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Genome assembly of the milky mangrove Excoecaria agallocha. GIGABYTE 2024; 2024:gigabyte119. [PMID: 38707633 PMCID: PMC11066562 DOI: 10.46471/gigabyte.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024] Open
Abstract
The milky mangrove Excoecaria agallocha is a latex-secreting mangrove that are distributed in tropical and subtropical regions. While its poisonous latex is regarded as a potential source of phytochemicals for biomedical applications, the genomic resources of E. agallocha remains limited. Here, we present a chromosomal level genome of E. agallocha, assembled from the combination of PacBio long-read sequencing and Omni-C data. The resulting assembly size is 1,332.45 Mb and has high contiguity and completeness with a scaffold N50 of 58.9 Mb and a BUSCO score of 98.4%, with 86.08% of sequences anchored to 18 pseudomolecules. 73,740 protein-coding genes were also predicted. The milky mangrove genome provides a useful resource for further understanding the biosynthesis of phytochemical compounds in E. agallocha.
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Liu L, Chen M, Folk RA, Wang M, Zhao T, Shang F, Soltis DE, Li P. Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids. Mol Ecol Resour 2023; 23:1673-1688. [PMID: 37449554 DOI: 10.1111/1755-0998.13833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep-level relationships, we constructed a high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen-fixing clade, while Picramniales, the Celastrales-Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an "expanded" malvid clade. The Celastrales-Oxalidales-Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well-supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.
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Affiliation(s)
- Luxian Liu
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengzhen Chen
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
| | - Meizhen Wang
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fude Shang
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, Henan, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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Tan F, Li W, Feng H, Huang Y, Banerjee AK. Interspecific variation and phylogenetic relationship between mangrove and non-mangrove species of a same family (Meliaceae)-insights from comparative analysis of complete chloroplast genome. PeerJ 2023; 11:e15527. [PMID: 37397021 PMCID: PMC10309054 DOI: 10.7717/peerj.15527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/19/2023] [Indexed: 07/04/2023] Open
Abstract
The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus: Xylocarpus. Two of the three species of the genus Xylocarpus are true mangroves (X. granatum and X. moluccensis), and one is a non-mangrove (X. rumphii). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of these Xylocarpus species along with two non-mangrove species of the Meliaceae family (Carapa guianensis and Swietenia macrophylla) and compared the genome features and variations across the five species. The five Meliaceae species shared 130 genes (85 protein-coding genes, 37 tRNA, and eight rRNA) with identical direction and order, with a few variations in genes and intergenic spacers. The repetitive sequences identified in the rpl22 gene region only occurred in Xylocarpus, while the repetitive sequences in accD were found in X. moluccensis and X. rumphii. The TrnH-GUG and rpl32 gene regions and four non-coding gene regions showed high variabilities between X. granatum and the two non-mangrove species (S. macrophylla and C. guianensis). In addition, among the Xylocarpus species, only two genes (accD and clpP) showed positive selection. Carapa guianensis and S. macrophylla owned unique RNA editing sites. The above genes played an important role in acclimation to different stress factors like heat, low temperature, high UV light, and high salinity. Phylogenetic analysis with 22 species in the order Sapindales supported previous studies, which revealed that the non-mangrove species X. rumphii is closer to X. moluccensis than X. granatum. Overall, our results provided important insights into the variation of genetic structure and adaptation mechanism at interspecific (three Xylocarpus species) and intergeneric (mangrove and non-mangrove genera) levels.
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Affiliation(s)
- Fengxiao Tan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Weixi Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hui Feng
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yelin Huang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Gong L, Ding X, Guan W, Zhang D, Zhang J, Bai J, Xu W, Huang J, Qiu X, Zheng X, Zhang D, Li S, Huang Z, Su H. Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification. BMC PLANT BIOLOGY 2022; 22:520. [PMID: 36352400 PMCID: PMC9644571 DOI: 10.1186/s12870-022-03898-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Species in genus Amomum always have important medicinal and economic values. Classification of Amomum using morphological characters has long been a challenge because they exhibit high similarity. The main goals of this study were to mine genetic markers from cp genomes for Amomum species identification and discover their evolutionary history through comparative analysis. RESULTS Three species Amomum villosum, Amomum maximum and Amomum longipetiolatum were sequenced and annotated for the complete chloroplast (cp) genomes, and the cp genomes of A. longipetiolatum and A. maximum were the first reported. Three cp genomes exhibited typical quadripartite structures with 163,269-163,591 bp in length. Each genome encodes 130 functional genes including 79 protein-coding, 26 tRNAs and 3 rRNAs genes. 113-152 SSRs and 99 long repeats were identified in the three cp genomes. By designing specific primers, we amplified the highly variable loci and the mined genetic marker ccsA exhibited a relatively high species identification resolution in Amomum. The nonsynonymous and synonymous substitution ratios (Ka/Ks) in Amomum and Alpinia showed that most genes were subjected to a purifying selection. Phylogenetic analysis revealed the evolutionary relationships of Amomum and Alpinia species and proved that Amomum is paraphyletic. In addition, the sequenced sample of A. villosum was found to be a hybrid, becoming the first report of natural hybridization of this genus. Meanwhile, the high-throughput sequencing-based ITS2 analysis was proved to be an efficient tool for interspecific hybrid identification and with the help of the chloroplast genome, the hybrid parents can be also be determined. CONCLUSION The comparative analysis and mined genetic markers of cp genomes were conducive to species identification and evolutionary relationships of Amomum.
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Affiliation(s)
- Lu Gong
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaoxia Ding
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Wan Guan
- Luqiao Hospital, Taizhou Enze Medical Center (Group), Taizhou, Zhejiang, China
| | - Danchun Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
| | - Jing Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Junqi Bai
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Wen Xu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Juan Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaohui Qiu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Danyan Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Shijie Li
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhihai Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
| | - He Su
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
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Fan ZF, Ma CL. Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora. Sci Rep 2022; 12:15984. [PMID: 36163343 PMCID: PMC9512918 DOI: 10.1038/s41598-022-16290-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022] Open
Abstract
Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data of Polyspora are scarce, and the gene evolution and interspecific relationship are still unclear. In this study, we sequenced and annotated Polyspora chrysandra cp genome and combined it with previously published genomes for other Chinese Polyspora species. The results showed that cp genomes of six Chinese Polyspora varied in length between 156,452 bp (P. chrysandra) and 157,066 bp (P. speciosa), but all contained 132 genes, with GC content of 37.3%, and highly similar genes distribution and codon usage. A total of eleven intergenic spacer regions were found having the highest levels of divergence, and eight divergence hotspots were identified as molecular markers for Phylogeography and genetic diversity studies in Polyspora. Gene selection pressure suggested that five genes were subjected to positive selection. Phylogenetic relationships among Polyspora species based on the complete cp genomes were supported strongly, indicating that the cp genomes have the potential to be used as super barcodes for further analysis of the phylogeny of the entire genus. The cp genomes of Chinese Polyspora species will provide valuable information for species identification, molecular breeding and evolutionary analysis of genus Polyspora.
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Affiliation(s)
- Zhi-Feng Fan
- Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, People's Republic of China.,Kunming University of Science and Technology, Kunming, 650500, People's Republic of China
| | - Chang-Le Ma
- Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, People's Republic of China.
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Ruang-Areerate P, Yoocha T, Kongkachana W, Phetchawang P, Maknual C, Meepol W, Jiumjamrassil D, Pootakham W, Tangphatsornruang S. Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests. BIOLOGY 2022; 11:383. [PMID: 35336757 PMCID: PMC8945693 DOI: 10.3390/biology11030383] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/19/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023]
Abstract
Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.
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Affiliation(s)
- Panthita Ruang-Areerate
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Phakamas Phetchawang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Wijarn Meepol
- Department of Marine and Coastal Resources, Ranong Mangrove Forest Research Center, Tambon Ngao, Muang District, Ranong 85000, Thailand
| | - Darunee Jiumjamrassil
- Marine and Coastal Resources Office 5, 199/6 Khanom, Khanom, Nakhon Si Thammarat 80210, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
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Nizam A, Meera SP, Kumar A. Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments. iScience 2022; 25:103547. [PMID: 34988398 PMCID: PMC8693430 DOI: 10.1016/j.isci.2021.103547] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mangroves are halophytic plants belonging to diverse angiosperm families that are adapted to highly stressful intertidal zones between land and sea. They are special, unique, and one of the most productive ecosystems that play enormous ecological roles and provide a large number of benefits to the coastal communities. To thrive under highly stressful conditions, mangroves have innovated several key morphological, anatomical, and physio-biochemical adaptations. The evolution of the unique adaptive modifications might have resulted from a host of genetic and molecular changes and to date we know little about the nature of these genetic and molecular changes. Although slow, new information has accumulated over the last few decades on the genetic and molecular regulation of the mangrove adaptations, a comprehensive review on it is not yet available. This review provides up-to-date consolidated information on the genetic, epigenetic, and molecular regulation of mangrove adaptive traits.
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Affiliation(s)
- Ashifa Nizam
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Suraj Prasannakumari Meera
- Department of Biotechnology and Microbiology, Dr. Janaki Ammal Campus, Kannur University, Palayad, Kerala 670661, India
| | - Ajay Kumar
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
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Yang J, Hu G, Hu G. Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales. BMC Genomics 2022; 23:27. [PMID: 34991482 PMCID: PMC8734052 DOI: 10.1186/s12864-021-08259-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. RESULTS The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. CONCLUSION This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.
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Affiliation(s)
- Jiaxin Yang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Guoxiong Hu
- College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Guangwan Hu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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Ruang-Areerate P, Kongkachana W, Naktang C, Sonthirod C, Narong N, Jomchai N, Maprasop P, Maknual C, Phormsin N, Shearman JR, Pootakham W, Tangphatsornruang S. Complete chloroplast genome sequences of five Bruguiera species (Rhizophoraceae): comparative analysis and phylogenetic relationships. PeerJ 2021; 9:e12268. [PMID: 34733586 PMCID: PMC8544253 DOI: 10.7717/peerj.12268] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022] Open
Abstract
Bruguiera is a genus of true mangroves that are mostly distributed in the Indo-West Pacific region. However, the number of published whole chloroplast genome sequences of Bruguiera species are limited. Here, the complete chloroplast sequences of five Bruguiera species were sequenced and assembled using Illumina data. The chloroplast genomes of B. gymnorhiza, B. hainesii, B. cylindrica, B. parviflora and B. sexangula were assembled into 161,195, 164,295, 164,297, 163,228 and 164,170 bp, respectively. All chloroplast genomes contain 37 tRNA and eight rRNA genes, with either 84 or 85 protein-coding genes. A comparative analysis of these genomes revealed high similarity in gene structure, gene order and boundary position of the LSC, SSC and two IR regions. Interestingly, B. gymnorhiza lost a rpl32 gene in the SSC region. In addition, a ndhF gene in B. parviflora straddles both the SSC and IRB boundary regions. These genes reveal differences in chloroplast evolution among Bruguiera species. Repeats and SSRs in the chloroplast genome sequences were found to be highly conserved between B. cylindrica and B. hainesii as well as B. gymnorhiza and B. sexangula indicating close genetic relationships based on maternal inheritance. Notably, B. hainesii, which is considered a hybrid between B. gymnorhiza and B. cylindrica, appears to have inherited the chloroplast from B. cylindrica. Investigating the effects of selection events on shared protein-coding genes showed a positive selection in rps7 and rpl36 genes in all species compared to land-plant species. A phylogenetic analysis, based on 59 conserved chloroplast protein-coding genes, showed strong support that all Bruguiera species are in the clade Rhizophoraceae. This study provides valuable genetic information for the study of evolutionary relationships and population genetics in Bruguiera and other mangrove species.
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Affiliation(s)
- Panthita Ruang-Areerate
- 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
| | - 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
| | - Nattapol Narong
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Pasin Maprasop
- Department of Marine and Coastal Resources, Bangkok, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, Bangkok, Thailand
| | - Nawin Phormsin
- Department of Marine and Coastal Resources, Bangkok, Thailand
| | - Jeremy R Shearman
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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Hu G, Hu C, Peng X, Lu S, Zhang Z. Complete chloroplast genome of a semi-mangrove plant Hibiscus tiliaceus (Malvaceae). Mitochondrial DNA B Resour 2021; 6:1904-1905. [PMID: 34179470 PMCID: PMC8204996 DOI: 10.1080/23802359.2021.1935337] [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: 12/02/2022] Open
Abstract
Hibiscus tiliaceus is a semi-mangrove species that is widely distributed in tropical and subtropical coastal areas around the world. Here, the complete chloroplast (cp) genome sequence of H. tiliaceus was assembled and characterized. The cp genome was 161,748 bp in length, consisting of a large single copy (LSC) region of 89,190 bp and a small single copy (SSC) region of 19,616 bp, which were separated by a pair of 26,471 bp inverted repeat (IR) regions. The overall GC content was 36.88%. A total of 131 genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified. Phylogenetic tree reconstructed by 15 complete cp genomes revealed that H. tiliaceus was sister to the congeneric species H. cannabinus.
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Affiliation(s)
- Gang Hu
- College of Environmental and Life Sciences, Nanning Normal University, Nanning, China
| | - Cong Hu
- College of Environmental and Life Sciences, Nanning Normal University, Nanning, China
| | - Xingbing Peng
- College of Environmental and Life Sciences, Nanning Normal University, Nanning, China
| | - Shaonuan Lu
- College of Environmental and Life Sciences, Nanning Normal University, Nanning, China
| | - Zhonghua Zhang
- College of Environmental and Life Sciences, Nanning Normal University, Nanning, China
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11
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Li YC, Li SY, Zhang TH, Qin LL, An YD, Pang YK, Jiang GF. Characterization of the complete chloroplast genome of mangrove Rhizophora apiculata Blume (Rhizophoraceae). Mitochondrial DNA B Resour 2021; 6:2071-2073. [PMID: 34222659 PMCID: PMC8231346 DOI: 10.1080/23802359.2021.1923421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/24/2021] [Indexed: 11/05/2022] Open
Abstract
The chloroplast (cp) genome sequence of Rhizophora apiculata was characterized. The cp genome length was 164,343 bp in length, containing a typical structure of a large single copy (LSC) of 93,155 bp, a small single copy (SSC) of 19,376 bp, and two inverted repeats (IRs) of 25,906 bp, with a GC content of 34.9%. There were 131 genes were annotated in the cp genome, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A phylogenetic analysis using cp genomes of mangroves and ecologically associated species resolved R. apiculata in Rhizophora with R. stylosa and R. x lamarckii. This complete chloroplast sequence offers a promising tool for further species identification and evolutionary studies of Rhizophora, as well as for mangroves.
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Affiliation(s)
- Yi-Chan Li
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Su-Yuan Li
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Tian-Hao Zhang
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Lan-Li Qin
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Yi-Dong An
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Yu-Kun Pang
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Guo-Feng Jiang
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
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12
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Li SY, Li YC, Zhang TH, Qin LL, An YD, Pang YK, Jiang GF. Characterization of the complete chloroplast genome of mangrove Bruguiera gymnorrhiza (L.) Lam. ex Savigny. Mitochondrial DNA B Resour 2021; 6:2076-2078. [PMID: 34222660 PMCID: PMC8231343 DOI: 10.1080/23802359.2021.1914220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022] Open
Abstract
The chloroplast (cp) genome sequence of Bruguiera gymnorrhiza was characterized. The cp genome length was 163,795 bp in length, with a GC content of 35.3%, containing a large single copy (LSC) of 90,830 bp, a small single copy (SSC) of 20,207 bp, and a pair of inverted repeats (IRs) of 26,379 bp. The genome contained 121 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A phylogenetic analysis using cp genomes of mangroves and ecologically associated species resolved B. gymnorrhiza in Bruguiera with B. sexangula var. rhynchopetala. This complete chloroplast sequence offers a promising tool for further species identification and evolutionary studies of Bruguiera, as well as for mangroves.
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Affiliation(s)
- Su-Yuan Li
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Yi-Chan Li
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Tian-Hao Zhang
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Lan-Li Qin
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Yi-Dong An
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Yu-Kun Pang
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
| | - Guo-Feng Jiang
- Guangxi Key Laboratory of Forest Ecology and Conservation and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, PR China
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13
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Wu JY, Ma XC, Ma L, Fang Y, Zhang YH, Liu LJ, Li XC, Zeng R, Sun WC. Complete chloroplast genome sequence and phylogenetic analysis of winter oil rapeseed ( Brassica rapa L.). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:723-731. [PMID: 33763561 PMCID: PMC7954489 DOI: 10.1080/23802359.2020.1860697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Winter oil rapeseed ‘18 R-1’ (Brassica rapa L.) is a new variety that can survive in northern China where the extreme low temperature is −20 °C to −32 °C. It is different from traditional B. rapa and Brassica napus. In this study, the complete chloroplast (cp) genome of ‘18 R-1’ was sequenced and analyzed to assess the genetic relationship. The size of cp genome is 153,494 bp, including one large single copy (LSC) region of 83,280 bp and one small single copy (SSC) region of 17,776 bp, separated by two inverted repeat (IR) regions of 26,219 bp. The GC content of the whole genome is 36.35%, while those of LSC, SSC, and IR are 34.12%, 29.20%, and 42.32%, respectively. The cp genome encodes 132 genes, including 87 protein-coding genes, eight rRNA genes, and 37 tRNA genes. In repeat structure analysis, 288 simple sequence repeats (SSRs) were identified. Cp genome of ‘18 R-1’ was closely related to Brassica chinensis, B. rapa and Brassica pekinesis.
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Affiliation(s)
- Jun Yan Wu
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Xue Cai Ma
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Li Ma
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Yan Fang
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Ya Hong Zhang
- Tianshui Institute of Agricultural Sciences, Tianshui Gansu, China
| | - Li Jun Liu
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Xue Cai Li
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Rui Zeng
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Wan Cang Sun
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
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