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Fleck SJ, Tomlin C, da Silva Coelho FA, Richter M, Danielson ES, Backenstose N, Krabbenhoft T, Lindqvist C, Albert VA. High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species. Commun Biol 2024; 7:54. [PMID: 38184717 PMCID: PMC10771460 DOI: 10.1038/s42003-023-05748-4] [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: 12/06/2022] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
With populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a hexaploidy event at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.
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Affiliation(s)
- Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
| | - Crystal Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Nathan Backenstose
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Trevor Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
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2
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Song Y, Du X, Li A, Fan A, He L, Sun Z, Niu Y, Qiao Y. Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl. BMC Genomics 2023; 24:708. [PMID: 37996801 PMCID: PMC10666317 DOI: 10.1186/s12864-023-09821-4] [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: 03/01/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, the genomic DNA of F. suspensa yellowish leaf material was extracted, sequenced by using a mixture of Illumina Novaseq6000 short reads and Oxford Nanopore PromethION long reads, and the sequencing data were assembled and annotated. RESULT The F. suspensa mitochondrial genome was obtained in the length of 535,692 bp with a circular structure, and the GC content was 44.90%. The genome contains 60 genes, including 36 protein-coding genes, 21 tRNA genes, and three rRNA genes. We further analyzed RNA editing of the protein-coding genes, relative synonymous codon usage, and sequence repeats based on the genomic data. There were 25 homologous sequences between F. suspensa mitochondria and chloroplast genome, which involved the transfer of 8 mitochondrial genes, and 9473 homologous sequences between mitochondrial and nuclear genomes. Analysis of the nucleic acid substitution rate, nucleic acid diversity, and collinearity of protein-coding genes of the F. suspensa mitochondrial genome revealed that the majority of genes may have undergone purifying selection, exhibiting a slower rate of evolution and a relatively conserved structure. Analysis of the phylogenetic relationships among different species revealed that F. suspensa was most closely related to Olea europaea subsp. Europaea. CONCLUSION In this study, we sequenced, assembled, and annotated a high-quality F. suspensa mitochondrial genome. The results of this study will enrich the mitochondrial genome data of Forsythia, lay a foundation for the phylogenetic development of Forsythia, and promote the evolutionary analysis of Oleaceae species.
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Affiliation(s)
- Yun Song
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Xiaorong Du
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Aoxuan Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Amei Fan
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Longjiao He
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Zhe Sun
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Yanbing Niu
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Yonggang Qiao
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
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3
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Patil AB, Kar D, Datta S, Vijay N. Genomic and Transcriptomic Analyses Illuminates Unique Traits of Elusive Night Flowering Jasmine Parijat (Nyctanthes arbor-tristis). PHYSIOLOGIA PLANTARUM 2023; 175:e14119. [PMID: 38148217 DOI: 10.1111/ppl.14119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
The night-flowering Jasmine, Nyctanthes arbor-tristis also known as Parijat, is a perennial woody shrub belonging to the family of Oleaceae. It is popular for its fragrant flowers that bloom in the night and is a potent source of secondary metabolites. However, knowledge about its genome and the expression of genes regulating flowering or secondary metabolite accumulation is lacking. In this study, we generated whole genome sequencing data to assemble the first de novo assembly of Parijat and use it for comparative genomics and demographic history reconstruction. The temporal dynamics of effective population size (Ne ) experienced a positive influence of colder climates suggesting the switch to night flowering may have provided an evolutionary advantage. We employed multi-tissue transcriptome sequencing of floral stages/parts to obtain insights into the transcriptional regulation of nocturnal flower development and the production of volatiles/metabolites. Tissue-specific transcripts for mature flowers revealed key players in circadian regulation and flower development, including the auxin pathway and cell wall modifying genes. Furthermore, we identified tissue-specific transcripts responsible for producing numerous secondary metabolites, mainly terpenoids and carotenoids. The diversity and specificity of Terpene Synthase (TPS) and CCDs (Carotenoid Cleavage Deoxygenases) mediate the bio-synthesis of specialised metabolites in Parijat. Our study establishes Parijat as a novel non-model species to understand the molecular mechanisms of nocturnal blooming and secondary metabolite production.
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Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
| | - Debojyoti Kar
- Plant Cell and Developmental Biology Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
| | - Sourav Datta
- Plant Cell and Developmental Biology Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
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Al-Karmalawy AA, Alnajjar R, Elmaaty AA, Binjubair FA, Al-Rashood ST, Mansour BS, Elkamhawy A, Eldehna WM, Mansour KA. Investigating the promising SARS-CoV-2 main protease inhibitory activity of secoiridoids isolated from Jasminum humile; in silico and in Vitro assessments with structure-activity relationship. J Biomol Struct Dyn 2023:1-13. [PMID: 37505066 DOI: 10.1080/07391102.2023.2240419] [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: 04/06/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
The proteolytic enzyme 3 C-like protease (3Clpro or Mpro) is considered the most important target for SARS-CoV-2 which could be attributed to its crucial role in viral maturation and/or replication. Besides, natural phytoconstituents from plant origin are always promising lead compounds in the drug discovery area. Herein, the previously isolated and identified seven compounds from Jasminum humile (J. humile) were examined in vitro and in silico against the SARS-CoV-2 Mpro. First, the Vero E6 cells were utilized to pursue the potential of the investigated compounds (both in fractions and individual isolates) using the MTT assay. The total extract (T1) displayed the most significant activity against SARS-CoV-2 with IC50 = 29.36 µg/mL. Besides, the fractions (Fr1 and Fr3) showed good activity against the SARS-CoV-2 with IC50 values of 70.42, and 73.09 µg/mL, respectively. Then, the SARS-CoV-2 Mpro inhibitory assay was utilized to emphasize the inhibitory potential of the investigated isolates. MJN, JMD, and IJM candidates displayed prominent Mpro inhibitory potentials with IC50 = 30.44, 30.24, and 56.25 µM, respectively. Moreover, molecular docking of the identified seven compounds against the Mpro of SARS-CoV-2 showed that the five secoiridoids achieved superior results. MJN, JSM, IJM, and JMD showed higher affinities towards the Mpro target compared to the co-crystallized antagonist. Furthermore, the most active complexes (MJN, JSM, IJM, and JMD-Mpro) were subjected to MD simulations run for 150 ns and MM-GBSA calculations, compared to the co-crystallized inhibitor (O6K-Mpro). Finally, the SAR study clarified that JMD achieved the best anti-SARS-CoV-2 Mpro activity followed by MJN.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ahmed A Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
- PharmD, Faculty of Pharmacy, Libyan International Medical University, Benghazi, Libya
| | - Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Faizah A Binjubair
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sara T Al-Rashood
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Basma S Mansour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Elkamhawy
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City, Egypt
| | - Khaled Ahmed Mansour
- Department of Pharmacognosy, Faculty of Pharmacy, Horus University in Egypt, New Damietta, Egypt
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Yang Z, Zhu Y, Zhang X, Zhang H, Zhang X, Liu G, Zhao Q, Bao Z, Ma F. Volatile secondary metabolome and transcriptome analysis reveals distinct regulation mechanism of aroma biosynthesis in Syringa oblata and S. vulgaris. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:965-973. [PMID: 36889235 DOI: 10.1016/j.plaphy.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/13/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Lilacs have high ornamental value due to their strong aroma. However, the molecular regulatory mechanisms of aroma biosynthesis and metabolism in lilac were largely unclear. In this study, two varieties with distinct aroma, Syringa oblata 'Zi Kui' (faint aroma) and Syringa vulgaris 'Li Fei' (strong aroma), were used for exploring the regulation mechanism of aroma difference. Via GC-MS analysis, a total of 43 volatile components were identified. Terpene volatiles was the most abundant volatiles constituting the aroma of two varieties. Notably, 3 volatile secondary metabolites were unique in 'Zi Kui' and 30 volatile secondary metabolites were unique in 'Li Fei'. Then, a transcriptome analysis was performed to clarify the regulation mechanism of aroma metabolism difference between these two varieties, and identified 6411 differentially expressed genes (DEGs). Interestingly, ubiquinone and other terpenoid-quinone biosynthesis genes were significantly enriched in DEGs. We further conducted a correlation analysis between the volatile metabolome and transcriptome and found that TPS, GGPPS, and HMGS genes might be the key contributors to the differences in floral fragrance composition between the two lilac varieties. Our study improves the understanding in the regulation mechanism of Lilac aroma and would help improve the aroma of ornamental crops by metabolic engineering.
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Affiliation(s)
- Zhiying Yang
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China
| | - Yuanyuan Zhu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xu Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Hailiang Zhang
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China
| | - Xiaoyu Zhang
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China
| | - Genzhong Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Qingzhu Zhao
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China.
| | - Zhilong Bao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Fangfang Ma
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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Wang Y, Lu L, Li J, Li H, You Y, Zang S, Zhang Y, Ye J, Lv Z, Zhang Z, Qin Y, Zhang H, Xia F, Li H, Zhang H, Fan P, Shi L, Liang Z, Cui H. A chromosome-level genome of Syringa oblata provides new insights into chromosome formation in Oleaceae and evolutionary history of lilacs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:836-848. [PMID: 35673966 DOI: 10.1111/tpj.15858] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Lilacs (Syringa L.), a group of well-known ornamental and aromatic woody plants, have long been used for gardening, essential oils and medicine purposes in East Asia and Europe. The lack of knowledge about the complete genome of Syringa not only hampers effort to better understand its evolutionary history, but also prevents genome-based functional gene mining that can help in the variety improvement and medicine development. Here, a chromosome-level genome of Syringa oblata is presented, which has a size of 1.12 Gb including 53 944 protein coding genes. Synteny analysis revealed that a recent duplication event and parallel evolution of two subgenomes formed the current karyotype. Evolutionary analysis, transcriptomics and metabolic profiling showed that segment and tandem duplications contributed to scent formation in the woody aromatic species. Moreover, phylogenetic analysis indicated that S. oblata shared a common ancestor with Osmanthus fragrans and Olea europaea approximately 27.61 million years ago (Mya). Biogeographic reconstruction based on a resequenced data set of 26 species suggested that Syringa originated in the northern part of East Asia during the Miocene (approximately 14.73 Mya) and that the five Syringa groups initially formed before the Late Miocene (approximately 9.97 Mya). Furthermore, multidirectional dispersals accompanied by gene introgression among Syringa species from Northern China during the Miocene were detected by biogeographic reconstruction. Taken together, the results showed that complex gene introgression, which occurred during speciation history, greatly contributed to Syringa diversity.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
- Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jingrui Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Huayang Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yichen You
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuying Zang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Yongqing Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, 250300, China
| | - Jianfei Ye
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Zemin Lv
- College of Forestry, Inner Mongolian Agricultural University, Hohhot, 010019, China
| | - Zhaoyu Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, 250300, China
| | - Yongsheng Qin
- Institute of Gardening, Hohhot, Inner Mongolia, Hohhot, 010030, China
| | - Hongling Zhang
- College of Forestry, Inner Mongolian Agricultural University, Hohhot, 010019, China
| | - Fei Xia
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Hui Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Huijin Zhang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Peige Fan
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
- Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Lei Shi
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Zhenchang Liang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
- Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Hongxia Cui
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
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Dong W, Li E, Liu Y, Xu C, Wang Y, Liu K, Cui X, Sun J, Suo Z, Zhang Z, Wen J, Zhou S. Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family. BMC Biol 2022; 20:92. [PMID: 35468824 PMCID: PMC9040247 DOI: 10.1186/s12915-022-01297-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/13/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Deep-branching phylogenetic relationships are often difficult to resolve because phylogenetic signals are obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, and incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- and shallow-scale relationships across all branches of the tree of life. The olive family (Oleaceae) is composed of 25 genera classified into five tribes with tribe Oleeae consisting of four subtribes. Previous phylogenetic analyses showed that ILS and/or hybridization led to phylogenetic incongruence in the family. It was essential to distinguish phylogenetic signal conflicts, and explore mechanisms for the uncertainties concerning relationships of the olive family, especially at the deep-branching nodes. RESULTS We used the whole plastid genome and nuclear single nucleotide polymorphism (SNP) data to infer the phylogenetic relationships and to assess the variation and rates among the main clades of the olive family. We also used 2608 and 1865 orthologous nuclear genes to infer the deep-branching relationships among tribes of Oleaceae and subtribes of tribe Oleeae, respectively. Concatenated and coalescence trees based on the plastid genome, nuclear SNPs and multiple nuclear genes suggest events of ILS and/or ancient introgression during the diversification of Oleaceae. Additionally, there was extreme heterogeneity in the substitution rates across the tribes. Furthermore, our results supported that introgression/hybridization, rather than ILS, is the main factor for phylogenetic discordance among the five tribes of Oleaceae. The tribe Oleeae is supported to have originated via ancient hybridization and polyploidy, and its most likely parentages are the ancestral lineage of Jasmineae or its sister group, which is a "ghost lineage," and Forsythieae. However, ILS and ancient introgression are mainly responsible for the phylogenetic discordance among the four subtribes of tribe Oleeae. CONCLUSIONS This study showcases that using multiple sequence datasets (plastid genomes, nuclear SNPs and thousands of nuclear genes) and diverse phylogenomic methods such as data partition, heterogeneous models, quantifying introgression via branch lengths (QuIBL) analysis, and species network analysis can facilitate untangling long and complex evolutionary processes of ancient introgression, paleopolyploidization, and ILS.
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Affiliation(s)
- Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yushuang Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Xingyong Cui
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA.
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Li Y, Li X, Sylvester SP, Zhang M, Wang X, Duan Y. Plastid genomes reveal evolutionary shifts in elevational range and flowering time of
Osmanthus
(Oleaceae). Ecol Evol 2022; 12:e8777. [PMID: 35386867 PMCID: PMC8975774 DOI: 10.1002/ece3.8777] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 11/20/2022] Open
Abstract
Species of Osmanthus are economically important ornamental trees, yet information regarding their plastid genomes (plastomes) have rarely been reported, thus hindering taxonomic and evolutionary studies of this small but enigmatic genus. Here, we performed comparative genomics and evolutionary analyses on plastomes of 16 of the 28 currently accepted species, with 11 plastomes newly sequenced. Phylogenetic studies identified four main lineages within the genus that are here designated the: “Caucasian Osmanthus” (corresponding to O. decorus), “Siphosmanthus” (corresponding to O. sect. Siphosmanthus), “O. serrulatus + O. yunnanensis,” and “Core Osmanthus: (corresponding to O. sect. Osmanthus + O. sect. Linocieroides). Molecular clock analysis suggested that Osmanthus split from its sister clade c. 15.83 Ma. The estimated crown ages of the lineages were the following: genus Osmanthus at 12.66 Ma; “Siphosmanthus” clade at 5.85 Ma; “O. serrulatus + O. yunnanensis” at 4.89 Ma; and “Core Osmanthus: clade at 6.2 Ma. Ancestral state reconstructions and trait mapping showed that ancestors of Osmanthus were spring flowering and originated at lower elevations. Phylogenetic principal component analysis clearly distinguished spring‐flowering species from autumn‐flowering species, suggesting that flowering time differentiation is related to the difference in ecological niches. Nucleotide substitution rates of 80 common genes showed slow evolutionary pace and low nucleotide variations, all genes being subjected to purifying selection.
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Affiliation(s)
- Yongfu Li
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment International Cultivar Registration Center for Osmanthus Nanjing Forestry University Nanjing China
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver British Columbia Canada
| | - Xuan Li
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment International Cultivar Registration Center for Osmanthus Nanjing Forestry University Nanjing China
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver British Columbia Canada
| | - Steven Paul Sylvester
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment International Cultivar Registration Center for Osmanthus Nanjing Forestry University Nanjing China
| | - Min Zhang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment International Cultivar Registration Center for Osmanthus Nanjing Forestry University Nanjing China
| | - Xianrong Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment International Cultivar Registration Center for Osmanthus Nanjing Forestry University Nanjing China
| | - Yifan Duan
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment International Cultivar Registration Center for Osmanthus Nanjing Forestry University Nanjing China
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Raimondeau P, Manzi S, Brucato N, Kinipi C, Leavesley M, Ricaut FX, Besnard G. Genome skims analysis of betel palms (Areca spp., Arecaceae) and development of a profiling method to assess their plastome diversity. Gene 2021; 800:145845. [PMID: 34274465 DOI: 10.1016/j.gene.2021.145845] [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: 04/03/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022]
Abstract
The betel nut (Areca catechu L., Arecaceae) is a monoecious cultivated palm tree that is widespread in tropical regions. It is mainly cultivated for producing areca nuts, from which seeds are extracted and chewed by local populations principally in the Indo-Pacific region. Seeds contain alkaloids which are central nervous system stimulants and are highly addictive. Wild relatives of the betel nut are distributed in South Asia and Australasia, with ca. 40-50 Areca species currently recognized. The geographic origin(s) of the betel nut and its subsequent diffusion and diversification remains poorly documented. Here, a genome skimming approach was applied to screen nucleotidic variation in the most abundant genomic regions. Low coverage sequencing data allowed us to assemble full plastomes, mitochondrial regions (either full mitogenomes or the full set of mitochondrial genes) and the nuclear ribosomal DNA cluster for nine representatives of the Areca genus collected in the field and herbarium collections (including a 182-years old specimen collected during the Dumont d'Urville's expedition). These three genomic compartments provided similar phylogenetic signals, and revealed very low genomic diversity in our sample of cultivated betel nut. We finally developed a genotyping method targeting 34 plastid DNA microsatellites. This plastome profiling approach is useful for tracing the spread of matrilineages, and in combination with nuclear genomic data, can resolve the history of the betel nut. Our method also proves to be efficient for analyzing herbarium specimens, even those collected >100 years ago.
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Affiliation(s)
- Pauline Raimondeau
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Sophie Manzi
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Nicolas Brucato
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Christopher Kinipi
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea; CABAH & College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France.
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10
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Akhtar N, Hafiz IA, Hayat MQ, Potter D, Abbasi NA, Habib U, Hussain A, Hafeez H, Bashir MA, Malik SI. ISSR-Based Genetic Diversity Assessment of Genus Jasminum L. (Oleaceae) from Pakistan. PLANTS (BASEL, SWITZERLAND) 2021; 10:1270. [PMID: 34206638 PMCID: PMC8308950 DOI: 10.3390/plants10071270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/01/2022]
Abstract
The genus Jasminum L., of the family Oleaceae, includes many species occurring in the wild, or cultivated worldwide. A preliminary investigation based on inter-simple sequence repeats (ISSR) was performed to assess the genetic diversity among 28 accessions, representing nine species of Jasminum from various regions, representing a range of altitudes in Pakistan. A total of 21 ISSR primers were used, which produced 570 amplified bands of different sizes, with a mean polymorphic band percentage of 98.26%. The maximum resolving power, polymorphism information content, and index values of the ISSR markers recorded for primers 6, 16, and 19 were 0.40, 12.32, and 24.21, respectively. Based on the data of the ISSR markers, the resulting UPGMA dendrogram with the Jaccard coefficient divided the 28 accessions into two main clades. At the species level, the highest values for Shannon's information index, polymorphism percentage, effective allele number, Nei's genetic variations, and genetic unbiased diversity were found in Jasminum sambac L. and J. humile L., while the lowest were observed in J. mesnyi Hance and J. nitidum Skan. Based on Nei's unbiased genetic identity pairwise population matrix, the maximum identity (0.804) was observed between J. elongatum Willd and J. multiflorum (Burm. f.) Andrews, and the lowest (0.566) between J. nitidum Skan. and J. azoricum L. Molecular variance analysis displayed a genetic variation of 79% among the nine populations. The study was aimed to established genetic diversity in Jasminum species using ISSR markers. With the help of this technique, we were able to establish immense intra- and interspecific diversity across the Jasminum species.
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Affiliation(s)
- Naeem Akhtar
- Department of Horticulture, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46000, Pakistan; (I.A.H.); (N.A.A.); (U.H.)
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA;
| | - Ishfaq Ahmad Hafiz
- Department of Horticulture, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46000, Pakistan; (I.A.H.); (N.A.A.); (U.H.)
| | - Muhammad Qasim Hayat
- Plant Systematics and Evolution Laboratory, Department of Plant Biotechnology, Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan;
| | - Daniel Potter
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA;
| | - Nadeem Akhtar Abbasi
- Department of Horticulture, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46000, Pakistan; (I.A.H.); (N.A.A.); (U.H.)
| | - Umer Habib
- Department of Horticulture, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46000, Pakistan; (I.A.H.); (N.A.A.); (U.H.)
| | - Adil Hussain
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara 56130, Pakistan;
| | - Hina Hafeez
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad 44000, Pakistan;
| | - Muhammad Ajmal Bashir
- Department of Horticulture, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46000, Pakistan; (I.A.H.); (N.A.A.); (U.H.)
- Department of Agriculture and Forestry Sciences, University of Tuscia, San Camillo de Lellis, snc, 01100 Viterbo, Italy
| | - Saad Imran Malik
- Department of Plant Breeding and Genetics, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46000, Pakistan;
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11
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Wang J, Tian T, Han X, Ye B, Ma X, Meng X, Xie J, Zhou H. The complete chloroplast genome and phylogenetic analysis of Syringa reticulata subsp. amurensis (Rupr.) P.S.Green & M.C.Chang from Qinghai Province, China. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1829-1831. [PMID: 34124358 PMCID: PMC8183553 DOI: 10.1080/23802359.2021.1934150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Syringa reticulata subsp. amurensis (Rupr.) P. S. Green & M. C. Chang (Oleaceae) is a shrub or tree with high medicinal value as well as great ecological significance as an urban garden plant. To better understand the molecular genetics and evolutionary of S. reticulata subsp. amurensis, its complete chloroplast genome was sequenced and annotated. The assembled chloroplast genome is a circular 156,141 bp sequence, consisting of 87,108 bp large single copy (LSC) region and 17,239 bp small single copy (SSC) region, which were flanked by a pair of 25,897 bp inverted repeats (IRs). The GC content of the chloroplast genome is 36.14%. Moreover, a total of 132 functional genes were annotated, including 88 protein-coding, 36 tRNA, and eight rRNA genes. Phylogenetic analysis showed that S. reticulata subsp. amurensis was most closely related to S. reticulata subsp. Pekinensis and the genus Syringa is paraphyletic group. This study provides important information for further phylogenetic studies on S. reticulata subsp. amurensis and its allies.
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Affiliation(s)
- Jiuli Wang
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China.,Qinghai Provincial Key Laboratory of Highvalue Utilization of Characteristic Economic Plants, Xining, China
| | - Tian Tian
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China
| | - Xia Han
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China
| | - Bin Ye
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China
| | - Xiuling Ma
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China
| | - Xianwen Meng
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China.,Qinghai Provincial Key Laboratory of Highvalue Utilization of Characteristic Economic Plants, Xining, China
| | - Jiuxiang Xie
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Huakun Zhou
- Key Laboratory of Restoration Ecology in Cold Region of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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