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Lian Z, Zhang J, Hao Z, Zhu L, Liu Y, Fang H, Lu Y, Li X, Shi J, Chen J, Cheng T. The Glutathione Peroxidase Gene Family in Nitraria sibirica: Genome-Wide Identification, Classification, and Gene Expression Analysis under Stress Conditions. Genes (Basel) 2023; 14:genes14040950. [PMID: 37107708 PMCID: PMC10137829 DOI: 10.3390/genes14040950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Plant glutathione peroxidases (GPXs) are the main enzymes in the antioxidant defense system that sustain H2O2 homeostasis and normalize plant reaction to abiotic stress conditions. However, the genome-wide identification of the GPX gene family and its responses to environmental stresses, especially salt stress, in Nitraria sibirica, which is a shrub that can survive in saline environments, has not yet been reported. Here, we first report the genome-wide analysis of the GPX gene family in N. sibirica, leading to a total of seven NsGPX genes that are distributed on six of the twelve chromosomes. Phylogenetic analysis showed that NsGPX genes were grouped into four major groups (Group I-IV). Three types of cis-acting elements were identified in the NsGPX promoters, mainly related to hormones and stress response. The quantitative real-time PCR (qRT-PCR) analysis indicated that NsGPX1 and NsGPX3 were significantly up-regulated in stem and leaf, while NsGPX7 transcriptionally in root in response to salt stress. The current study identified a total seven NsGPX genes in N. sibirica via genome-wide analysis, and discovered that NsGPXs may play an important role in response to salt stress. Taken together, our findings provide a basis for further functional studies of NsGPX genes, especially in regarding to the resistance to salt stress of this halophyte plant N. sibirica, eventually aid in the discovery of new methods to restore overtly saline soil.
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Affiliation(s)
- Ziming Lian
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jingbo Zhang
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, China
| | - Zhaodong Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Liming Zhu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuxin Liu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hao Fang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Ye Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xinle Li
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, China
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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Banaev EV, Tomoshevich MA, Khozyaykina SA, Erst AA, Erst AS. Integrative Taxonomy of Nitraria (Nitrariaceae), Description of the New Enigmatic Species and Key to All Currently Known Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:593. [PMID: 36771680 PMCID: PMC9921022 DOI: 10.3390/plants12030593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
A new species, Nitraria iliensis sp. nov., is described from the Ili basin, Almaty region, Kazakhstan. It belongs to section Nitraria ser. Sibiricae and is morphologically similar to N. sibirica Pall. An integrative taxonomic approach based on molecular, biochemical and morphological analyses, along with palynological data, was used to delimit this new species. The studied species of the genus are illustrated, and photographs of authentic specimens of the new species, as well as a distribution map of the new species and segregate taxa, are provided. Morphological characters were investigated, more important traits for identification were found, and a new key to distinguish between all species of the genus was prepared.
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Affiliation(s)
| | | | | | - Anna A. Erst
- Correspondence: (A.A.E.); (A.S.E.); Tel.: +7-(383)339-9842 (A.A.E.)
| | - Andrey S. Erst
- Correspondence: (A.A.E.); (A.S.E.); Tel.: +7-(383)339-9842 (A.A.E.)
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Mao C, Zhang F, Li X, Yang T, Zhao Q, Wu Y. Complete chloroplast genome sequences of Myristicaceae species with the comparative chloroplast genomics and phylogenetic relationships among them. PLoS One 2023; 18:e0281042. [PMID: 36940204 PMCID: PMC10027215 DOI: 10.1371/journal.pone.0281042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 01/14/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Myristicaceae was widly distributed from tropical Asia to Oceania, Africa, and tropical America. There are 3 genera and 10 species of Myristicaceae present in China, mainly distributed in the south of Yunnan Province. Most research on this family focuses on fatty acids, medicine, and morphology. Based on the morphology, fatty acid chemotaxonomy, and a few of molecular data, the phylogenetic position of Horsfieldia pandurifolia Hu was controversial. RESULTS In this study, the chloroplast genomes of two Knema species, Knema globularia (Lam.) Warb. and Knema cinerea (Poir.) Warb., were characterized. Comparing the genome structure of these two species with those of other eight published species, including three Horsfieldia species, four Knema species, and one Myristica species, it was found that the chloroplast genomes of these species were relatively conserved, retaining the same gene order. Through sequence divergence analysis, there were 11 genes and 18 intergenic spacers were subject to positive selection, which can be used to analyze the population genetic structure of this family. Phylogenetic analysis showed that all Knema species were clustered in the same group and formed a sister clade with Myristica species support by both high maximum likelihood bootstrap values and Bayesian posterior probabilities; among Horsfieldia species, Horsfieldia amygdalina (Wall.) Warb., Horsfieldia kingii (Hook.f.) Warb., Horsfieldia hainanensis Merr. and Horsfieldia tetratepala C.Y.Wu. were grouped together, but H. pandurifolia formed a single group and formed a sister clade with genus Myristica and Knema. Through the phylogenetic analysis, we support de Wilde' view that the H. pandurifolia should be separated from Horsfieldia and placed in the genus Endocomia, namely Endocomia macrocoma subsp. prainii (King) W.J.de Wilde. CONCLUSION The findings of this study provide a novel genetic resources for future research in Myristicaceae and provide a molecular evidence for the taxonomic classification of Myristicaceae.
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Affiliation(s)
- Changli Mao
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | | | - Xiaoqin Li
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Tian Yang
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Qi Zhao
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Yu Wu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
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Huang S, Kang Z, Chen Z, Deng Y. Comparative Analysis of the Chloroplast Genome of Cardamine hupingshanensis and Phylogenetic Study of Cardamine. Genes (Basel) 2022; 13:2116. [PMID: 36421792 PMCID: PMC9690686 DOI: 10.3390/genes13112116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 05/04/2024] Open
Abstract
Cardamine hupingshanensis (K. M. Liu, L. B. Chen, H. F. Bai and L. H. Liu) is a perennial herbal species endemic to China with narrow distribution. It is known as an important plant for investigating the metabolism of selenium in plants because of its ability to accumulate selenium. However, the phylogenetic position of this particular species in Cardamine remains unclear. In this study, we reported the chloroplast genome (cp genome) for the species C. hupingshanensis and analyzed its position within Cardamine. The cp genome of C. hupingshanensis is 155,226 bp in length and exhibits a typical quadripartite structure: one large single copy region (LSC, 84,287 bp), one small single copy region (17,943 bp) and a pair of inverted repeat regions (IRs, 26,498 bp). Guanine-Cytosine (GC) content makes up 36.3% of the total content. The cp genome contains 111 unique genes, including 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. A total of 115 simple sequences repeats (SSRs) and 49 long repeats were identified in the genome. Comparative analyses among 17 Cardamine species identified the five most variable regions (trnH-GUG-psbA, ndhK-ndhC, trnW-CCA-trnP-UGG, rps11-rpl36 and rpl32-trnL-UAG), which could be used as molecular markers for the classification and phylogenetic analyses of various Cardamine species. Phylogenetic analyses based on 79 protein coding genes revealed that the species C. hupingshanensis is more closely related to the species C. circaeoides. This relationship is supported by their shared morphological characteristics.
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Affiliation(s)
- Sunan Huang
- Key Laboratory of Plant Resources Conservation & Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zujie Kang
- Management Bureau of Hunan Hupingshan National Nature Reserve, Shimen 415300, China
| | - Zhenfa Chen
- Management Bureau of Hunan Hupingshan National Nature Reserve, Shimen 415300, China
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation & Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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Kadoglidou K, Irakli M, Boutsika A, Mellidou I, Maninis N, Sarrou E, Georgiadou V, Tourvas N, Krigas N, Moysiadis T, Grigoriadou K, Maloupa E, Xanthopoulou A, Ganopoulos I. Metabolomic Fingerprinting and Molecular Characterization of the Rock Samphire Germplasm Collection from the Balkan Botanic Garden of Kroussia, Northern Greece. PLANTS 2022; 11:plants11040573. [PMID: 35214906 PMCID: PMC8879136 DOI: 10.3390/plants11040573] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 11/19/2022]
Abstract
The traditionally edible aerial parts of rock samphire (Crithmum maritimum L.) could be a valuable functional food or feed ingredient due to their high antioxidant capacity, ascorbic acid content, and rich content in secondary metabolites such as phenolics and flavonoids. The first objective of this study was to evaluate eighteen genotypes derived from different regions of Greece regarding the phytochemical contents of their soluble extracts in total phenolics, total flavonoids, and individual polyphenols as determined by LC-MS analysis, as well as ascorbic acid content and their antioxidant capacity as determined by different assays, including ABTS (2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid), DPPH (2,2-diphenyl-1-picrylhydrazyl radical scavenging activity), and FRAP (ferric reducing antioxidant power) assays. The second objective of the study was the molecular characterization of native Greek C. maritimum genotypes. Great variation among genotypes was observed in terms of the antioxidant capacity, ascorbic acid content, and phenolic compounds (total phenolic content and total flavonoid content), as well as in caffeolquinic acids and flavonoids. The principal component analysis highlighted genotypes with a higher potential in antioxidants and polyphenolics. The most promising genotypes were G9 from Kefalonia, followed by G4 from Ikaria, where both clearly exhibited a similar response with high values of evaluated traits. The molecular characterization of genotypes revealed low variability and low to moderate genetic diversity between populations. Our data indicated that the rock samphire germplasm collection from the Balkan Botanic Garden of Kroussia could serve as an important source of documented genetic material and, thus, it is suggested for further investigation to provide insight regarding cultivation and agro-processing aspects, artificial selection, or plant breeding aimed at developing C. maritimum genotypes of high-bioactive value.
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Affiliation(s)
- Kalliopi Kadoglidou
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
- Correspondence: (K.K.); (I.G.)
| | - Maria Irakli
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Anastasia Boutsika
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Nikolas Maninis
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Eirini Sarrou
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Vasiliki Georgiadou
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Nikolaos Tourvas
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Nikos Krigas
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Theodoros Moysiadis
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
- Department of Computer Science, School of Sciences and Engineering, University of Nicosia, Nicosia 2417, Cyprus
| | - Katerina Grigoriadou
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Eleni Maloupa
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Aliki Xanthopoulou
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thermi, GR-57001 Thessaloniki, Greece; (M.I.); (A.B.); (I.M.); (N.M.); (E.S.); (V.G.); (N.T.); (N.K.); (T.M.); (K.G.); (E.M.); (A.X.)
- Correspondence: (K.K.); (I.G.)
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Lu L, Chen X, Zhu L, Li M, Zhang J, Yang X, Wang P, Lu Y, Cheng T, Shi J, Yi Y, Chen J. NtCIPK9: A Calcineurin B-Like Protein-Interacting Protein Kinase From the Halophyte Nitraria tangutorum, Enhances Arabidopsis Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:1112. [PMID: 32973820 PMCID: PMC7472804 DOI: 10.3389/fpls.2020.01112] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 07/06/2020] [Indexed: 05/20/2023]
Abstract
Calcineurin B-like protein-interacting protein kinases (CIPKs) play essential roles in plant abiotic stress response. In order to better understand salt tolerance, we cloned and analyzed the NtCIPK9 gene from the halophyte Nitraria tangutorum. Phylogenetic analysis shows that NtCIPK9 belongs to a sister clade with the Arabidopsis AtCIPK9 gene and is thought to localize to the plasma membrane. NtCIPK9 shows the highest expression level in the Nitraria tangutorum root under normal growth conditions, whereas after NaCl treatment, the highest expression was found in the blade. NtCIPK9-overexpressing Arabidopsis plants have a higher seed germination rate, longer root length, and displayed higher salt tolerance than wild type seedlings under salt stress conditions. Furthermore, NtCIPK9 overexpression might enhance the expression of genes related to K+ transportation after NaCl treatment. Thus, we conclude that NtCIPK9 increases transgenic plant salt tolerance and reduces damage associated with salt stress by promoting the expression of genes controlling ion homeostasis. Our results suggest that NtCIPK9 could serve as an ideal candidate gene to genetically engineer salt-tolerant plants.
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Affiliation(s)
- Lu Lu
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinying Chen
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Mengjuan Li
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jingbo Zhang
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, China
| | - Xiuyan Yang
- Research Center of Saline and Alkali Land of National Forestry and Grassland Administration, China Academy of Forestry, Beijing, China
| | - Pengkai Wang
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Tielong Cheng
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yin Yi
- State Forestry Administration Key Laboratory of Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, China
- Guizhou Provincial Key Laboratory of Plant Physiology and Developmental Regulation, Guizhou Normal University, Guiyang, China
| | - Jinhui Chen
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Areces-Berazain F, Wang Y, Hinsinger DD, Strijk JS. Plastome comparative genomics in maples resolves the infrageneric backbone relationships. PeerJ 2020; 8:e9483. [PMID: 32742784 PMCID: PMC7365138 DOI: 10.7717/peerj.9483] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/15/2020] [Indexed: 12/28/2022] Open
Abstract
Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples.
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Affiliation(s)
- Fabiola Areces-Berazain
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
| | - Yixi Wang
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
| | - Damien D. Hinsinger
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commisariat à l’Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Joeri S. Strijk
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, China
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Alzahrani DA, Yaradua SS, Albokhari EJ, Abba A. Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae. BMC Genomics 2020; 21:393. [PMID: 32532210 PMCID: PMC7291470 DOI: 10.1186/s12864-020-06798-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 05/27/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The plastome of medicinal and endangered species in Kingdom of Saudi Arabia, Barleria prionitis was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, spot the microsatellite, assess the dissimilarities within the sampled plastomes and to infer their phylogenetic relationships. RESULTS The plastome of B. prionitis was 152,217 bp in length with Guanine-Cytosine and Adenine-Thymine content of 38.3 and 61.7% respectively. It is circular and quadripartite in structure and constitute of a large single copy (LSC, 83, 772 bp), small single copy (SSC, 17, 803 bp) and a pair of inverted repeat (IRa and IRb 25, 321 bp each). 131 genes were identified in the plastome out of which 113 are unique and 18 were repeated in IR region. The genome consists of 4 rRNA, 30 tRNA and 80 protein-coding genes. The analysis of long repeat showed all types of repeats were present in the plastome and palindromic has the highest frequency. A total number of 98 SSR were also identified of which mostly were mononucleotide Adenine-Thymine and are located at the non coding regions. Comparative genomic analysis among the plastomes revealed that the pair of the inverted repeat is more conserved than the single copy region. In addition high variation is observed in the intergenic spacer region than the coding region. The genes, ycf1and ndhF and are located at the border junction of the small single copy region and IRb region of all the plastome. The analysis of sequence divergence in the protein coding genes indicates that the following genes undergo positive selection (atpF, petD, psbZ, rpl20, petB, rpl16, rps16, rpoC, rps7, rpl32 and ycf3). Phylogenetic analysis indicated sister relationship between Ruellieae and Justcieae. In addition, Barleria, Justicia and Ruellia are paraphyletic, suggesting that Justiceae, Ruellieae, Andrographideae and Barlerieae should be treated as tribes. CONCLUSIONS This study sequenced and assembled the first plastome of the taxon Barleria and reported the basics resources for evolutionary studies of B. prionitis and tools for phylogenetic relationship studies within the core Acanthaceae.
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Affiliation(s)
- Dhafer A Alzahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Samaila S Yaradua
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. .,Department of Biology, Umaru Musa Yaradua University, Centre for Biodiversity and Conservation, Katsina, Nigeria.
| | - Enas J Albokhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Biological Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Abidina Abba
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Liao YY, Liu Y, Liu X, Lü TF, Mbichi RW, Wan T, Liu F. The complete chloroplast genome of Myriophyllum spicatum reveals a 4-kb inversion and new insights regarding plastome evolution in Haloragaceae. Ecol Evol 2020; 10:3090-3102. [PMID: 32211179 PMCID: PMC7083656 DOI: 10.1002/ece3.6125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 09/11/2019] [Accepted: 02/05/2020] [Indexed: 12/13/2022] Open
Abstract
Myriophyllum, among the most species-rich genera of aquatic angiosperms with ca. 68 species, is an extensively distributed hydrophyte lineage in the cosmopolitan family Haloragaceae. The chloroplast (cp) genome is useful in the study of genetic evolution, phylogenetic analysis, and molecular dating of controversial taxa. Here, we sequenced and assembled the whole chloroplast genome of Myriophyllum spicatum L. and compared it to other species in the order Saxifragales. The complete chloroplast genome sequence of M. spicatum is 158,858 bp long and displays a quadripartite structure with two inverted repeats (IR) separating the large single copy (LSC) region from the small single copy (SSC) region. Based on sequence identification and the phylogenetic analysis, a 4-kb phylogenetically informative inversion between trnE-trnC in Myriophyllum was determined, and we have placed this inversion on a lineage specific to Myriophyllum and its close relatives. The divergence time estimation suggested that the trnE-trnC inversion possibly occurred between the upper Cretaceous (72.54 MYA) and middle Eocene (47.28 MYA) before the divergence of Myriophyllum from its most recent common ancestor. The unique 4-kb inversion might be caused by an occurrence of nonrandom recombination associated with climate changes around the K-Pg boundary, making it interesting for future evolutionary investigations.
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Affiliation(s)
- Yi-Ying Liao
- Key Laboratory of Southern Subtropical Plant Diversity Fairy Lake Botanical Garden Shenzhen China
| | - Yu Liu
- Key Laboratory of Southern Subtropical Plant Diversity Fairy Lake Botanical Garden Shenzhen China
| | - Xing Liu
- Laboratory of Plant Systematics and Evolutionary Biology College of Life Science Wuhan University Wuhan China
| | - Tian-Feng Lü
- Laboratory of Plant Systematics and Evolutionary Biology College of Life Science Wuhan University Wuhan China
| | - Ruth Wambui Mbichi
- Sino-Africa Joint Research Centre Chinese Academy of Science Wuhan China
| | - Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity Fairy Lake Botanical Garden Shenzhen China
| | - Fan Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden Chinese Academy of Sciences Wuhan China
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10
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Xu Y, Zhao Y, Zhao X, Chen X, Yuan Z. Characterization of complete chloroplast genome of Malus sylvestris L. Mitochondrial DNA B Resour 2019; 4:2357-2358. [PMID: 33365542 PMCID: PMC7687612 DOI: 10.1080/23802359.2019.1629352] [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: 11/30/2022] Open
Abstract
The European wild apple (Malus sylvestris L.) is an important economical fruit crop. In this present study, we characterized the complete chloroplast (cp) genome sequence of Malus sylvestris L. The complete cp genome is 159,926 bp in length with a typical quadripartite structure, containing a large single-copy region (88,064 bp), a small single-copy region (26,353 bp) and a pair of inverted repeat regions (19,157 bp each). A total of 110 unique genes were found in the newly sequenced genome, including 78 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. Of these, 6 protein-coding genes, 7 tRNA genes, and all 4 rRNA genes are duplicated in the inverted regions. A phylogenetic tree was reconstructed using the neighbor-joining method based on the full length of cp genomes within genus Malus. The result showed that M. sylvestris L. was clustered together with the cultivated apple. The complete cp genome could provide valuable information for understanding the phylogenetic relationships within the genus Malus.
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Affiliation(s)
- Yunfang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yujie Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xuesen Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
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11
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Wang X, Zhou T, Bai G, Zhao Y. Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships. Sci Rep 2018; 8:12379. [PMID: 30120274 PMCID: PMC6098159 DOI: 10.1038/s41598-018-30398-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
Fagopyrum dibotrys, belongs to Polygonaceae family, is one of national key conserved wild plants of China with important medicinal and economic values. Here, the complete chloroplast (cp) genome sequence of F. dibotrys is reported. The cp genome size is 159,919 bp with a typical quadripartite structure and consisting of a pair of inverted repeat regions (30,738 bp) separated by large single copy region (85,134 bp) and small single copy region (13,309 bp). Sequencing analyses indicated that the cp genome encodes 131 genes, including 80 protein-coding genes, 28 tRNA genes and 4 rRNA genes. The genome structure, gene order and codon usage are typical of angiosperm cp genomes. We also identified 48 simple sequence repeats (SSR) loci, fewer of them are distributed in the protein-coding sequences compared to the noncoding regions. Comparison of F. dibotrys cp genome to other Polygonaceae cp genomes indicated the inverted repeats (IRs) and coding regions were more conserved than single copy and noncoding regions, and several variation hotspots were detected. Coding gene sequence divergence analyses indicated that five genes (ndhK, petL rpoC2, ycf1, ycf2) were subject to positive selection. Phylogenetic analysis among 42 species based on cp genomes and 50 protein-coding genes indicated a close relationship between F. dibotrys and F. tataricum. In summary, the complete cp genome sequence of F. dibotrys reported in this study will provide useful plastid genomic resources for population genetics and pave the way for resolving phylogenetic relationships of order Caryophyllales.
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Affiliation(s)
- Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Guoqing Bai
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Xi'an, 710061, China
| | - Yuemei Zhao
- College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo, 726000, China
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12
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Zhou T, Wang J, Jia Y, Li W, Xu F, Wang X. Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers. Int J Mol Sci 2018; 19:E1962. [PMID: 29976857 PMCID: PMC6073106 DOI: 10.3390/ijms19071962] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 11/30/2022] Open
Abstract
Gentiana section Cruciata is widely distributed across Eurasia at high altitudes, and some species in this section are used as traditional Chinese medicine. Accurate identification of these species is important for their utilization and conservation. Due to similar morphological and chemical characteristics, correct discrimination of these species still remains problematic. Here, we sequenced three complete chloroplast (cp) genomes (G. dahurica, G. siphonantha and G. officinalis). We further compared them with the previously published plastomes from sect. Cruciata and developed highly polymorphic molecular markers for species authentication. The eight cp genomes shared the highly conserved structure and contained 112 unique genes arranged in the same order, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. We found that four genes (accD, clpP, matK and ycf1) were subject to positive selection, and sixteen InDel-variable loci with high discriminatory powers were selected as candidate barcodes. Our phylogenetic analyses based on plastomes further confirmed the monophyly of sect. Cruciata and primarily elucidated the phylogeny of Gentianales. This study indicated that cp genomes can provide more integrated information for better elucidating the phylogenetic pattern and improving discriminatory power during species authentication.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Jian Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), School of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Wenli Li
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Fusheng Xu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
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13
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Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses. Int J Mol Sci 2018; 19:ijms19030701. [PMID: 29494509 PMCID: PMC5877562 DOI: 10.3390/ijms19030701] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 01/02/2023] Open
Abstract
The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously published Azadirachta indica plastome. The five plastomes are circular and exhibit a quadripartite structure with high conservation of gene content and order. They include 130 genes encoding 85 proteins, 37 tRNAs and 8 rRNAs. Inverted repeat expansion resulted in a duplication of rps19 in the five Meliaceae species, which is consistent with that in many other Sapindales, but different from many other rosids. Compared to Azadirachta indica, the four newly sequenced Meliaceae individuals share several large deletions, which mainly contribute to the decreased genome sizes. A whole-plastome phylogeny supports previous findings that the four species form a monophyletic sister clade to Azadirachta indica within the Meliaceae. SNPs and indels identified in all complete Meliaceae plastomes might be suitable targets for the future development of genetic markers at different taxonomic levels. The extended analysis of SNPs in the matK gene led to the identification of four potential Meliaceae-specific SNPs as a basis for future validation and marker development.
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