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Joshi V, Bachhar V, Mishra SS, Shukla RK, Gangal A, Duseja M. GC-MS fingerprinting, nutritional composition, in vitro pharmacological activities and molecular docking studies of Piper chaba from Uttarakhand region. 3 Biotech 2024; 14:158. [PMID: 38766322 PMCID: PMC11101386 DOI: 10.1007/s13205-024-03996-7] [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: 02/27/2024] [Accepted: 04/23/2024] [Indexed: 05/22/2024] Open
Abstract
This study aimed to evaluate the potential therapeutic effects of Piper chaba (PC) growing in the northern region of India, having differences in the phytochemicals, nutritional content, antimicrobial and antioxidant properties by reducing power assay (RPA), 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, phosphomolybdate assay, and antidiabetic potential by α-amylase assay with change in the geographical location. Outcomes of the gas chromatography-mass spectrometry (GC-MS) analysis revealed that phytochemicals such as piperine (46.69%), kusunokinin (8.9%), and sitostenone (7.57%) are the prominent compounds found in PC. The plant has also shown a good nutritional value, i.e., iron (11.25 mg), calcium (147 mg), and vitamin C (9.30 mg) per 100 g. PC has a higher phenolic content than other species (⁓ 13.75 g/100 g plant powder). Among the four tested bacterial strains, the extract is best responsive toward Escherichia coli (35 ± 0.68 mm) which is more than the standard ciprofloxacin (24 ± 0.8 mm). Similarly, among two tested fungal strains, Saccharomyces cerevisiae shows the best zone of inhibition (ZOI) (27.5 ± 0.8 mm), which is greater than tat of standard amphotericin (20.25 ± 0.28 mm). The DDPH method demonstrated the highest antioxidant activity (⁓ 42.61 ± 1.82 µg/ml). IC50 for the antidiabetic potential of PC was found to be 23.09 ± 0.3 µg/ml against α-amylase assay. A molecular docking study revealed that three compounds, piperine, sitostenone and kusunokinin, showed strong binding affinity toward bacterial tyrosyl-tRNA synthetases, fungal dihydrofolate reductase, and α-amylase, respectively. Therefore, the findings of the current study indicate that PC can be considered as a source of food and medicines, either in the form of traditional preparations or as pure active constituents. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03996-7.
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Affiliation(s)
- Vibha Joshi
- Analytical Chemistry Lab, Department of Chemistry, School of Physical Sciences, DIT University, Dehradun, Uttarakhand 248009 India
| | - Vishwajeet Bachhar
- Analytical Chemistry Lab, Department of Chemistry, School of Physical Sciences, DIT University, Dehradun, Uttarakhand 248009 India
| | - Shashank Shekher Mishra
- School of Pharmaceutical and Population Health Informatics, Faculty of Pharmacy, DIT University, Dehradun, Uttarakhand 248009 India
| | - Ravi K. Shukla
- Advanced Functional Smart Materials Laboratory, Department of Physics, School of Physical Sciences, DIT University, Dehradun, Uttarakhand 248009 India
| | - Avinash Gangal
- Analytical Chemistry Lab, Department of Chemistry, School of Physical Sciences, DIT University, Dehradun, Uttarakhand 248009 India
| | - Manisha Duseja
- Analytical Chemistry Lab, Department of Chemistry, School of Physical Sciences, DIT University, Dehradun, Uttarakhand 248009 India
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Hu X, Li Y, Meng F, Duan Y, Sun M, Yang S, Liu H. Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae. Funct Integr Genomics 2024; 24:109. [PMID: 38797780 DOI: 10.1007/s10142-024-01389-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
For the study of species evolution, chloroplast gene expression, and transformation, the chloroplast genome is an invaluable resource. Codon usage bias (CUB) analysis is a tool that is utilized to improve gene expression and investigate evolutionary connections in genetic transformation. In this study, we analysed chloroplast genome differences, codon usage patterns and the sources of variation on CUB in 14 Annonaceae species using bioinformatics tools. The study showed that there was a significant variation in both gene sizes and numbers between the 14 species, but conservation was still maintained. It's worth noting that there were noticeable differences in the IR/SC sector boundary and the types of SSRs among the 14 species. The mono-nucleotide repeat type was the most common, with A/T repeats being more prevalent than G/C repeats. Among the different types of repeats, forward and palindromic repeats were the most abundant, followed by reverse repeats, and complement repeats were relatively rare. Codon composition analysis revealed that all 14 species had a frequency of GC lower than 50%. Additionally, it was observed that the proteins in-coding sequences of chloroplast genes tend to end with A/T at the third codon position. Among these species, 21 codons exhibited bias (RSCU > 1), and there were 8 high-frequency (HF) codons and 5 optimal codons that were identical across the species. According to the ENC-plot and Neutrality plot analysis, natural selection had less impact on the CUB of A. muricate and A. reticulata. Based on the PR2-plot, it was evident that base G had a higher frequency than C, and T had a higher frequency A. The correspondence analysis (COA) revealed that codon usage patterns different in Annonaceae.
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Affiliation(s)
- Xiang Hu
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Yaqi Li
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, 678000, China
| | - Fuxuan Meng
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Yuanjie Duan
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Manying Sun
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Shiying Yang
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China
| | - Haigang Liu
- Tropical Eco-agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, 651300, China.
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Ware I, Franke K, Frolov A, Bureiko K, Kysil E, Yahayu M, El Enshasy HA, Wessjohann LA. Comparative metabolite analysis of Piper sarmentosum organs approached by LC-MS-based metabolic profiling. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:30. [PMID: 38743199 PMCID: PMC11093948 DOI: 10.1007/s13659-024-00453-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024]
Abstract
Piper sarmentosum Roxb. (Piperaceae) is a traditional medicinal and food plant widely distributed in the tropical and subtropical regions of Asia, offering both health and culinary benefits. In this study the secondary metabolites in different organs of P. sarmentosum were identified and their relative abundances were characterized. The metabolic profiles of leaves, roots, stems and fruits were comprehensively investigated by liquid chromatography high-resolution mass spectrometry (LC-HR-MS) and the data subsequently analyzed using multivariate statistical methods. Manual interpretation of the tandem mass spectrometric (MS/MS) fragmentation patterns revealed the presence of 154 tentatively identified metabolites, mostly represented by alkaloids and flavonoids. Principle component analysis and hierarchical clustering indicated the predominant occurrence of flavonoids, lignans and phenyl propanoids in leaves, aporphines in stems, piperamides in fruits and lignan-amides in roots. Overall, this study provides extensive data on the metabolite composition of P. sarmentosum, supplying useful information for bioactive compounds discovery and patterns of their preferential biosynthesis or storage in specific organs. This can be used to optimize production and harvesting as well as to maximize the plant's economic value as herbal medicine or in food applications.
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Affiliation(s)
- Ismail Ware
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
| | - Katrin Franke
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany.
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, 06108, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Kseniia Bureiko
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Elana Kysil
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Maizatulakmal Yahayu
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
| | - Hesham Ali El Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), 81310 Johor Bahru, Johor, Malaysia
- City of Scientific Research and Technology Applications, New Borg Al Arab, Alexandria, 21934, Egypt
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.
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Geng LY, Jiang TY, Chen X, Li Q, Ma JH, Hou WX, Tang CQ, Wang Q, Deng YF. Plastome structure, phylogeny and evolution of plastid genes in Reevesia (Helicteroideae, Malvaceae). JOURNAL OF PLANT RESEARCH 2024:10.1007/s10265-024-01547-y. [PMID: 38739241 DOI: 10.1007/s10265-024-01547-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/29/2024] [Indexed: 05/14/2024]
Abstract
Reevesia is an eastern Asian-eastern North American disjunction genus in the family Malvaceae s.l. and comprises approximately 25 species. The relationships within the genus are not well understood. Here, 15 plastomes representing 12 Reevesia species were compared, with the aim of better understanding the species circumscription and phylogenetic relationships within the genus and among genera in the family Malvaceae s.l. The 11 newly sequenced plastomes range between 161,532 and 161, 945 bp in length. The genomes contain 114 unique genes, 18 of which are duplicated in the inverted repeats (IRs). Gene content of these plastomes is nearly identical. All the protein-coding genes are under purifying selection in the Reevesia plastomes compared. The top ten hypervariable regions, SSRs, and the long repeats identified are potential molecular markers for future population genetic and phylogenetic studies. Phylogenetic analysis based on the whole plastomes confirmed the monophyly of Reevesia and a close relationship with Durio (traditional Bombacaceae) in subfamily Helicteroideae, but not with the morphologically similar genera Pterospermum and Sterculia (both of traditional Sterculiaceae). Phylogenetic relationships within Reevesia suggested that two species, R. pubescens and R. thyrsoidea, as newly defined, are not monophyletic. Six taxa, R. membranacea, R. xuefengensis, R. botingensis, R. lofouensis, R. longipetiolata and R. pycnantha, are suggested to be recognized.
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Affiliation(s)
- Li-Yang Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Tian-Yi Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China.
| | - Qiang Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Jian-Hui Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Wen-Xiang Hou
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Chen-Qian Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Qin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yun-Fei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
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Long J, He WC, Peng HW, Erst AS, Wang W, Xiang KL. Comparative plastome analysis of the sister genera Ceratocephala and Myosurus (Ranunculaceae) reveals signals of adaptive evolution to arid and aquatic environments. BMC PLANT BIOLOGY 2024; 24:202. [PMID: 38509479 PMCID: PMC10953084 DOI: 10.1186/s12870-024-04891-2] [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: 01/17/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Expansion and contraction of inverted repeats can cause considerable variation of plastid genomes (plastomes) in angiosperms. However, little is known about whether structural variations of plastomes are associated with adaptation to or occupancy of new environments. Moreover, adaptive evolution of angiosperm plastid genes remains poorly understood. Here, we sequenced the complete plastomes for four species of xerophytic Ceratocephala and hydrophytic Myosurus, as well as Ficaria verna. By an integration of phylogenomic, comparative genomic, and selection pressure analyses, we investigated evolutionary patterns of plastomes in Ranunculeae and their relationships with adaptation to dry and aquatic habitats. RESULTS Owing to the significant contraction of the boundary of IRA/LSC towards the IRA, plastome sizes and IR lengths of Myosurus and Ceratocephala are smaller within Ranunculeae. Compared to other Ranunculeae, the Myosurus plastome lost clpP and rps16, one copy of rpl2 and rpl23, and one intron of rpoC1 and rpl16, and the Ceratocephala plastome added an infA gene and lost one copy of rpl2 and two introns of clpP. A total of 11 plastid genes (14%) showed positive selection, two genes common to Myosurus and Ceratocephala, seven in Ceratocephala only, and two in Myosurus only. Four genes showed strong signals of episodic positive selection. The rps7 gene of Ceratocephala and the rpl32 and ycf4 genes of Myosurus showed an increase in the rate of variation close to 3.3 Ma. CONCLUSIONS The plastomic structure variations as well as the positive selection of two plastid genes might be related to the colonization of new environments by the common ancestor of Ceratocephala and Myosurus. The seven and two genes under positive selection might be related to the adaptation to dry and aquatic habitats in Ceratocephala and Myosurus, respectively. Moreover, intensified aridity and frequent sea-level fluctuations, as well as global cooling, might have favored an increased rate of change in some genes at about 3.3 Ma, associated with adaptation to dry and aquatic environments, respectively. These findings suggest that changing environments might have influenced structural variations of plastomes and fixed new mutations arising on some plastid genes owing to adaptation to specific habitats.
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Affiliation(s)
- Jing Long
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Wen-Chuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Huan-Wen Peng
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Andrey S Erst
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya Str. 101, Novosibirsk, 630090, Russia
| | - Wei Wang
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- China National Botanical Garden, Beijing, 100093, China.
| | - Kun-Li Xiang
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
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Jost M, Wanke S. A comparative analysis of plastome evolution in autotrophic Piperales. AMERICAN JOURNAL OF BOTANY 2024; 111:e16300. [PMID: 38469876 DOI: 10.1002/ajb2.16300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
PREMISE Many plastomes of autotrophic Piperales have been reported to date, describing a variety of differences. Most studies focused only on a few species or a single genus, and extensive, comparative analyses have not been done. Here, we reviewed publicly available plastome reconstructions for autotrophic Piperales, reanalyzed publicly available raw data, and provided new sequence data for all previously missing genera. Comparative plastome genomics of >100 autotrophic Piperales were performed. METHODS We performed de novo assemblies to reconstruct the plastomes of newly generated sequence data. We used Sanger sequencing and read mapping to verify the assemblies and to bridge assembly gaps. Furthermore, we reconstructed the phylogenetic relationships as a foundation for comparative plastome genomics. RESULTS We identified a plethora of assembly and annotation issues in published plastome data, which, if unattended, will lead to an artificial increase of diversity. We were able to detect patterns of missing and incorrect feature annotation and determined that the inverted repeat (IR) boundaries were the major source for erroneous assembly. Accounting for the aforementioned issues, we discovered relatively stable junctions of the IRs and the small single-copy region (SSC), whereas the majority of plastome variations among Piperales stems from fluctuations of the boundaries of the IR and the large single-copy (LSC) region. CONCLUSIONS This study of all available plastomes of autotrophic Piperales, expanded by new data for previously missing genera, highlights the IR-LSC junctions as a potential marker for discrimination of various taxonomic levels. Our data indicates a pseudogene-like status for cemA and ycf15 in various Piperales. Based on a review of published data, we conclude that incorrect IR-SSC boundary identification is the major source for erroneous plastome assembly. We propose a gold standard for assembly and annotation of high-quality plastomes based on de novo assembly methods and appropriate references for gene annotation.
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Affiliation(s)
- Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Botanik und Molekulare Evolutionsforschung, Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Biodiversität, Goethe-Universität, Frankfurt am Main, Germany
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Phillips AL, Ferguson S, Burton RA, Watson-Haigh NS. CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data. PLoS Comput Biol 2024; 20:e1011870. [PMID: 38335225 PMCID: PMC10883564 DOI: 10.1371/journal.pcbi.1011870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 02/22/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Chloroplasts are photosynthetic organelles in algal and plant cells that contain their own genome. Chloroplast genomes are commonly used in evolutionary studies and taxonomic identification and are increasingly becoming a target for crop improvement studies. As DNA sequencing becomes more affordable, researchers are collecting vast swathes of high-quality whole-genome sequence data from laboratory and field settings alike. Whole tissue read libraries sequenced with the primary goal of understanding the nuclear genome will inadvertently contain many reads derived from the chloroplast genome. These whole-genome, whole-tissue read libraries can additionally be used to assemble chloroplast genomes with little to no extra cost. While several tools exist that make use of short-read second generation and third-generation long-read sequencing data for chloroplast genome assembly, these tools may have complex installation steps, inadequate error reporting, poor expandability, and/or lack scalability. Here, we present CLAW (Chloroplast Long-read Assembly Workflow), an easy to install, customise, and use Snakemake tool to assemble chloroplast genomes from chloroplast long-reads found in whole-genome read libraries (https://github.com/aaronphillips7493/CLAW). Using 19 publicly available reference chloroplast genome assemblies and long-read libraries from algal, monocot and eudicot species, we show that CLAW can rapidly produce chloroplast genome assemblies with high similarity to the reference assemblies. CLAW was designed such that users have complete control over parameterisation, allowing individuals to optimise CLAW to their specific use cases. We expect that CLAW will provide researchers (with varying levels of bioinformatics expertise) with an additional resource useful for contributing to the growing number of publicly available chloroplast genome assemblies.
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Affiliation(s)
- Aaron L Phillips
- Department of Food Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Rachel A Burton
- Department of Food Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Nathan S Watson-Haigh
- South Australian Genomics Centre (SAGC), SAHMRI, Adelaide, South Australia, Australia
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
- Alkahest Inc., San Carlos, California, United States of America
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Yang Z, Ferguson DK, Yang Y. New insights into the plastome evolution of Lauraceae using herbariomics. BMC PLANT BIOLOGY 2023; 23:387. [PMID: 37563571 PMCID: PMC10413609 DOI: 10.1186/s12870-023-04396-4] [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: 03/08/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND The family Lauraceae possesses ca. 50 genera and 2,500-3,000 species that are distributed in the pantropics. Only half of the genera of the family were represented in previously published plastome phylogenies because of the difficulty of obtaining research materials. Plastomes of Hypodaphnideae and the Mezilaurus group, two lineages with unusual phylogenetic positions, have not been previously reported and thus limit our full understanding on the plastome evolution of the family. Herbariomics, promoted by next generation sequencing technology, can make full use of herbarium specimens, and provides opportunities to fill the sampling gap. RESULTS In this study, we sequenced five new plastomes (including four genera which are reported for the first time, viz. Chlorocardium, Hypodaphnis, Licaria and Sextonia) from herbarium specimens using genome skimming to conduct a comprehensive analysis of plastome evolution of Lauraceae as a means of sampling representatives of all major clades of the family. We identified and recognized six types of plastomes and revealed that at least two independent loss events at the IR-LSC boundary and an independent expansion of SSC occurred in the plastome evolution of the family. Hypodaphnis possesses the ancestral type of Lauraceae with trnI-CAU, rpl23 and rpl2 duplicated in the IR regions (Type-I). The Mezilaurus group shares the same plastome structure with the core Lauraceae group in the loss of trnI-CAU, rpl23 and rpl2 in the IRa region (Type-III). Two new types were identified in the Ocotea group: (1) the insertion of trnI-CAU between trnL-UAG and ccsA in the SSC region of Licaria capitata and Ocotea bracteosa (Type-IV), and (2) trnI-CAU and pseudogenizated rpl23 inserted in the same region of Nectandra angustifolia (Type-V). Our phylogeny suggests that Lauraceae are divided into nine major clades largely in accordance with the plastome types. The Hypodaphnideae are the earliest diverged lineage supported by both robust phylogeny and the ancestral plastome type. The monophyletic Mezilaurus group is sister to the core Lauraceae. CONCLUSIONS By using herbariomics, we built a more complete picture of plastome evolution and phylogeny of the family, thus providing a convincing case for further use of herbariomics in phylogenetic studies of the Lauraceae.
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Affiliation(s)
- Zhi Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing, 210037, China
| | | | - Yong Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing, 210037, China.
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Liu SH, Hung KH, Hsu TW, Hoch PC, Peng CI, Chiang TY. New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae). BOTANICAL STUDIES 2023; 64:14. [PMID: 37269434 DOI: 10.1186/s40529-023-00387-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/17/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa. RESULTS Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported. CONCLUSIONS The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.
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Affiliation(s)
- Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan
| | - Tsai-Wen Hsu
- Endemic Species Research Institute, Nantou, 552, Taiwan
| | - Peter C Hoch
- Missouri Botanical Garden, St. Louis, MO, 63166, USA
| | - Ching-I Peng
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
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Valarezo E, Herrera-García M, Astudillo-Dávila P, Rosales-Demera I, Jaramillo-Fierro X, Cartuche L, Meneses MA, Morocho V. Study of the Chemical Composition and Biological Activity of the Essential Oil from Congona ( Peperomia inaequalifolia Ruiz and Pav.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1504. [PMID: 37050130 PMCID: PMC10097166 DOI: 10.3390/plants12071504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
The species Peperomia inaequalifolia, commonly known as congona, is a succulent herbaceous plant belonging to the Piperaceae family, which is used for different purposes in traditional medicine. In this study, the chemical composition, enantiomeric distribution, and biological activity of essential oil isolated from the leaves of this species was determined. Hydrodistillation was used to isolate the essential oil. Gas chromatography coupled to mass spectrometry was used to determine the qualitative composition, a gas chromatograph equipped with a flame ionization detector was used to determine quantitative composition, and gas chromatography on an enantioselective column was used to determine enantiomeric distribution. Antibacterial activity was determined using the broth microdilution method, for which we used three Gram-positive cocci bacteria, a Gram-positive bacilli bacterium, and three Gram-negative bacilli bacteria. 2,2'-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical cations and 2,2-diphenyl-1-picrylhydryl (DPPH) radicals were used as reagents for determining the antioxidant activity of the essential oil. The spectrophotometric method was used to analyze the acetylcholinesterase inhibitory effect of the essential oil. The yield of leaves in essential oil was 0.16 ± 0.01% (v/w). Forty-three chemical compounds were identified in the essential oil, which represent 97.46% of the total composition. Sesquiterpene hydrocarbons were the most representative group, with 24 compounds (21.63%). The principal constituents were found to be elemicin (27.44 ± 1.35%), bisabolol <α-> (17.76 ± 1.38), myristicin (15.45 ± 0.86), methyl eugenol (6.22 ± 0.24), viridiflorene (6.81 ± 0.10), and safrole (6.68 ± 0.23). Three pairs of enantiomers were identified in the essential oil of Peperomia inaequalifolia. Essential oil presented a minimum inhibitory concentration (MIC) of 4000 μg/mL against Enterococcus faecalis, Enterococcus faecium, Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli. The antioxidant activity of the essential oil was strong according to the DPPH and ABTS methods, with a half radical scavenging capacity (SC50) of 293.76 ± 3.12 µg/mL and 226.86 ± 0.05 µg/mL, respectively. Additionally, the essential oil reported moderate anticholinesterase activity, with an IC50 of 43.93 ± 1.05 µg/mL.
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Phylogenomics, plastome structure and species identification in Mahonia (Berberidaceae). BMC Genomics 2022; 23:766. [PMID: 36418947 PMCID: PMC9682747 DOI: 10.1186/s12864-022-08964-0] [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: 08/01/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Elucidating the phylogenetic relationships within species-rich genera is essential but challenging, especially when lineages are assumed to have been going through radiation events. Mahonia Nutt. (Berberidaceae) is a genus with cosmopolitan distribution, comprising approximately 100 species, two of which are known as Caulis Mahoniae (M. bealei and M. fortunei) with crucial pharmacological significance in Chinese herbal medicine. Mahonia is a taxonomically challenging genus, and intrageneric phylogenetic relationships still need to be explored using genome data. Universal DNA barcodes and floral morphological attributes have limited discriminatory power in Mahonia. RESULTS We sequenced 17 representative plastomes and integrated three published plastome data together to conduct comparative and phylogenetic analyses. We found that Mahonia and Berberis share a large IR expansion (~ 12 kb), which is recognized as a typical character of Berberideae. Repeated sequences are revealed in the species of Mahonia, which are valuable for further population genetic studies. Using a comparative plastome analysis, we determined eight hypervariable regions whose discriminative power is comparable to that of the whole plastid genomes. The incongruence of the ITS and the plastome tree topologies may be ascribed to ancestral hybridization events and/or to incomplete lineage sorting. In addition, we suggest that leaf epidermal characters could help to distinguish closely related species in Mahonia. CONCLUSIONS We propose an integrative approach combining special barcodes and micromorphological traits to circumscribe Mahonia species. The results cast a new light on the development of an integrative method for accurate species circumscription and provide abundant genetic resources for further research on Mahonia.
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Hay T, Prakash S, Daygon VD, Fitzgerald M. Review of edible Australian flora for colour and flavour additives: Appraisal of suitability and ethicality for bushfoods as natural additives to facilitate new industry growth. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Li J, Fan R, Xu J, Hu L, Su F, Hao C. Comparative analysis of the chloroplast genomes of eight Piper species and insights into the utilization of structural variation in phylogenetic analysis. Front Genet 2022; 13:925252. [PMID: 36246585 PMCID: PMC9556897 DOI: 10.3389/fgene.2022.925252] [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] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
With more than 2000 species, Piper is regarded as having high medicinal, cosmetic, and edible value. There also remain some taxonomic and evolutionary uncertainties about the genus. This study performed chloroplast genome sequencing of eight poorly studied Piper species and a comparative analysis with black pepper (Piper nigrum). All examined species were highly similar in gene content, with 79 protein-coding genes, 24 tRNAs, and four rRNAs. They also harbored significant structural differences: The number of SSRs ranged from 63 to 87, over 10,000 SNPs were detected, and over 1,000 indels were found. The spatial distribution of structural differences was uneven, with the IR and LSC being relatively more conserved and the SSC region highly variable. Such structural variations of the chloroplast genome can help in evaluating the phylogenetic relationships between species, deciding some hard-to-distinguish evolutionary relationships, or eliminating improper markers. The SSC region may be evolving at high speed, and some species showed a high degree of sequence variation in the SSC region, which seriously affected marker sequence detection. Conversely, CDS sequences tended to lack variation, and some CDSs can serve as ideal markers for phylogenetic reconstruction. All told, this study provides an effective strategy for selecting chloroplast markers, analyzing difficult-to-distinguish phylogenetic relationships and avoiding the taxonomic errors caused by high degree of sequence variations.
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Affiliation(s)
- Jing Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Jintao Xu
- Yangtze Normal University, Chongqing, China
| | - Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Fan Su
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, Hainan, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, Hainan, China
- Academician Soonliang Sim of Hainan Province Research Station, Wanning, Hainan, China
- *Correspondence: Chaoyun Hao,
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Li QJ, Liu Y, Wang AH, Chen QF, Wang JM, Peng L, Yang Y. Plastome comparison and phylogenomics of Fagopyrum (Polygonaceae): insights into sequence differences between Fagopyrum and its related taxa. BMC PLANT BIOLOGY 2022; 22:339. [PMID: 35831794 PMCID: PMC9281083 DOI: 10.1186/s12870-022-03715-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/23/2022] [Indexed: 05/09/2023]
Abstract
BACKGROUND Fagopyrum (Polygonaceae) is a small plant lineage comprised of more than fifteen economically and medicinally important species. However, the phylogenetic relationships of the genus are not well explored, and the characteristics of Fagopyrum chloroplast genomes (plastomes) remain poorly understood so far. It restricts the comprehension of species diversity in Fagopyrum. Therefore, a comparative plastome analysis and comprehensive phylogenomic analyses are required to reveal the taxonomic relationship among species of Fagopyrum. RESULTS In the current study, 12 plastomes were sequenced and assembled from eight species and two varieties of Fagopyrum. In the comparative analysis and phylogenetic analysis, eight previously published plastomes of Fagopyrum were also included. A total of 49 plastomes of other genera in Polygonaceae were retrieved from GenBank and used for comparative analysis with Fagopyrum. The variation of the Fagopyrum plastomes is mainly reflected in the size and boundaries of inverted repeat/single copy (IR/SC) regions. Fagopyrum is a relatively basal taxon in the phylogenomic framework of Polygonaceae comprising a relatively smaller plastome size (158,768-159,985 bp) than another genus of Polygonaceae (158,851-170,232 bp). A few genera of Polygonaceae have nested distribution of the IR/SC boundary variations. Although most species of Fagopyrum show the same IRb/SC boundary with species of Polygonaceae, only a few species show different IRa/SC boundaries. The phylogenomic analyses of Fagopyrum supported the cymosum and urophyllum groups and resolved the systematic position of subclades within the urophyllum group. Moreover, the repeat sequence types and numbers were found different between groups of Fagopyrum. The plastome sequence identity showed significant differences between intra-group and inter-group. CONCLUSIONS The deletions of intergenic regions cause a short length of Fagopyrum plastomes, which may be the main reason for plastome size diversity in Polygonaceae species. The phylogenomic reconstruction combined with the characteristics comparison of plastomes supports grouping within Fagopyrum. The outcome of these genome resources may facilitate the taxonomy, germplasm resources identification as well as plant breeding of Fagopyrum.
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Affiliation(s)
- Qiu-Jie Li
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yu Liu
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - An-Hu Wang
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, 615013, China
| | - Qing-Fu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China
| | - Jian-Mei Wang
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lu Peng
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yi Yang
- College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Ellestad P, Farrera MAP, Forest F, Buerki S. Uncovering haplotype diversity in cultivated Mexican vanilla species. AMERICAN JOURNAL OF BOTANY 2022; 109:1120-1138. [PMID: 35709340 DOI: 10.1002/ajb2.16024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Although vanilla is one of the best-known spices, there is only a limited understanding of its biology and genetics within Mexico, where its cultivation originated and where phenotypic variability is high. This study aims to augment our understanding of vanilla's genetic resources by assessing species delimitation and genetic, geographic, and climatic variability within Mexican cultivated vanilla. METHODS Using nuclear and plastid DNA sequence data from 58 Mexican samples collected from three regions and 133 ex situ accessions, we assessed species monophyly using phylogenetic analyses and genetic distances. Intraspecific genetic variation was summarized through the identification of haplotypes. Within the primarily cultivated species, Vanilla planifolia, haplotype relationships were further verified using plastome and rRNA gene sequences. Climatic niche and haplotype composition were assessed across the landscape. RESULTS Three species (Vanilla planifolia, V. pompona, and V. insignis) and 13 haplotypes were identified among Mexican vanilla. Within V. planifolia haplotypes, hard phylogenetic incongruences between plastid and nuclear sequences suggest past hybridization events. Eight haplotypes consisted exclusively of Mexican samples. The dominant V. planifolia haplotype occurred throughout all three regions as well as outside of its country of origin. Haplotype richness was found to be highest in regions around Papantla and Chinantla. CONCLUSIONS Long histories of regional cultivation support the consideration of endemic haplotypes as landraces shaped by adaptation to local conditions and/or hybridization. Results may aid further genomic investigations of vanilla's genetic resources and ultimately support the preservation of genetic diversity within the economically important crop.
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Affiliation(s)
- Paige Ellestad
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, USA
| | - Miguel Angel Perez Farrera
- Herbario Eizi Matuda, Laboratorio de Ecología Evolutiva, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes, Chiapas, Mexico, Libramiento Norte Poniente 1151, Col. Lajas Maciel, Tuxtla Gutiérrez, Chiapas, CP, 29039, Mexico
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, USA
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Cárdenas-Laverde D, Rincón-Aceldas S, Coy-Barrera E. Identification of Antifungal Compounds from Piper Plants Against Fusarium oxysporum: An Untargeted Metabolite Profiling-Based Approach. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221089995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The phytopathogen Fusarium oxysporum produces considerable losses in economically important crops, making alternative control measures urgently required. Piper plants are widely distributed in tropical regions, and they are also known to produce metabolites with biological activity against infectious agents. As part of our continuous search for antifungals, 18 Piper-derived ethanolic extracts were evaluated by their in vitro effect on F oxysporum mycelial growth inhibition. The total content of phenol and flavonoid measurements and liquid chromatography-electrospray ionization-mass spectrometry analysis served as the chemical characterization of the investigated extracts. Piper pulchrum, Piper barcoense, and Piper tuberculatum exhibited the highest mycelial growth inhibition (>74%). The integration of chemical fingerprints and bioactivity datasets led to recognizing 4 bioactive candidates among extracts through single- Y orthogonal partial least squares regression and univariate statistics. These candidates were 2 amides (1,3), an alkyl lactone (2), and a prenylated benzoquinone (4), subsequently isolated and identified by nuclear magnetic resonance spectroscopy. These isolated compounds exhibited reasonable antifungal activity (IC50 < 50 µM). The findings indicated that the correlative association is advantageous for identifying bioactive metabolites within active extracts.
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Affiliation(s)
- Diego Cárdenas-Laverde
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Sebastián Rincón-Aceldas
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, Colombia
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Plastid Phylogenomic Analysis of Tordylieae Tribe (Apiaceae, Apioideae). PLANTS 2022; 11:plants11050709. [PMID: 35270181 PMCID: PMC8912408 DOI: 10.3390/plants11050709] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
Abstract
Based on the nrDNA ITS sequence data, the Tordylieae tribe is recognized as monophyletic with three major lineages: the subtribe Tordyliinae, the Cymbocarpum clade, and the Lefebvrea clade. Recent phylogenomic investigations showed incongruence between the nuclear and plastid genome evolution in the tribe. To assess phylogenetic relations and structure evolution of plastomes in Tordylieae, we generated eleven complete plastome sequences using the genome skimming approach and compared them with the available data from this tribe and close relatives. Newly assembled plastomes had lengths ranging from 141,148 to 150,103 base pairs and contained 122–127 genes, including 79–82 protein-coding genes, 35–37 tRNAs, and 8 rRNAs. We observed substantial differences in the inverted repeat length and gene content, accompanied by a complex picture of multiple JLA and JLB shifts. In concatenated phylogenetic analyses, Tordylieae plastomes formed at least three not closely related lineages with plastomes of the Lefebvrea clade as a sister group to plastomes from the Selineae tribe. The newly obtained data have increased our knowledge on the range of plastome variability in Apiaceae.
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Ogoma CA, Liu J, Stull GW, Wambulwa MC, Oyebanji O, Milne RI, Monro AK, Zhao Y, Li DZ, Wu ZY. Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:870949. [PMID: 35668809 PMCID: PMC9164014 DOI: 10.3389/fpls.2022.870949] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/15/2022] [Indexed: 05/09/2023]
Abstract
Urticeae s.l., a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data-CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions-for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110-112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.
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Affiliation(s)
- Catherine A. Ogoma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Gregory W. Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Moses C. Wambulwa
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya
| | - Oyetola Oyebanji
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Richard I. Milne
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ying Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: De-Zhu Li,
| | - Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Zeng-Yuan Wu,
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