, Department of Biotechnology and Bioscience, Piazza della Scienza 2, 20126, Milano, Italy
- NBFC, National Biodiversity Future Center, Palermo 90133, Italy
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Peng JY, Zhang XS, Zhang DG, Wang Y, Deng T, Huang XH, Kuang TH, Zhou Q. Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu & Q. E. Yang and comparative analyses with other Sinosenecio species. BMC Genomics 2022; 23:639. [PMID: 36076168 PMCID: PMC9454173 DOI: 10.1186/s12864-022-08872-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/31/2022] [Indexed: 11/10/2022] Open
Abstract
Background Sinosenecio B. Nordenstam (Asteraceae) currently comprises 44 species. To investigate the interspecific relationship, several chloroplast markers, including ndhC-trnV, rpl32-trnL, matK, and rbcL, are used to analyze the phylogeny of Sinosenecio. However, the chloroplast genomes of this genus have not been thoroughly investigated. We sequenced and assembled the Sinosenecio albonervius chloroplast genome for the first time. A detailed comparative analysis was performed in this study using the previously reported chloroplast genomes of three Sinosenecio species. Results The results showed that the chloroplast genomes of four Sinosenecio species exhibit a typical quadripartite structure. There are equal numbers of total genes, protein-coding genes and RNA genes among the annotated genomes. Per genome, 49–56 simple sequence repeats and 99 repeat sequences were identified. Thirty codons were identified as RSCU values greater than 1 in the chloroplast genome of S. albonervius based on 54 protein-coding genes, indicating that they showed biased usage. Among 18 protein-coding genes, 46 potential RNA editing sites were discovered. By comparing these chloroplast genomes' structures, inverted repeat regions and coding regions were more conserved than single-copy and non-coding regions. The junctions among inverted repeat and single-copy regions showed slight difference. Several hot spots of genomic divergence were detected, which can be used as new DNA barcodes for species identification. Phylogenetic analysis of the whole chloroplast genome showed that the four Sinosenecio species have close interspecific relationships. Conclusions The complete chloroplast genome of Sinosenecio albonervius was revealed in this study, which included a comparison of Sinosenecio chloroplast genome structure, variation, and phylogenetic analysis for related species. These will help future research on Sinosenecio taxonomy, identification, origin, and evolution to some extent. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08872-3.
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Affiliation(s)
- Jing-Yi Peng
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China
| | - Xiao-Shuang Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Dai-Gui Zhang
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China.,Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, College of Hunan Province, Jishou, 416000, Hunan, China
| | - Yi Wang
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Xian-Han Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Tian-Hui Kuang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Qiang Zhou
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China. .,Key Laboratory of Plant Resources Conservation and Utilization, Jishou University, College of Hunan Province, Jishou, 416000, Hunan, China.
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Dong S, Zhou M, Zhu J, Wang Q, Ge Y, Cheng R. The complete chloroplast genomes of Tetrastigma hemsleyanum (Vitaceae) from different regions of China: molecular structure, comparative analysis and development of DNA barcodes for its geographical origin discrimination. BMC Genomics 2022; 23:620. [PMID: 36028808 PMCID: PMC9412808 DOI: 10.1186/s12864-022-08755-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tetrastigma hemsleyanum is a valuable traditional Chinese medicinal plant widely distributed in the subtropical areas of China. It belongs to the Cayratieae tribe, family Vitaceae, and exhibited significant anti-tumor and anti-inflammatory activities. However, obvious differences were observed on the quality of T. hemsleyanum root from different regions, requiring the discrimination strategy for the geographical origins. RESULT This study characterized five complete chloroplast (cp) genomes of T. hemsleynum samples from different regions, and conducted a comparative analysis with other representing species from family Vitaceae to reveal the structural variations, informative markers and phylogenetic relationships. The sequenced cp genomes of T. hemsleyanum exhibited a conserved quadripartite structure with full length ranging from 160,124 bp of Jiangxi Province to 160,618 bp of Zhejiang Province. We identified 112 unique genes (80 protein-coding, 28 tRNA and 4 rRNA genes) in the cp genomes of T. hemsleyanum with highly similar gene order, content and structure. The IR contraction/expansion events occurred on the junctions of ycf1, rps19 and rpl2 genes with different degrees, causing the differences of genome sizes in T. hemsleyanum and Vitaceae plants. The number of SSR markers discovered in T. hemsleyanum was 56-57, exhibiting multiple differences among the five geographic groups. Phylogenetic analysis based on conserved cp genome proteins strongly grouped the five T. hemsleyanum species into one clade, showing a sister relationship with T. planicaule. Comparative analysis of the cp genomes from T. hemsleyanum and Vitaceae revealed five highly variable spacers, including 4 intergenic regions and one protein-coding gene (ycf1). Furthermore, five mutational hotspots were observed among T. hemsleyanum cp genomes from different regions, providing data for designing DNA barcodes trnL and trnN. The combination of molecular markers of trnL and trnN clustered the T. hemsleyanum samples from different regions into four groups, thus successfully separating specimens of Sichuan and Zhejiang from other areas. CONCLUSION Our study obtained the chloroplast genomes of T. hemsleyanum from different regions, and provided a potential molecular tracing tool for determining the geographical origins of T. hemsleyanum, as well as important insights into the molecular identification approach and and phylogeny in Tetrastigma genus and Vitaceae family.
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Affiliation(s)
- Shujie Dong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Manjia Zhou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinxing Zhu
- Bureau of Agricultural and Rural Affairs of Suichang, Suichang, China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China. .,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China.
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Javaid N, Ramzan M, Khan IA, Alahmadi TA, Datta R, Fahad S, Danish S. The chloroplast genome of Farsetia hamiltonii Royle, phylogenetic analysis, and comparative study with other members of Clade C of Brassicaceae. BMC PLANT BIOLOGY 2022; 22:384. [PMID: 35918648 PMCID: PMC9344719 DOI: 10.1186/s12870-022-03750-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/13/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Farsetia hamiltonii Royle is a medicinally important annual plant from the Cholistan desert that belongs to the tribe Anastaticeae and clade C of the Brassicaceae family. We provide the entire chloroplast sequence of F.hamiltonii, obtained using the Illumina HiSeq2500 and paired-end sequencing. We compared F. hamiltonii to nine other clade C species, including Farsetia occidentalis, Lobularia libyca, Notoceras bicorne, Parolinia ornata, Morettia canescens, Cochlearia borzaeana, Megacarpaea polyandra, Biscutella laevigata, and Iberis amara. We conducted phylogenetic research on the 22 Brassicaceae species, which included members from 17 tribes and six clades. RESULTS The chloroplast genome sequence of F.hamiltonii of 154,802 bp sizes with 36.30% GC content and have a typical structure comprised of a Large Single Copy (LSC) of 83,906 bp, a Small Single Copy (SSC) of 17,988 bp, and two copies of Inverted Repeats (IRs) of 26,454 bp. The genomes of F. hamiltonii and F. occidentalis show shared amino acid frequencies and codon use, RNA editing sites, simple sequence repeats, and oligonucleotide repeats. The maximum likelihood tree revealed Farsetia as a monophyletic genus, closely linked to Morettia, with a bootstrap score of 100. The rate of transversion substitutions (Tv) was higher than the rate of transition substitutions (Ts), resulting in Ts/Tv less than one in all comparisons with F. hamiltonii, indicating that the species are closely related. The rate of synonymous substitutions (Ks) was greater than non-synonymous substitutions (Ka) in all comparisons with F. hamiltonii, with a Ka/Ks ratio smaller than one, indicating that genes underwent purifying selection. Low nucleotide diversity values range from 0.00085 to 0.08516, and IR regions comprise comparable genes on junctions with minimal change, supporting the conserved status of the selected chloroplast genomes of the clade C of the Brassicaceae family. We identified ten polymorphic regions, including rps8-rpl14, rps15-ycf1, ndhG-ndhI, psbK-psbI, ccsA-ndhD, rpl36-rps8, petA-psbJ, ndhF-rpl32, psaJ-rpl3, and ycf1 that might be exploited to construct genuine and inexpensive to solve taxonomic discrepancy and understand phylogenetic relationship amongst Brassicaceae species. CONCLUSION The entire chloroplast sequencing of F. hamiltonii sheds light on the divergence of genic chloroplast sequences among members of the clade C. When other Farsetia species are sequenced in the future, the full F. hamiltonii chloroplast will be used as a source for comprehensive taxonomical investigations of the genus. The comparison of F. hamiltonii and other clade C species adds new information to the phylogenetic data and evolutionary processes of the clade. The results of this study will also provide further molecular uses of clade C chloroplasts for possible plant genetic modifications and will help recognise more Brassicaceae family species.
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Affiliation(s)
- Nida Javaid
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Musarrat Ramzan
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences University of Karachi, Karachi, 75270 Pakistan
| | - Tahani Awad Alahmadi
- Department of Pediatrics, College of Medicine and King Khalid University Hospital, King Saud University, Medical City, PO Box-2925, Riyadh, 11461 Saudi Arabia
| | - Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska1, 61300 Brno, Czech Republic
| | - Shah Fahad
- Department of Agronomy, The University of Haripur, Khyber Pakhtunkhwa, Haripur, 22620 Pakistan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
| | - Subhan Danish
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60800 Punjab Pakistan
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He X, Dong S, Gao C, Wang Q, Zhou M, Cheng R. The complete chloroplast genome of Carpesium abrotanoides L. (Asteraceae): structural organization, comparative analysis, mutational hotspots and phylogenetic implications within the tribe Inuleae. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Complete Chloroplast Genome Sequence of Fortunella venosa (Champ. ex Benth.) C.C.Huang (Rutaceae): Comparative Analysis, Phylogenetic Relationships, and Robust Support for Its Status as an Independent Species. FORESTS 2021. [DOI: 10.3390/f12080996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fortunella venosa (Rutaceae) is an endangered species endemic to China and its taxonomic status has been controversial. The genus Fortunella contains a variety of important economic plants with high value in food, medicine, and ornamental. However, the placement of Genus Fortunella into Genus Citrus has led to controversy on its taxonomy and Systematics. In this present research, the Chloroplast genome of F. venosa was sequenced using the second-generation sequencing, and its structure and phylogenetic relationship analyzed. The results showed that the Chloroplast genome size of F. venosa was 160,265 bp, with a typical angiosperm four-part ring structure containing a large single copy region (LSC) (87,597 bp), a small single copy region (SSC) (18,732 bp), and a pair of inverted repeat regions (IRa\IRb) (26,968 bp each). There are 134 predicted genes in Chloroplast genome, including 89 protein-coding genes, 8 rRNAs, and 37 tRNAs. The GC-content of the whole Chloroplast genome was 43%, with the IR regions having a higher GC content than the LSC and the SSC regions. There were no rearrangements present in the Chloroplast genome; however, the IR regions showed obvious contraction and expansion. A total of 108 simple sequence repeats (SSRs) were present in the entire chloroplast genome and the nucleotide polymorphism was high in LSC and SSC. In addition, there is a preference for codon usage with the non-coding regions being more conserved than the coding regions. Phylogenetic analysis showed that species of Fortunella are nested in the genus of Citrus and the independent species status of F. venosa is supported robustly, which is significantly different from F. japonica. These findings will help in the development of DNA barcodes that can be useful in the study of the systematics and evolution of the genus Fortunella and the family Rutaceae.
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Huang X, Zhou Q, Qin C, Mao C, Sun K, Qin B, Tang Q. The complete chloroplast genome of Tetrastigma planicaule, one important folk medicinal plant in China. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1745-1746. [PMID: 34104758 PMCID: PMC8158278 DOI: 10.1080/23802359.2021.1930598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]
Abstract
We announce here the first complete chloroplast genome sequence of Tetrastigma planicaule, one important Chinese folk medicinal plant. This complete chloroplast genome is 160,323 bp in length. In total, 131 genes were identified, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The results of phylogenetic analysis indicated that Tetrastigma is a separate genus and is closely related to Vitis.
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Affiliation(s)
- Xin Huang
- Guangxi Forestry Research Institute, Nanning, China
| | - Qihua Zhou
- Guangxi State-Owned Qipo Forest Farm, Nanning, China
| | - Cimei Qin
- Guangxi State-Owned Huangmian Forest Farm, Liuzhou, China
| | - Chun Mao
- Guangxi State-Owned Qipo Forest Farm, Nanning, China
| | - Kaidao Sun
- Guangxi Forestry Research Institute, Nanning, China
| | - Bo Qin
- Guangxi Forestry Research Institute, Nanning, China
| | - Qing Tang
- Guangxi Forestry Research Institute, Nanning, China
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13
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Yu X, Wang W, Yang H, Zhang X, Wang D, Tian X. Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication. Front Genet 2021; 12:602528. [PMID: 33747039 PMCID: PMC7970127 DOI: 10.3389/fgene.2021.602528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Vincetoxicum versicolor (Bunge) Decne is the original plant species of the Chinese herbal medicine Cynanchi Atrati Radix et Rhizoma. The lack of information on the transcriptome and chloroplast genome of V. versicolor hinders its evolutionary and taxonomic studies. Here, the V. versicolor transcriptome and chloroplast genome were assembled and functionally annotated. In addition, the comparative chloroplast genome analysis was conducted between the genera Vincetoxicum and Cynanchum. A total of 49,801 transcripts were generated, and 20,943 unigenes were obtained from V. versicolor. One thousand thirty-two unigenes from V. versicolor were classified into 73 functional transcription factor families. The transcription factors bHLH and AP2/ERF were the most significantly abundant, indicating that they should be analyzed carefully in the V. versicolor ecological adaptation studies. The chloroplast genomes of Vincetoxicum and Cynanchum exhibited a typical quadripartite structure with highly conserved gene order and gene content. They shared an analogous codon bias pattern in which the codons of protein-coding genes had a preference for A/U endings. The natural selection pressure predominantly influenced the chloroplast genes. A total of 35 RNA editing sites were detected in the V. versicolor chloroplast genome by RNA sequencing (RNA-Seq) data, and one of them restored the start codon in the chloroplast ndhD of V. versicolor. Phylogenetic trees constructed with protein-coding genes supported the view that Vincetoxicum and Cynanchum were two distinct genera.
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Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wenxiu Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hongxia Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoying Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Dan Wang
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Dong F, Lin Z, Lin J, Ming R, Zhang W. Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. PLANTS 2021; 10:plants10020283. [PMID: 33540810 PMCID: PMC7912957 DOI: 10.3390/plants10020283] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023]
Abstract
Rambutan (Nephelium lappaceum L.) is an important fruit tree that belongs to the family Sapindaceae and is widely cultivated in Southeast Asia. We sequenced its chloroplast genome for the first time and assembled 161,321 bp circular DNA. It is characterized by a typical quadripartite structure composed of a large (86,068 bp) and small (18,153 bp) single-copy region interspersed by two identical inverted repeats (IRs) (28,550 bp). We identified 132 genes including 78 protein-coding genes, 29 tRNA and 4 rRNA genes, with 21 genes duplicated in the IRs. Sixty-three simple sequence repeats (SSRs) and 98 repetitive sequences were detected. Twenty-nine codons showed biased usage and 49 potential RNA editing sites were predicted across 18 protein-coding genes in the rambutan chloroplast genome. In addition, coding gene sequence divergence analysis suggested that ccsA, clpP, rpoA, rps12, psbJ and rps19 were under positive selection, which might reflect specific adaptations of N. lappaceum to its particular living environment. Comparative chloroplast genome analyses from nine species in Sapindaceae revealed that a higher similarity was conserved in the IR regions than in the large single-copy (LSC) and small single-copy (SSC) regions. The phylogenetic analysis showed that N. lappaceum chloroplast genome has the closest relationship with that of Pometia tomentosa. The understanding of the chloroplast genomics of rambutan and comparative analysis of Sapindaceae species would provide insight into future research on the breeding of rambutan and Sapindaceae evolutionary studies.
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Affiliation(s)
- Fei Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Zhicong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Jing Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
| | - Wenping Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
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15
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Yu X, Tan W, Gao H, Miao L, Tian X. Development of a Specific Mini-Barcode From Plastome and its Application for Qualitative and Quantitative Identification of Processed Herbal Products Using DNA Metabarcoding Technique: A Case Study on Senna. Front Pharmacol 2021; 11:585687. [PMID: 33390955 PMCID: PMC7773718 DOI: 10.3389/fphar.2020.585687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/26/2020] [Indexed: 01/04/2023] Open
Abstract
Herbal products play an important role globally in the pharmaceutical and healthcare industries. However, some specific groups of herbal products are easily adulterated by confused materials on the market, which seriously reduces the products’ quality. Universal conventional DNA barcodes would function poorly since the processed herbal products generally suffer from varying degrees of DNA degradation and DNA mixing during processing or manufacturing. For quality control purposes, an accurate and effective method should be provided for species identification of these herbal products. Here, we provided a strategy of developing the specific mini-barcode using Senna as an example, and by coupling with the metabarcoding technique, it realized the qualitative and quantitative identification of processed herbal products. The plastomes of Senna obtusifolia (L.) H.S.Irwin & Barneby and Senna occidentalis (L.) Link were newly assembled, and the hypervariable coding-regions were identified by comparing their genomes. Then, the specific mini-barcodes were developed based on the identified hypervariable regions. Finally, we applied the DNA metabarcoding technique to the developed mini-barcodes. Results showed that the lengths of plastomes of S. obtusifolia and S. occidentalis were 162,426 and 159,993 bp, respectively. Four hypervariable coding-regions ycf1, rpl23, petL, and matK were identified. Two specific mini-barcodes were successfully developed from matK, and the mini-barcode of primer 647F-847R was proved to be able to qualitatively and quantitatively identify these two processed Senna seeds. Overall, our study established a valuable way to develop the specific mini-barcode, which may provide a new idea for the quality control of processed herbal products.
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Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wei Tan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Han Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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16
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Gou W, Jia SB, Price M, Guo XL, Zhou SD, He XJ. Complete Plastid Genome Sequencing of Eight Species from Hansenia, Haplosphaera and Sinodielsia (Apiaceae): Comparative Analyses and Phylogenetic Implications. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1523. [PMID: 33182384 PMCID: PMC7695273 DOI: 10.3390/plants9111523] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 11/17/2022]
Abstract
Hansenia Turcz., Haplosphaera Hand.-Mazz. and Sinodielsia H.Wolff are three Apiaceae genera endemic to the Hengduan Mountains and the Himalayas, which usually inhabit elevations greater than 2000 m. The phylogenetic relationships between and within the genera were uncertain, especially the placement of Hap. himalayensis and S. microloba. Therefore, we aimed to conduct comparative (simple sequence repeat (SSR) structure, codon usage bias, nucleotide diversity (Pi) and inverted repeat (IR) boundaries) and phylogenetic analyses of Hansenia, Haplosphaera and Sinodielsia (also compared with Chamaesium and Bupleurum) to reduce uncertainties in intergeneric and interspecific relationships. We newly assembled eight plastid genomes from Hansenia, Haplosphaera and Sinodielsia species, and analyzed them with two plastid genomes from GenBank of Hap. phaea,S. yunnanensis. Phylogenetic analyses used these ten genomes and another 22 plastid genome sequences of Apiaceae. We found that the newly assembled eight genomes ranged from 155,435 bp to 157,797 bp in length and all had a typical quadripartite structure. Fifty-five to 75 SSRs were found in Hansenia, Haplosphaera and Sinodielsia species, and the most abundant SSR was mononucleotide, which accounted for 58.47% of Hansenia, 60.21% of Haplosphaera and 48.01% of Sinodielsia. There was no evident divergence of codon usage frequency between the three genera, where codons ranged from 21,134 to 21,254. The Pi analysis showed that trnE(UUC)-trnT(GGU), trnH(GUG)-psbA and trnE(UUC)-trnT(GGU) spacer regions had the highest Pi values in the plastid genomes of Hansenia (0.01889), Haplosphaera (0.04333) and Sinodielsia (0.01222), respectively. The ndhG-ndhI spacer regions were found in all three genera to have higher diversity values (Pi values: 0.01028-0.2), and thus may provide potential DNA barcodes in phylogenetic analysis. IR boundary analysis showed that the length of rps19 and ycf1 genes entering IRs were usually stable in the same genus. Our phylogenetic tree demonstrated that Hap. himalayensis is sister to Han. weberbaueriana; meanwhile, Haplosphaera and Hansenia are nested together in the East Asia clade, and S. microloba is nested within individuals of S. yunnanensis in the Acronema clade. This study will enrich the complete plastid genome dataset of the Apiaceae genera and has provided a new insight into phylogeny reconstruction using complete plastid genomes of Hansenia, Haplosphaera and Sinodielsia.
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Affiliation(s)
- Wei Gou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (W.G.); (S.-B.J.); (X.-L.G.); (S.-D.Z.)
| | - Sheng-Bin Jia
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (W.G.); (S.-B.J.); (X.-L.G.); (S.-D.Z.)
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, China;
| | - Xian-Lin Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (W.G.); (S.-B.J.); (X.-L.G.); (S.-D.Z.)
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (W.G.); (S.-B.J.); (X.-L.G.); (S.-D.Z.)
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (W.G.); (S.-B.J.); (X.-L.G.); (S.-D.Z.)
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Tan W, Gao H, Jiang W, Zhang H, Yu X, Liu E, Tian X. The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes. Sci Rep 2020; 10:16309. [PMID: 33005000 PMCID: PMC7529812 DOI: 10.1038/s41598-020-73392-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/07/2020] [Indexed: 11/09/2022] Open
Abstract
Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.
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Affiliation(s)
- Wei Tan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Han Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Weiling Jiang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Huanyu Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Erwei Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
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Yang CH, Liu X, Cui YX, Nie LP, Lin YL, Wei XP, Wang Y, Yao H. Molecular structure and phylogenetic analyses of the complete chloroplast genomes of three original species of Pyrrosiae Folium. Chin J Nat Med 2020; 18:573-581. [PMID: 32768164 DOI: 10.1016/s1875-5364(20)30069-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Indexed: 12/12/2022]
Abstract
Pyrrosia petiolosa, Pyrrosia lingua and Pyrrosia sheareri are recorded as original plants of Pyrrosiae Folium (PF) and commonly used as Chinese herbal medicines. Due to the similar morphological features of PF and its adulterants, common DNA barcodes cannot accurately distinguish PF species. Knowledge of the chloroplast (cp) genome is widely used in species identification, molecular marker and phylogenetic analyses. Herein, we determined the complete cp genomes of three original species of PF via high-throughput sequencing technologies. The three cp genomes exhibited a typical quadripartite structure with sizes ranging from 158 165 to 163 026 bp. The cp genomes of P. petiolosa and P. lingua encoded 130 genes, whilst that of P. sheareri encoded 131 genes. The complete cp genomes were compared, and five highly divergent regions of petA-psbJ, matK-rps16, ndhC-trnM, psbM-petN and psaC-ndhE were screened as potential DNA barcodes for identification of Pyrrosia genus species. The phylogenetic tree we obtained indicated that P. petiolosa and P. lingua are clustered in a single clade and, thus, share a close relationship. This study provides invaluable information for further studies on the species identification, taxonomy and phylogeny of Pyrrosia genus species.
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Affiliation(s)
- Chu-Hong Yang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Xia Liu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Ying-Xian Cui
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Li-Ping Nie
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Yu-Lin Lin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Xue-Ping Wei
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Yu Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China.
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China.
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Chang L, Yu X, Wang W, Tian X. The complete chloroplast genome of Apocynum venetum (Apocynaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2601-2602. [PMID: 33457875 PMCID: PMC7782900 DOI: 10.1080/23802359.2020.1781567] [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: 11/08/2022]
Abstract
Apocynum venetum (A. venetum) has high medicinal value that belongs to the family Apocynaceae. Here, we reported the complete chloroplast (cp) genome of A. venetum, which was 150,858 bp in length. The cp genome was characterized by a typical quadripartite structure composed of a large single-copy region (LSC 81,919 bp) and a small single-copy region (SSC 17,257 bp) interspersed by a pair of 25,841 bp inverted repeat regions (IRs), and it contained 86 protein-coding genes, eight rRNAs, and 37 tRNAs. A maximum-likelihood (ML) phylogenetic tree indicated that A. venetum was closely related to Trachelospermum jasminoides.
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Affiliation(s)
- Lianying Chang
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaolei Yu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wenxiu Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxuan Tian
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Guo L, Guo S, Liu G, Hou X. Structure and phylogenetic analysis of Paeonia lactiflora ‘Lv He’ chloroplast genome. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1749156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Lili Guo
- College of Agriculture/Tree Peony, Henan University of Science and Technology, Luoyang, China
| | - Shuai Guo
- College of Agriculture/Tree Peony, Henan University of Science and Technology, Luoyang, China
| | - Gaixiu Liu
- National Peony Gene Bank of Luoyang, Luoyang, Henan, China
| | - Xiaogai Hou
- College of Agriculture/Tree Peony, Henan University of Science and Technology, Luoyang, China
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21
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Liu Z, Yu X, Cui P, Tian X. The complete chloroplast genome of Iris tectorum (Iridaceae). MITOCHONDRIAL DNA PART B 2020. [DOI: 10.1080/23802359.2020.1742599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Zhenzhen Liu
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaolei Yu
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Pengdi Cui
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxuan Tian
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Munyao JN, Dong X, Yang JX, Mbandi EM, Wanga VO, Oulo MA, Saina JK, Musili PM, Hu GW. Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E296. [PMID: 32121524 PMCID: PMC7154914 DOI: 10.3390/plants9030296] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022]
Abstract
The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus.
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Affiliation(s)
- Jacinta N. Munyao
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Dong
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Xin Yang
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Elijah M. Mbandi
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Vincent O. Wanga
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Millicent A. Oulo
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Josphat K. Saina
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Paul M. Musili
- East Africa Herbarium, National Museums of Kenya, P.O. Box 45166 00100 Nairobi, Kenya;
| | - Guang-Wan Hu
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Henriquez CL, Ahmed I, Carlsen MM, Zuluaga A, Croat TB, McKain MR. Molecular evolution of chloroplast genomes in Monsteroideae (Araceae). PLANTA 2020; 251:72. [PMID: 32112137 DOI: 10.1007/s00425-020-03365-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/14/2020] [Indexed: 05/02/2023]
Abstract
This study provides broad insight into the chloroplast genomes of the subfamily Monsteroideae. The identified polymorphic regions may be suitable for designing unique and robust molecular markers for phylogenetic inference. Monsteroideae is the third largest subfamily (comprises 369 species) and one of the early diverging lineages of the monocot plant family Araceae. The phylogeny of this important subfamily is not well resolved at the species level due to scarcity of genomic resources and suitable molecular markers. Here, we report annotated chloroplast genome sequences of four Monsteroideae species: Spathiphyllum patulinervum, Stenospermation multiovulatum, Monstera adansonii, and Rhaphidophora amplissima. The quadripartite chloroplast genomes (size range 163,335-164,751 bp) consist of a pair of inverted repeats (25,270-25,931 bp), separating a small single copy region (21,448-22,346 bp) from a large single copy region (89,714-91,841 bp). The genomes contain 114 unique genes, including four rRNA genes, 80 protein-coding genes, and 30 tRNA genes. Gene features, amino acid frequencies, codon usage, GC contents, oligonucleotide repeats, and inverted repeats dynamics exhibit similarities among the four genomes. Higher rate of synonymous substitutions was observed as compared to non-synonymous substitutions in 76 protein-coding genes. Positive selection was observed in seven protein-coding genes, including psbK, ndhK, ndhD, rbcL, accD, rps8, and ycf2. Our included species of Araceae showed the monophyly in Monsteroideae and other subfamilies. We report 30 suitable polymorphic regions. The polymorphic regions identified here might be suitable for designing unique and robust markers for inferring the phylogeny and phylogeography among closely related species within the genus Spathiphyllum and among distantly related species within the subfamily Monsteroideae. The chloroplast genomes presented here are a valuable contribution towards understanding the molecular evolutionary dynamics in the family Araceae.
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Affiliation(s)
- Claudia L Henriquez
- University of California, Department of Ecology and Evolutionary Biology, Los Angeles, USA.
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, 45710, Pakistan
| | | | - Alejandro Zuluaga
- Departamento de Biología, Universidad del Valle, Calle 13, 100-00, Cali, Colombia
| | | | - Michael R McKain
- The University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, USA
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Henriquez CL, Abdullah, Ahmed I, Carlsen MM, Zuluaga A, Croat TB, McKain MR. Evolutionary dynamics of chloroplast genomes in subfamily Aroideae (Araceae). Genomics 2020; 112:2349-2360. [PMID: 31945463 DOI: 10.1016/j.ygeno.2020.01.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/31/2019] [Accepted: 01/11/2020] [Indexed: 12/21/2022]
Abstract
Aroideae is the largest and most diverse subfamily of the plant family Araceae. Despite its agricultural and horticultural importance, the genomic resources are sparse for this subfamily. Here, we report de novo assembled and fully annotated chloroplast genomes of 13 Aroideae species. The quadripartite chloroplast genomes (size range of 158,177-170,037 bp) are comprised of a large single copy (LSC; 75,594-94,702 bp), a small single copy (SSC; 12,903-23,981 bp) and a pair of inverted repeats (IRs; 25,266-34,840 bp). Notable gene rearrangements and IRs contraction / expansions were found for Anchomanes hookeri and Zantedeschia aethiopica. Codon usage, amino acid frequencies, oligonucleotide repeats, GC contents, and gene features revealed similarities among the 13 species. The number of oligonucleotide repeats was uncorrelated with genome size or phylogenetic position of the species. Phylogenetic analyses corroborated the monophyly of Aroideae but were unable to resolve the positions of Calla and Schismatoglottis.
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Affiliation(s)
- Claudia L Henriquez
- University of California, Los Angeles, Department of Ecology and Evolutionary Biology, United States of America.
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, 45320 Islamabad, Pakistan.
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad 45710, Pakistan
| | - Monica M Carlsen
- Missouri Botanical Garden, St. Louis, MO, United States of America
| | - Alejandro Zuluaga
- Universidad del Valle, Departamento de Biología, Calle 13, #100-00 Cali, Colombia
| | - Thomas B Croat
- Missouri Botanical Garden, St. Louis, MO, United States of America
| | - Michael R McKain
- The University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, United States of America
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