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Francisconi AF, Marroquín JAM, Cauz-Santos LA, van den Berg C, Martins KKM, Costa MF, Picanço-Rodrigues D, de Alencar LD, Zanello CA, Colombo CA, Hernández BGD, Amaral DT, Lopes MTG, Veasey EA, Zucchi MI. Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns. Sci Rep 2023; 13:20635. [PMID: 37996522 PMCID: PMC10667357 DOI: 10.1038/s41598-023-44631-4] [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: 01/25/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023] Open
Abstract
The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.
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Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Jonathan Andre Morales Marroquín
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Luiz Augusto Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina S/N-Novo Horizonte, Feira de SantanaFeira de Santana, Bahia, CEP 44036-900, Brazil
| | - Kauanne Karolline Moreno Martins
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Marcones Ferreira Costa
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
- Universidade Federal do Piauí, BR-343 Km 3.5, Floriano, Piauí, CEP 64808-605, Brazil
| | - Doriane Picanço-Rodrigues
- Departamento de Biologia, Universidade Federal do Amazonas, Avenida Gen. Rodrigo Octávio Jordão Ramos, 3000-Coroado I-Campus Universitário-Senador Arthur Virgílio Filho-Setor Sul, Bloco H, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Luciano Delmodes de Alencar
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Cesar Augusto Zanello
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Carlos Augusto Colombo
- Instituto Agronômico, Av. Theodureto de Almeida Camargo, 1500, Campinas, São Paulo, CEP 13075-630, Brazil
| | | | - Danilo Trabuco Amaral
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo, CEP 09040-040, Brazil
| | - Maria Teresa Gomes Lopes
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Avenida Rodrigo Otávio Ramos, 3000-Bairro Coroado, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11-Bairro São Dimas, Piracicaba, São Paulo, CEP 13418-900, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia dos Agronegócios (APTA), Polo Centro Sul, Rodovia SP 127 Km 30, CP 28, Piracicaba, São Paulo, CEP 13400-970, Brazil.
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Nahar K, Zohora FT, Begum R, Hasan M, Aziz A, Jui Y, Al-Mansur MA, Anwar MR. Isolation and Evaluation of Cytotoxic, Anti-Inflammatory, Anti-Ulcer Activity of Methanolic Extract of Ceriops decandra leaves. BIOMEDICAL AND PHARMACOLOGY JOURNAL 2023; 16:1681-1691. [DOI: 10.13005/bpj/2746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2024]
Abstract
The current study was undertaken to provide scientific validation for the traditional medicinal applications of Ceriops decandra leaves in treating gastrointestinal disorders and inflammation. Additionally, the study aimed to isolate a pure component from the extracted leaves for further analysis. Lupeol was extracted from the crude methanolic extract of Ceriops decandra leaves by column chromatography as part of a phytochemical inquiry. Its structure was determined using 1H and 13C NMR spectroscopy. In order to assess the cytotoxicity, the unrefined methanolic extract was divided into two fractions: a petroleum fraction and an aqueous fraction, employing the modified Kupchan method. The brine shrimp lethality test revealed that both the aqueous and petroleum ether fractions had significant cytotoxic activity, with LC50 values of 1.93 µg/l and 2.04 µg/l, respectively. These values were compared to the LC50 value of the standard Vincristine Sulphate, which was found to be 0.02 µg/l. The results of the anti-inflammatory trial demonstrated that the administration of the extract at doses of 250mg/kg and 500mg/kg resulted in protection rates of 62.5% and 87.5%, respectively, as compared to the carrageenan control group after 3 hours post-injection. It is worth noting that Ibuprofen exhibited a higher level of protection, with a rate of 91.7%. In the context of ethanol-induced stomach ulcer, the administration of extracts at doses of 250 mg/kg and 500 mg/kg resulted in 45.5% and 59.1% protection against gastric ulcer, respectively. These findings were compared to the protective effect of Omeprazole, which demonstrated 63.6% protection and served as the standard reference. The findings suggest that the methanolic leaf extract of Ceriops decandra possesses robust cytotoxic and potent anti-inflammatory and anti-ulcer properties. These results provide support for the traditional application of this extract in the management of gastrointestinal diseases, inflammation, and cancer.
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Affiliation(s)
- Kamrun Nahar
- 1Department of Pharmacy, Primeasia University, Bangladesh. Star Tower, 12 Kemal Ataturk Ave, Dhaka
| | - Fatema-Tuz- Zohora
- 2Department of Pharmacy, University of Asia Pacific, Bangladesh. 74/A Green Rd, Dhaka
| | - Rayhana Begum
- 1Department of Pharmacy, Primeasia University, Bangladesh. Star Tower, 12 Kemal Ataturk Ave, Dhaka
| | - Maruf Hasan
- 1Department of Pharmacy, Primeasia University, Bangladesh. Star Tower, 12 Kemal Ataturk Ave, Dhaka
| | - Abdul Aziz
- 1Department of Pharmacy, Primeasia University, Bangladesh. Star Tower, 12 Kemal Ataturk Ave, Dhaka
| | - Yasmin Jui
- 1Department of Pharmacy, Primeasia University, Bangladesh. Star Tower, 12 Kemal Ataturk Ave, Dhaka
| | - Muhammad Abdullah Al-Mansur
- 3Institute of National Analytical Research and Service (INARS), BCSIR; P9RP+375, Dr. Qudrat-E-Khuda Road Dhaka
| | - Md. Rafi Anwar
- 4University of Louisiana at Monroe, College of Pharmacy, Louisiana, USA
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Zhou Y, She J, Jin C, Zhu X, Xiao F, Zhao J. Characterization of the complete chloroplast genome of Carallia brachiata (Lour.) Merr. (Rhizophoraceae). Mitochondrial DNA B Resour 2023; 8:867-871. [PMID: 37600503 PMCID: PMC10435000 DOI: 10.1080/23802359.2023.2238935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/15/2023] [Indexed: 08/22/2023] Open
Abstract
Carallia brachiata (Lour.) Merr. (1919) is an important medical resource distributed across subtropical Asia. In this study, the complete chloroplast genome of C. brachiata was sequenced, revealing a total length of 162,460 bp, including four regions - a large single copy (89,814 bp), a small single copy (18,804 bp), and a pair of inverted repeats (26,921 bp each). The overall guanine + cytosine content was 35.76%. In total, 130 genes were annotated within the chloroplast genome, comprising 85 protein-coding, 37 tRNA, and 8 rRNA genes. Subsequent phylogenetic analyses revealed that C. brachiata is closely related to Carallia diplopetala.
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Affiliation(s)
- You Zhou
- Institute of Forestry, Central South University of Forestry and Technology, Changsha, China
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Jiyun She
- Institute of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Chenzhong Jin
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Xiongmei Zhu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Fen Xiao
- Institute of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Jian Zhao
- Analysis Department, Biomarker Technologies Corporation, Beijing, China
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Lin N, Liu R, Wang Y, Guo P, Wang Y, Liu Y, Shang F. The complete chloroplast genome of Ulmus mianzhuensis with insights into structural variations, adaptive evolution, and phylogenetic relationships of Ulmus (Ulmaceae). BMC Genomics 2023; 24:366. [PMID: 37386355 DOI: 10.1186/s12864-023-09430-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/06/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Ulmus mianzhuensis is an endemic tree species in China with high ornamental and economic value. Currently, little is known regarding its genomic architecture, phylogenetic position, or adaptive evolution. Here, we sequenced the complete chloroplast genome (cp genome) of U. mianzhuensis and further compared the variations in gene organization and structure within Ulmus species to define their genomic evolution, then reconstructed the phylogenomic relationship of 31 related Ulmus species to explore the systematic position of U. mianzhuensis and the utility of cp genome for resolving phylogenetics among Ulmus species. RESULTS Our results revealed that all the Ulmus species exhibited a typical quadripartite structure, with a large single copy (LSC) region of 87,170 - 88,408 bp, a small single copy (SSC) region of 18,650 - 19,038 bp and an inverted repeat (IR) region of 26,288 - 26,546 bp. Within Ulmus species, gene structure and content of cp genomes were highly conserved, although slight variations were found in the boundary of SC/IR regions. Moreover, genome-wide sliding window analysis uncovered the variability of ndhC-trnV-UAC, ndhF-rpl32, and psbI-trnS-GCU were higher among 31 Ulmus that may be useful for the population genetics and potential DNA barcodes. Two genes (rps15 and atpF) were further detected under a positive selection of Ulmus species. Comparative phylogenetic analysis based on the cp genome and protein-coding genes revealed consistent topology that U. mianzhuensis is a sister group to U. parvifolia (sect. Microptelea) with a relatively low-level nucleotide variation of the cp genome. Additionally, our analyses also found that the traditional taxonomic system of five sections in Ulmus is not supported by the current phylogenomic topology with a nested evolutionary relationship between sections. CONCLUSIONS Features of the cp genome length, GC content, organization, and gene order were highly conserved within Ulmus. Furthermore, molecular evidence from the low variation of the cp genome suggested that U. mianzhuensis should be merged into U. parvifolia and regarded as a subspecies of U. parvifolia. Overall, we demonstrated that the cp genome provides valuable information for understanding the genetic variation and phylogenetic relationship in Ulmus.
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Affiliation(s)
- Nan Lin
- College of Life Science, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Rui Liu
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Yakun Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Peng Guo
- College of Life Science, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Yihan Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Yanpei Liu
- College of Life Science, Henan Agricultural University, Zhengzhou, China.
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China.
| | - Fude Shang
- College of Life Science, Henan Agricultural University, Zhengzhou, China.
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China.
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Agduma AR, Cao KF. Species richness, extent and potential threats to mangroves of Sarangani Bay Protected Seascape, Philippines. Biodivers Data J 2023; 11:e100050. [PMID: 38327299 PMCID: PMC10848689 DOI: 10.3897/bdj.11.e100050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Mangroves form one of the most vital tropical ecosystems that support many species and surrounding communities. The Sarangani Bay Protected Seascape (SBPS) in the south of Mindanao Islands in the Philippines is home to a large number of mangrove species, which have not been fully explored. We updated the list of true mangrove species for SBPS from 10 to 24 by integrating the results of our survey and other past mangrove assessments. A practical spatial analysis approach was used to estimate the current mangrove forest extent of SBPS at 514 ha, as compared to 479 ha and 332 ha in 1998 and 2016, respectively, from other independent reports. Mangrove cover was negatively related to built area, cropland, bare ground, rangeland and total human population, but positively related to the number of fishing boats and total tree cover. In addition, we identified other potential anthropogenic threats to mangroves and categorised them into forest clearing or deforestation, over-extraction and pollution. The benefits of mangrove cover expansion, adoption of mangrove-friendly aquaculture and revitalising degraded mangrove forests outweigh their constraints. Our work provided a locally relevant understanding of the potential causes of mangrove loss and the values of human actions in mangrove dynamics, which will contribute to reliable and informed decision-making for the conservation of mangrove species and restoration of mangrove forests in SBPS.
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Affiliation(s)
- Angelo Rellama Agduma
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, Guangxi University, Nanning 530004, Guangxi, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, Guangxi UniversityNanning 530004, GuangxiChina
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, Guangxi, ChinaGuangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi UniversityNanning 530004, GuangxiChina
- Ecology and Conservation Research Laboratory, Department of Biological Sciences, College of Science and Mathematics, University of Southern Mindanao, Kabacan 9407, Cotabato, PhilippinesEcology and Conservation Research Laboratory, Department of Biological Sciences, College of Science and Mathematics, University of Southern MindanaoKabacan 9407, CotabatoPhilippines
- Environmental Conservation and Protection Center, Provincial Capitol Compound, Alabel 9501, Sarangani, PhilippinesEnvironmental Conservation and Protection Center, Provincial Capitol CompoundAlabel 9501, SaranganiPhilippines
| | - Kun-Fang Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, Guangxi University, Nanning 530004, Guangxi, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, Guangxi UniversityNanning 530004, GuangxiChina
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, Guangxi, ChinaGuangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi UniversityNanning 530004, GuangxiChina
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Mei Y, Chen D, Cai S. The characteristics of the complete chloroplast genome of Staurogyne concinnula (Hance) O. Kuntze (Acanthaceae). Mitochondrial DNA B Resour 2023; 8:507-511. [PMID: 37091578 PMCID: PMC10116917 DOI: 10.1080/23802359.2023.2199894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Staurogyne concinnula (Hance) O. Kuntze (Acanthaceae) is an important ornamental herb mainly distributed in the southern region of China, including Fujian, Guangdong, Hainan, and Taiwan provinces. However, the complete chloroplast genome of S. concinnula, which could serve as a genetic resource for studies on its taxonomy and evolution, is poorly studied at present. In this study, we reported the complete chloroplast genome of S. concinnula that was assembled using high-throughput sequencing data. The chloroplast genome was 153,783 bp long, with a typical quadripartite structure containing a small single-copy region (SSC; 17,855 bp), a large single-copy region (LSC; 84,636 bp) and a pair of inverted repeats (IRs; each 25,646 bp). The overall GC content of the chloroplast genome was 38.04%. A total of 86 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes were predicted. Phylogenetic analysis based on the combined sequences of 86 PCGs with the other 16 closely related species of Acanthaceae indicated that S. concinnula is closely related to Avicennia marina. The genomic data and finding from the phylogenetic studies of S. concinnula could provide useful information and give light to in-depth studies on the evolution pattern of the understudied species, as well as Staurogyne.
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Affiliation(s)
- Yu Mei
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P.R. China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, P.R. China
| | - Dongming Chen
- Guangdong Taihetang Industrial Co., LTD, Huizhou, P.R. China
| | - Shike Cai
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P.R. China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, P.R. China
- CONTACT Shike Cai Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P.R. China
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Wang R, Liao N, Liu X, Qin Y, Xiao Y, Wang Y, Huang R. Characterization of the complete chloroplast genome of Carallia diplopetala (Rhizophoraceae). Mitochondrial DNA B Resour 2022; 7:1870-1872. [PMID: 36325279 PMCID: PMC9621227 DOI: 10.1080/23802359.2022.2135398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Carallia diplopetala (Rhizophoraceae) is an important economic tree species narrowly distributed endemic to East Asia. In this study, We generate the complete chloroplast genome of C. diplopetala using next-generation sequencing technology, which is 162,052 bp in size and consists of a large single copy (LSC) of 89,556 bp and a small single copy (SSC) of 18,814 bp, separated a pair of inverted repeats (IRb and IRa) of 26,841 bp. The overall GC content is 36.4%. A total of 130 genes are annotated, including 83 protein-coding genes, 37 tRNAs, eight rRNAs and two pseudogenes (ψycf1 and ψrps19). The phylogenetic analysis indicated that C. diplopetala and C. brachiate formed a monophyletic clade with strong support and then sister to Pellacalyx yunnanensis. The plastome of C. diplopetala will provide informative genomic resources for further conservation applications.
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Affiliation(s)
- Renjie Wang
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - Nanyan Liao
- Guangxi Fangcheng Golden, Camellias National Nature Reserve, Fangchenggang, China
| | - Xiongsheng Liu
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - Yi Qin
- Guangxi Fangcheng Golden, Camellias National Nature Reserve, Fangchenggang, China
| | - Yufei Xiao
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - Yong Wang
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - Ronglin Huang
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China,CONTACT Ronglin Huang Guangxi Forestry Research Institute, Nanning, China
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Sangsrakru D, Sonthirod C, Nawae W, Yundaeng C, Promchoo W, Pootakham W, Tangphatsornruang S. The complete chloroplast genome of Sonneratia griffithii Kurz (Lythraceae). Mitochondrial DNA B Resour 2022; 7:1761-1763. [PMID: 36237205 PMCID: PMC9553166 DOI: 10.1080/23802359.2022.2119818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Sonneratia griffithii Kurz is a critically endangered mangrove species that can be found along the western coast of Thailand. In this study, we reported the complete chloroplast genome of S. griffithii. The chloroplast genome is 152,730 bp, consisting of one large single-copy (LSC) region, one small single-copy (SSC) region and a pair of inverted repeats (IRs). The LSC, SSC, and IR lengths are 87,226, 17,764, and 23,870 bp, respectively. The genome contains 113 unique genes, including 79 protein-coding, 30 tRNA, and 4 rRNA genes. The GC content of the chloroplast genome is 37.31%. The phylogenetic analysis based on 76 protein-coding genes showed a monophyletic group of S. griffithii and other Sonneratia species.
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Affiliation(s)
- Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutintorn Yundaeng
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Waratthaya Promchoo
- Department of Marine and Coastal Resources, Royal Thai Government Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand,CONTACT Sithichoke Tangphatsornruang National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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Pootakham W, Naktang C, Sonthirod C, Kongkachana W, Narong N, Sangsrakru D, Maknual C, Jiumjamrassil D, Chumriang P, Tangphatsornruang S. Chromosome-level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome-wide duplication event predating the divergence of Rhizophoraceae mangrove species. THE PLANT GENOME 2022; 15:e20217. [PMID: 35608212 DOI: 10.1002/tpg2.20217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
Mangrove ecosystems are unique, highly diverse, provide benefits to humans, and aid in coastal protection. The Indian mangrove, or spurred mangrove, [Ceriops tagal (Perr.) C. B. Rob.] is a member of the Rhizophoraceae family and is commonly found along the intertidal zones in tropical regions in Southeast Asia, southern Asia, and Africa. Here, we present the first high-quality reference genome assembly of the Ceriops species. A preliminary draft assembly, generated from the 10× Genomics linked-read library, was scaffolded using the proximity ligation chromatin contact mapping technique (Hi-C) to obtain a chromosome-scale assembly of 231,919,005 bases with an N50 length of 11,408,429 bases. The benchmarking universal single-copy orthologs (BUSCO) analysis revealed that C. tagal gene predictions recovered 95.8% of the highly conserved orthologs. Phylogenetic analyses suggested that C. tagal diverged from the last common ancestor of flat-leaf spurred mangrove [C. decandra (Griff.) Ding Hou] and C. zippeliana Blume ∼10.4 million yr ago (MYA), and the last common ancestor of genera Ceriops, Kandelia, and Rhizophora diverged from that of genus Bruguiera ∼49.4 MYA. In addition, our analysis of the transversion rate at fourfold-degenerate sites from orthologous gene pairs provided evidence supporting a recent whole-genome duplication in C. tagal. The STRUCTURE and principal component analyses illustrated that C. tagal individuals investigated in this study were the admixture of two subpopulations, the genetic background of which was influenced primarily by location. The availability of genomic and transcriptomic resources and biodiversity data reported in this work will be useful for future studies that may shed light on adaptive evolutions of mangrove species.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nattapol Narong
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chatree Maknual
- Dep. of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok, 10210, Thailand
| | - Darunee Jiumjamrassil
- Dep. of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok, 10210, Thailand
| | - Pranom Chumriang
- Dep. of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok, 10210, Thailand
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