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Ogutcen E, de Lima Ferreira P, Wagner ND, Marinček P, Vir Leong J, Aubona G, Cavender-Bares J, Michálek J, Schroeder L, Sedio BE, Vašut RJ, Volf M. Phylogenetic insights into the Salicaceae: The evolution of willows and beyond. Mol Phylogenet Evol 2024; 199:108161. [PMID: 39079595 DOI: 10.1016/j.ympev.2024.108161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 07/05/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024]
Abstract
The Salicaceae includes approximately 54 genera and over 1,400 species with a cosmopolitan distribution. Members of the family are well-known for their diverse secondary plant metabolites, and they play crucial roles in tropical and temperate forest ecosystems. Phylogenetic reconstruction of the Salicaceae has been historically challenging due to the limitations of molecular markers and the extensive history of hybridization and polyploidy within the family. Our study employs whole-genome sequencing of 74 species to generate an extensive phylogeny of the Salicaceae. We generated two RAD-Seq enriched whole-genome sequence datasets and extracted two additional gene sets corresponding to the universal Angiosperms353 and Salicaceae-specific targeted-capture arrays. We reconstructed maximum likelihood-based molecular phylogenies using supermatrix and coalescent-based supertree approaches. Our fossil-calibrated phylogeny estimates that the Salicaceae originated around 128 million years ago and unravels the complex taxonomic relationships within the family. Our findings confirm the non-monophyly of the subgenus Salix s.l. and further support the merging of subgenera Chamaetia and Vetrix, both of which exhibit intricate patterns within and among different sections. Overall, our study not only enhances our understanding of the evolution of the Salicaceae, but also provides valuable insights into the complex relationships within the family.
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Affiliation(s)
- Ezgi Ogutcen
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Department of Environment and Biodiversity, Paris Lodron University of Salzburg, Salzburg, Austria.
| | - Paola de Lima Ferreira
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Department of Biology, Aarhus University, Aarhus, Denmark
| | - Natascha D Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Pia Marinček
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Jing Vir Leong
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Gibson Aubona
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | | | - Jan Michálek
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Trebon, Czech Republic
| | - Lucy Schroeder
- College of Biological Sciences, University of Minnesota, St. Paul, MN, United States
| | - Brian E Sedio
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States; Smithsonian Tropical Research Institute, Apartado, 0843-03092 Balboa, Ancón, Republic of Panama
| | - Radim J Vašut
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic; Department of Biology, Faculty of Education, Palacký University Olomouc, Olomouc, Czech Republic
| | - Martin Volf
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
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Khodaeiaminjan M, Gomes C, Pagano A, Kruszka D, Sulima P, Przyborowski JA, Krajewski P, Paiva JAP. Impacts of in-vitro zebularine treatment on genome-wide DNA methylation and transcriptomic profiles in Salix purpurea L. PHYSIOLOGIA PLANTARUM 2024; 176:e14403. [PMID: 38923551 DOI: 10.1111/ppl.14403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Renewable energy resources such as biomass are crucial for a sustainable global society. Trees are a major source of lignocellulosic biomass, which can vary in response to different environmental factors owing to epigenetic regulation, such as DNA C-methylation. To investigate the effects of DNA methylation on plant development and wood formation, and its impacts on gene expression, with a focus on secondary cell wall (SCW)-associated genes, Salix purpurea plantlets were cloned from buds derived from a single hybrid tree for both treatment and control conditions. For the treatment condition, buds were exposed to 50 μM zebularine in vitro and a combined strategy of whole-genome bisulfite sequencing (WGBS) and RNA-seq was employed to examine the methylome and transcriptome profiles of different tissues collected at various time points under both conditions. Transcriptomic and methylome data revealed that most of the promoter and gene body demethylation had no marked effects on the expression profiles of genes. Nevertheless, gene expression tended to decrease with the increased methylation levels of genes with highly methylated promoters. Results indicated that demethylation is less evident in centromeric regions and sex chromosomes. Promoters of secondary cell wall-associated genes, such as 4-coumarate-CoA ligase-like and Rac-like GTP-binding protein RHO, were differentially methylated in the secondary xylem samples collected from two-month potted treated plants compared to control samples. Our results provide novel insights into DNA methylation and gene expression landscapes and a basis for investigating the epigenetic regulation of wood formation in S. purpurea as a model plant for bioenergy species.
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Affiliation(s)
- Mortaza Khodaeiaminjan
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Carolina Gomes
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Andrea Pagano
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Dariusz Kruszka
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Paweł Sulima
- Department of Genetics, Plant Breeding and Bioresource Engineering, University of Warmia and Mazury, Olsztyn, Poland
| | - Jerzy Andrzej Przyborowski
- Department of Genetics, Plant Breeding and Bioresource Engineering, University of Warmia and Mazury, Olsztyn, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Jorge Almiro Pinto Paiva
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Michell CT, Wagner N, Mutanen M, Lee KM, Nyman T. Genomic evidence for contrasting patterns of host-associated genetic differentiation across shared host-plant species in leaf- and bud-galling sawflies. Mol Ecol 2023; 32:1791-1809. [PMID: 36626108 DOI: 10.1111/mec.16844] [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: 08/02/2021] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Resource specialization and ecological speciation arising through host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary timescales. We applied genome-wide single nucleotide polymorphism and mitochondrial DNA sequence data obtained through genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae) collected from seven shared willow (Salicaceae: Salix) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species compared with most bud gallers. In contrast to bud gallers, leaf gallers also exhibited statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and host shifts in two related galler groups that have radiated in parallel across a shared resource base indicate a lack of evolutionary repeatability in the focal system, and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.
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Affiliation(s)
- Craig T Michell
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Natascha Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
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Marinček P, Pittet L, Wagner ND, Hörandl E. Evolution of a hybrid zone of two willow species ( Salix L.) in the European Alps analyzed by RAD-seq and morphometrics. Ecol Evol 2023; 13:e9700. [PMID: 36620405 PMCID: PMC9811612 DOI: 10.1002/ece3.9700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/30/2022] [Accepted: 12/14/2022] [Indexed: 01/06/2023] Open
Abstract
Natural hybridization of plants can result in many outcomes with several evolutionary consequences, such as hybrid speciation and introgression. Natural hybrid zones can arise in mountain systems as a result of fluctuating climate during the exchange of glacial and interglacial periods, where species retract and expand their territories, resulting in secondary contacts. Willows are a large genus of woody plants with an immense capability of interspecific crossing. In this study, the sympatric area of two diploid sister species, S. foetida and S. waldsteiniana in the eastern European Alps, was investigated to study the genomic structure of populations within and outside their contact zone and to analyze congruence of morphological phenotypes with genetic data. Eleven populations of the two species were sampled across the Alps and examined using phylogenetic network and population genetic structure analyses of RAD Seq data and morphometric analyses of leaves. The results showed that a homoploid hybrid zone between the two species was established within their sympatric area. Patterns of genetic admixture in homoploid hybrids indicated introgression with asymmetric backcrossing to not only one of the parental species but also one hybrid population forming a separate lineage. The lack of F1 hybrids indicated a long-term persistence of the hybrid populations. Insignificant isolation by distance suggests that gene flow can act over large geographical scales. Morphometric characteristics of hybrids supported the molecular data and clearly separated populations of the parental species, but showed intermediacy in the hybrid zone populations with a bias toward S. waldsteiniana. The homoploid hybrid zone might have been established via secondary contact hybridization, and its establishment was fostered by the low genetic divergence of parental species and a lack of strong intrinsic crossing barriers. Incomplete ecological separation and the ability of long-distance dispersal of willows could have contributed to the spatial expansion of the hybrid zone.
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Affiliation(s)
- Pia Marinček
- Department of Systematics, Biodiversity, and Evolution of Plants (with Herbarium)University of GöttingenGöttingenGermany
| | - Loïc Pittet
- Department of Systematics, Biodiversity, and Evolution of Plants (with Herbarium)University of GöttingenGöttingenGermany
| | - Natascha D. Wagner
- Department of Systematics, Biodiversity, and Evolution of Plants (with Herbarium)University of GöttingenGöttingenGermany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity, and Evolution of Plants (with Herbarium)University of GöttingenGöttingenGermany
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Unweaving the population structure and genetic diversity of Canadian shrub willow. Sci Rep 2022; 12:17254. [PMID: 36241753 PMCID: PMC9568530 DOI: 10.1038/s41598-022-20498-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/14/2022] [Indexed: 01/06/2023] Open
Abstract
Perennial shrub willow are increasingly being promoted in short-rotation coppice systems as biomass feedstocks, for phytoremediation applications, and for the diverse ecosystem services that can accrue. This renewed interest has led to widespread willow cultivation, particularly of non-native varieties. However, Canadian willow species have not been widely adopted and their inherent diversity has not yet been thoroughly investigated. In this study, 324 genotypes of Salix famelica and Salix eriocephala collected from 33 sites of origin were analyzed using 26,016 single nucleotide polymorphisms to reveal patterns of population structure and genetic diversity. Analyses by Bayesian methods and principal component analysis detected five main clusters that appeared to be largely shaped by geoclimatic variables including mean annual precipitation and the number of frost-free days. The overall observed (HO) and expected (HE) heterozygosity were 0.126 and 0.179, respectively. An analysis of molecular variance revealed that the highest genetic variation occurred within genotypes (69%), while 8% of the variation existed among clusters and 23% between genotypes within clusters. These findings provide new insights into the extent of genetic variation that exists within native shrub willow species which could be leveraged in pan-Canadian willow breeding programs.
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Wang D, Li Y, Li M, Yang W, Ma X, Zhang L, Wang Y, Feng Y, Zhang Y, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, DiFazio SP, Liu J, Olson M, Ma T. Repeated turnovers keep sex chromosomes young in willows. Genome Biol 2022; 23:200. [PMID: 36151581 PMCID: PMC9502649 DOI: 10.1186/s13059-022-02769-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/08/2022] [Indexed: 01/10/2023] Open
Abstract
Background Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively. Results Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the “deleterious mutation load” and “sexually antagonistic selection” theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration. Conclusions Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02769-w.
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Affiliation(s)
- Deyan Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Wenlu Yang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Lei Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yubo Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yanlin Feng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yuanyuan Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV, USA.,Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
| | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
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Ren W, Jiang Z, Zhang M, Kong L, Zhang H, Liu Y, Fu Q, Ma W. The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements. FRONTIERS IN PLANT SCIENCE 2022; 13:987443. [PMID: 36092427 PMCID: PMC9459086 DOI: 10.3389/fpls.2022.987443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Salix floderusii is a rare alpine tree species in the Salix genus. Unfortunately, no extensive germplasm identification, molecular phylogeny, and chloroplast genomics of this plant have been conducted. We sequenced the chloroplast (cp) genome of S. floderusii for the first time using second-generation sequencing technology. The cp genome was 155,540 bp long, including a large single-copy region (LSC, 84,401 bp), a small single-copy region (SSC, 16,221 bp), and inverted repeat regions (IR, 54,918 bp). A total of 131 genes were identified, including 86 protein genes, 37 tRNA genes, and 8 rRNA genes. The S. floderusii cp genome contains 1 complement repeat, 24 forward repeats, 17 palindromic repeats, and 7 reverse repeats. Analysis of the IR borders showed that the IRa and IRb regions of S. floderusii and Salix caprea were shorter than those of Salix cinerea, which may affect plastome evolution. Furthermore, four highly variable regions were found, including the rpl22 coding region, psbM/trnD-GUC non-coding region, petA/psbJ non-coding region, and ycf1 coding region. These high variable regions can be used as candidate molecular markers and as a reference for identifying future Salix species. In addition, phylogenetic analysis indicated that the cp genome of S. floderusii is sister to Salix cupularis and belongs to the Subgenus Vetrix. Genes (Sf-trnI, Sf-PpsbA, aadA, Sf-TpsbA, Sf-trnA) obtained via cloning were inserted into the pBluescript II SK (+) to yield the cp expression vectors, which harbored the selectable marker gene aadA. The results of a spectinomycin resistance test indicated that the cp expression vector had been successfully constructed. Moreover, the aadA gene was efficiently expressed under the regulation of predicted regulatory elements. The present study provides a solid foundation for establishing subsequent S. floderusii cp transformation systems and developing strategies for the genetic improvement of S. floderusii.
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Affiliation(s)
- Weichao Ren
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhehui Jiang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Meiqi Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Lingyang Kong
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Houliang Zhang
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Yunwei Liu
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Qifeng Fu
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Ma
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
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Gulyaev S, Cai XJ, Guo FY, Kikuchi S, Applequist WL, Zhang ZX, Hörandl E, He L. The phylogeny of Salix revealed by whole genome re-sequencing suggests different sex-determination systems in major groups of the genus. ANNALS OF BOTANY 2022; 129:485-498. [PMID: 35134824 PMCID: PMC8944726 DOI: 10.1093/aob/mcac012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS The largest genus of Salicaceae sensu lato, Salix, has been shown to consist of two main clades: clade Salix, in which species have XY sex-determination systems (SDSs) on chromosome 7, and clade Vetrix including species with ZW SDSs on chromosome 15. Here, we test the utility of whole genome re-sequencing (WGR) for phylogenomic reconstructions of willows to infer changes between different SDSs. METHODS We used more than 1 TB of WGR data from 70 Salix taxa to ascertain single nucleotide polymorphisms on the autosomes, the sex-linked regions (SLRs) and the chloroplast genomes, for phylogenetic and species tree analyses. To avoid bias, we chose reference genomes from both groups, Salix dunnii from clade Salix and S. purpurea from clade Vetrix. KEY RESULTS Two main largely congruent groups were recovered: the paraphyletic Salix grade and the Vetrix clade. The autosome dataset trees resolved four subclades (C1-C4) in Vetrix. C1 and C2 comprise species from the Hengduan Mountains and adjacent areas and from Eurasia, respectively. Section Longifoliae (C3) grouped within the Vetrix clade but fell into the Salix clade in trees based on the chloroplast dataset analysis. Salix triandra from Eurasia (C4) was revealed as sister to the remaining species of clade Vetrix. In Salix, the polyploid group C5 is paraphyletic to clade Vetrix and subclade C6 is consistent with Argus's subgenus Protitea. Chloroplast datasets separated both Vetrix and Salix as monophyletic, and yielded C5 embedded within Salix. Using only diploid species, both the SLR and autosomal datasets yielded trees with Vetrix and Salix as well-supported clades. CONCLUSION WGR data are useful for phylogenomic analyses of willows. The different SDSs may contribute to the isolation of the two major groups, but the reproductive barrier between them needs to be studied.
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Affiliation(s)
- Sergey Gulyaev
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin-Jie Cai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fei-Yi Guo
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Satoshi Kikuchi
- Hokkaido Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization. Hitsujigaoka 7, Toyohira, Sapporo City, Hokkaido, 062-8516, Japan
| | - Wendy L Applequist
- William L. Brown Center, Missouri Botanical Garden, St. Louis, MO 63110, USA
| | - Zhi-Xiang Zhang
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, 37073, Germany
| | - Li He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
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9
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Wagner ND, Volf M, Hörandl E. Highly Diverse Shrub Willows ( Salix L.) Share Highly Similar Plastomes. FRONTIERS IN PLANT SCIENCE 2021; 12:662715. [PMID: 34539686 PMCID: PMC8448165 DOI: 10.3389/fpls.2021.662715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/23/2021] [Indexed: 05/23/2023]
Abstract
Plastome phylogenomics is used in a broad range of studies where single markers do not bear enough information. Phylogenetic reconstruction in the genus Salix is difficult due to the lack of informative characters and reticulate evolution. Here, we use a genome skimming approach to reconstruct 41 complete plastomes of 32 Eurasian and North American Salix species representing different lineages, different ploidy levels, and separate geographic regions. We combined our plastomes with published data from Genbank to build a comprehensive phylogeny of 61 samples (50 species) using RAxML (Randomized Axelerated Maximum Likelihood). Additionally, haplotype networks for two observed subclades were calculated, and 72 genes were tested to be under selection. The results revealed a highly conserved structure of the observed plastomes. Within the genus, we observed a variation of 1.68%, most of which separated subg. Salix from the subgeneric Chamaetia/Vetrix clade. Our data generally confirm previous plastid phylogenies, however, within Chamaetia/Vetrix phylogenetic results represented neither taxonomical classifications nor geographical regions. Non-coding DNA regions were responsible for most of the observed variation within subclades and 5.6% of the analyzed genes showed signals of diversifying selection. A comparison of nuclear restriction site associated DNA (RAD) sequencing and plastome data on a subset of 10 species showed discrepancies in topology and resolution. We assume that a combination of (i) a very low mutation rate due to efficient mechanisms preventing mutagenesis, (ii) reticulate evolution, including ancient and ongoing hybridization, and (iii) homoplasy has shaped plastome evolution in willows.
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Affiliation(s)
- Natascha D. Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (With Herbarium), University of Goettingen, Göttingen, Germany
| | - Martin Volf
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (With Herbarium), University of Goettingen, Göttingen, Germany
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10
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Gervais-Bergeron B, Chagnon PL, Labrecque M. Willow Aboveground and Belowground Traits Can Predict Phytoremediation Services. PLANTS 2021; 10:plants10091824. [PMID: 34579357 PMCID: PMC8471398 DOI: 10.3390/plants10091824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/20/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
The increasing number of contaminated sites worldwide calls for sustainable remediation, such as phytoremediation, in which plants are used to decontaminate soils. We hypothesized that better anchoring phytoremediation in plant ecophysiology has the potential to drastically improve its predictability. In this study, we explored how the community composition, diversity and coppicing of willow plantations, influenced phytoremediation services in a four-year field trial. We also evaluated how community-level plant functional traits might be used as predictors of phytoremediation services, which would be a promising avenue for plant selection in phytoremediation. We found no consistent impact of neither willow diversity nor coppicing on phytoremediation services directly. These services were rather explained by willow traits related to resource economics and management strategy along the plant "fast-slow" continuum. We also found greater belowground investments to promote plant bioconcentration and soil decontamination. These traits-services correlations were consistent for several trace elements investigated, suggesting high generalizability among contaminants. Overall, our study provides evidence, even using a short taxonomic (and thus functional) plant gradient, that traits can be used as predictors for phytoremediation efficiency for a broad variety of contaminants. This suggests that a trait-based approach has great potential to develop predictive plant selection strategies in phytoremediation trials, through a better rooting of applied sciences in fundamental plant ecophysiology.
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11
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Lynch SC, Eskalen A, Gilbert GS. Host evolutionary relationships explain tree mortality caused by a generalist pest-pathogen complex. Evol Appl 2021; 14:1083-1094. [PMID: 33897822 PMCID: PMC8061262 DOI: 10.1111/eva.13182] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
The phylogenetic signal of transmissibility (competence) and attack severity among hosts of generalist pests is poorly understood. In this study, we examined the phylogenetic effects on hosts differentially affected by an emergent generalist beetle-pathogen complex in California and South Africa. Host types (non-competent, competent and killed-competent) are based on nested types of outcomes of interactions between host plants, the beetles and the fungal pathogens. Phylogenetic dispersion analysis of each host type revealed that the phylogenetic preferences of beetle attack and fungal growth were a nonrandom subset of all available tree and shrub species. Competent hosts were phylogenetically narrower by 62 Myr than the set of all potential hosts, and those with devastating impacts were the most constrained by 107 Myr. Our results show a strong phylogenetic signal in the relative effects of a generalist pest-pathogen complex on host species, demonstrating that the strength of multi-host pest impacts in plants can be predicted by host evolutionary relationships. This study presents a unifying theoretical approach to identifying likely disease outcomes across multiple host-pest combinations.
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Affiliation(s)
- Shannon Colleen Lynch
- Department of Environmental StudiesUniversity of California Santa CruzSanta CruzCaliforniaUSA
- Department of Plant PathologyUniversity of California DavisDavisCaliforniaUSA
| | - Akif Eskalen
- Department of Plant PathologyUniversity of California DavisDavisCaliforniaUSA
| | - Gregory S. Gilbert
- Department of Environmental StudiesUniversity of California Santa CruzSanta CruzCaliforniaUSA
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12
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The Evolutionary History, Diversity, and Ecology of Willows (Salix L.) in the European Alps. DIVERSITY-BASEL 2021. [DOI: 10.3390/d13040146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The genus Salix (willows), with 33 species, represents the most diverse genus of woody plants in the European Alps. Many species dominate subalpine and alpine types of vegetation. Despite a long history of research on willows, the evolutionary and ecological factors for this species richness are poorly known. Here we will review recent progress in research on phylogenetic relationships, evolution, ecology, and speciation in alpine willows. Phylogenomic reconstructions suggest multiple colonization of the Alps, probably from the late Miocene onward, and reject hypotheses of a single radiation. Relatives occur in the Arctic and in temperate Eurasia. Most species are widespread in the European mountain systems or in the European lowlands. Within the Alps, species differ ecologically according to different elevational zones and habitat preferences. Homoploid hybridization is a frequent process in willows and happens mostly after climatic fluctuations and secondary contact. Breakdown of the ecological crossing barriers of species is followed by introgressive hybridization. Polyploidy is an important speciation mechanism, as 40% of species are polyploid, including the four endemic species of the Alps. Phylogenomic data suggest an allopolyploid origin for all taxa analyzed so far. Further studies are needed to specifically analyze biogeographical history, character evolution, and genome evolution of polyploids.
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13
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He L, Jia KH, Zhang RG, Wang Y, Shi TL, Li ZC, Zeng SW, Cai XJ, Wagner ND, Hörandl E, Muyle A, Yang K, Charlesworth D, Mao JF. Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7. Mol Ecol Resour 2021; 21:1966-1982. [PMID: 33609314 PMCID: PMC8359994 DOI: 10.1111/1755-0998.13362] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 12/23/2022]
Abstract
Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 scaffolds, and includes 31,501 predicted genes. Analyses of short-read sequence data that included female and male plants suggested a male heterogametic sex-determining factor on chromosome 7, implying that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii sex-linked region occupies about 3.21 Mb of chromosome 7 in females (representing its position in the X chromosome), probably within a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one-third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for further studies of sex-determining regions in the family Salicaceae, and sex chromosome evolution.
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Affiliation(s)
- Li He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai-Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ren-Gang Zhang
- Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, China
| | - Yuan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tian-Le Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhi-Chao Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Si-Wen Zeng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin-Jie Cai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Natascha Dorothea Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Aline Muyle
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Ke Yang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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14
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Tawfeek N, Mahmoud MF, Hamdan DI, Sobeh M, Farrag N, Wink M, El-Shazly AM. Phytochemistry, Pharmacology and Medicinal Uses of Plants of the Genus Salix: An Updated Review. Front Pharmacol 2021; 12:593856. [PMID: 33643045 PMCID: PMC7908037 DOI: 10.3389/fphar.2021.593856] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/07/2021] [Indexed: 01/18/2023] Open
Abstract
The Willows (genus Salix), with more than 330–500 species and 200 hybrids, are trees, shrubs or prostrate plants that are widely distributed in Africa, North America, Europe, and Asia. The genus is traditionally used in folk medicine and represents a valuable source of biologically active compounds among them salicin, a prodrug for salicylic acid. Altogether, 322 secondary metabolites were characterized in the genus including flavonoids 94) (flavonols, flavones, flavanones, isoflavones, flavan-3-ols (catechins and procyanidins), chalcones, dihydrochalcone, anthocyanins, dihydroflavonols), phenolic glycosides (76), organic acids (28), and non-phenolic glycosides (17), sterols and terpenes (17), simple phenolics 13) and lignans 7) in addition to volatiles and fatty acids (69). Furthermore, willows exert analgesic, anti-inflammatory, antioxidant, anticancer, cytotoxic, antidiabetic, antimicrobial, antiobesity, neuroprotective and hepatoprotective activities. The current review provides an updated summary of the importance of willows, their chemical composition and pharmacological activities.
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Affiliation(s)
- Nora Tawfeek
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.,Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mona F Mahmoud
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Dalia I Hamdan
- Department of Pharmacognosy, Faculty of Pharmacy, Menoufia University, Shibin Elkom, Egypt
| | - Mansour Sobeh
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.,AgroBioSciences Research Division, Mohammed VI Polytechnic University, Ben-Guerir, Morocco
| | - Nawaal Farrag
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Assem M El-Shazly
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
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15
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Butterfield BJ, Palmquist EC, Hultine KR. Regional coordination between riparian dependence and atmospheric demand in willows (
Salix
L.) of western North America. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Bradley J. Butterfield
- Center for Ecosystem Science and Society (ECOSS) Northern Arizona University Flagstaff AZ USA
| | - Emily C. Palmquist
- Center for Ecosystem Science and Society (ECOSS) Northern Arizona University Flagstaff AZ USA
- U.S. Geological Survey Southwest Biological Science Center Grand Canyon Monitoring and Research Center Flagstaff AZ USA
| | - Kevin R. Hultine
- Department of Research, Conservation, and Collections Desert Botanical Garden Phoenix AZ USA
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16
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Sato S, Harris KM, Collet DM, Kim W, Yukawa J. Genetic variation in intraspecific populations of Rabdophaga rosaria (Diptera: Cecidomyiidae) indicating possible diversification scenarios into sibling species along with host range expansion on willows (Salicaceae: Salix). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
We analysed the COI gene of mitochondrial DNA extracted from larvae of Rabdophaga (Diptera: Cecidomyiidae) that induce rosette galls on Salix in the Holarctic Region. Genetic data show that they belong to species groups of Rabdophaga rosaria and Rabdophaga strobiloides. A maximum likelihood tree indicates that R. rosaria and R. strobiloides populations are divided into clades 1 and 2, respectively. Clade 1 is divided into subclades 1 and 2, and the latter is further divided into subclades 2A and 2B. Subclade 1 consists of populations on several Salix species of section Cinerella in subgenus Vetrix in Georgia and the UK. Subclade 2A contains populations on Salix alba (section Salix, subgenus Salix) in The Netherlands and the UK. Subclade 2B consists of populations on section Helix in Poland, Phylicifoliae in Alaska and Salix species in the Eastern Palaearctic Region. The genetic differences between populations of subclades 1, 2A and 2B range from 1.06 to 3.46%. We propose a possible diversification scenario of R. rosaria into sibling species through the expansion of host plant ranges. Clade 2 consists of R. strobiloides populations on two Alaskan Salix species of the sections Hastatae and Sitchenses in subgenus Vetrix.
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Affiliation(s)
- Shinsuke Sato
- Horticultural Institute, Ibaraki Agricultural Center, Ibaraki, Japan
| | | | | | - Wanggyu Kim
- Institute of Life Science and Natural Resources, Korea University, Seoul, South Korea
| | - Junichi Yukawa
- Entomological Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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17
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Wagner ND, He L, Hörandl E. Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data. FRONTIERS IN PLANT SCIENCE 2020; 11:1077. [PMID: 32765560 PMCID: PMC7379873 DOI: 10.3389/fpls.2020.01077] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/30/2020] [Indexed: 05/19/2023]
Abstract
Polyploidy is common in the genus Salix. However, little is known about the origin, parentage and genomic composition of polyploid species because of a lack of suitable molecular markers and analysis tools. We established a phylogenomic framework including species of all described sections of Eurasian shrub willows. We analyzed the genomic composition of seven polyploid willow species in comparison to putative diploid parental species to draw conclusions on their origin and the effects of backcrossing and post-origin evolution. We applied recently developed programs like SNAPP, HyDe, and SNiPloid to establish a bioinformatic pipeline for unravelling the complexity of polyploid genomes. RAD sequencing revealed 23,393 loci and 320,010 high quality SNPs for the analysis of relationships of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix). Polyploid willow species appear to be predominantly of allopolyploid origin. More ancient allopolyploidization events were observed for two hexaploid and one octoploid species, while our data suggested a more recent allopolyploid origin for the included tetraploids and identified putative parental taxa. SNiPloid analyses disentangled the different genomic signatures resulting from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid species. Our RAD sequencing data demonstrate that willow genomes are shaped by ancient and recent reticulate evolution, polyploidization, and post-origin divergence of species.
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Affiliation(s)
- Natascha D. Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Li He
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
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18
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Noleto-Dias C, Harflett C, Beale MH, Ward JL. Sulfated flavanones and dihydroflavonols from willow. PHYTOCHEMISTRY LETTERS 2020; 35:88-93. [PMID: 32025274 PMCID: PMC6988443 DOI: 10.1016/j.phytol.2019.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Phytochemical profiling of a hybrid species of willow, Salix × alberti L. (S. integra Thunb. × Salix suchowensis W.C. Cheng ex G.Zhu) revealed four sulfated flavonoids, which were then isolated from young stem tissue. The structures of dihydroflavonols (flavanonols) taxifolin-7-sulfate (1) and dihydrokaempferol-7-sulfate (2) and flavanones, eridictyol-7-sulfate (3) and naringenin-7-sulfate (4) were elucidated through NMR spectroscopy and high-resolution mass spectrometry. The identified sulfated flavanones and dihydroflavonols have not been previously seen in plants, but the former have been partially characterised as metabolites in mammalian metabolism of dietary flavonoids. In addition to providing full spectroscopic characterisation of these metabolites for the first time, we also compared the in vitro antioxidant properties, via the DPPH radical scavenging assay, of the parent and sulfated flavanones, which showed that 7-sulfation of taxifolin and eriodictyol attenuates but does not remove anti-oxidant activity.
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19
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Li MM, Wang DY, Zhang L, Kang MH, Lu ZQ, Zhu RB, Mao XX, Xi ZX, Tao M. Intergeneric Relationships within the Family Salicaceae s.l. based on Plastid Phylogenomics. Int J Mol Sci 2019; 20:ijms20153788. [PMID: 31382526 PMCID: PMC6696080 DOI: 10.3390/ijms20153788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022] Open
Abstract
Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l.
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Affiliation(s)
- Meng-Meng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - De-Yan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ming-Hui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhi-Qiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Ren-Bin Zhu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Xing-Xing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhen-Xiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ma Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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20
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Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5190425. [PMID: 31380427 PMCID: PMC6662467 DOI: 10.1155/2019/5190425] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/13/2019] [Indexed: 11/18/2022]
Abstract
Salix wilsonii is an important ornamental willow tree widely distributed in China. In this study, an integrated circular chloroplast genome was reconstructed for S. wilsonii based on the chloroplast reads screened from the whole-genome sequencing data generated with the PacBio RSII platform. The obtained pseudomolecule was 155,750 bp long and had a typical quadripartite structure, comprising a large single copy region (LSC, 84,638 bp) and a small single copy region (SSC, 16,282 bp) separated by two inverted repeat regions (IR, 27,415 bp). The S. wilsonii chloroplast genome encoded 115 unique genes, including four rRNA genes, 30 tRNA genes, 78 protein-coding genes, and three pseudogenes. Repetitive sequence analysis identified 32 tandem repeats, 22 forward repeats, two reverse repeats, and five palindromic repeats. Additionally, a total of 118 perfect microsatellites were detected, with mononucleotide repeats being the most common (89.83%). By comparing the S. wilsonii chloroplast genome with those of other rosid plant species, significant contractions or expansions were identified at the IR-LSC/SSC borders. Phylogenetic analysis of 17 willow species confirmed that S. wilsonii was most closely related to S. chaenomeloides and revealed the monophyly of the genus Salix. The complete S. wilsonii chloroplast genome provides an additional sequence-based resource for studying the evolution of organelle genomes in woody plants.
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21
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Xi H, Park J, Kim Y. The complete chloroplast genome sequence of rose-gold pussy willow, Salix gracilistyla Miq. (Salicaceae). Mitochondrial DNA B Resour 2019; 4:2118-2120. [PMID: 33365434 PMCID: PMC7687643 DOI: 10.1080/23802359.2019.1623115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/17/2019] [Indexed: 11/18/2022] Open
Abstract
To understand genetic background of Salix gracilistyla Miq., we presented its complete chloroplast genome which is 155,557 bp and has four sub regions: 84,530 bp of large single copy (LSC) and 16,218 bp of small single copy (SSC) regions are separated by 27,405 bp of inverted repeat (IR) regions including 130 genes (84 protein-coding gene, eight rRNAs, and 38 tRNAs). The overall GC content of the chloroplast genome is 36.7% and those in the LSC, SSC, and IR regions are 34.5%, 31.0%, and 41.9%, respectively. Phylogenetic trees show phylogenetic position of S. gracilistyla with low level of inter-species sequence variations.
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Affiliation(s)
- Hong Xi
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Jongsun Park
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Yongsung Kim
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
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22
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Zhao YJ, Liu XY, Guo R, Hu KR, Cao Y, Dai F. Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny. BMC Genomics 2019; 20:253. [PMID: 30925896 PMCID: PMC6440167 DOI: 10.1186/s12864-019-5627-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/20/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis to study the evolution patterns with the different origin and geographical distributions in the Salix phylogeny. RESULTS Transcript sequences of 10 Salicaceae species were downloaded from public databases. All pairwise of orthologues were identified by comparative analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of diverse. Divergence times were estimated in the 10 Salicaceae using comparative transcriptomic analysis. All of the fast-evolving positive selection sequences were identified, and some cold-, drought-, light-, universal-, and heat- resistance genes were discovered. CONCLUSIONS The divergence time of subgenus Vetrix and Salix was about 17.6-16.0 Mya during the period of Middle Miocene Climate Transition (21-14 Mya). Subgenus Vetrix diverged to migratory and resident groups when the climate changed to the cool and dry trend by 14 Mya. Cold- and light- stress genes were involved in positive selection among the resident Vetrix, and which would help them to adapt the cooling stage. Universal- stress genes exhibited positive selection among the migratory group and subgenus Salix. These data are useful for comprehending the adaptive evolution and speciation in the Salix lineage.
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Affiliation(s)
- You-jie Zhao
- Key Laboratory of Forestry and Ecological Big Data State Forestry Administration, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Xin-yi Liu
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Ran Guo
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Kun-rong Hu
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Yong Cao
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Fei Dai
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
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Kim J, Kim Y, Park J. Complete chloroplast genome sequence of the Salix koriyanagi Kimura ex Goerz (Salicaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1553521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Juhyeon Kim
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Korea
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Park J, Kim Y, Xi H. The complete chloroplast genome sequence of male individual of Korean endemic willow, Salix koriyanagi Kimura ex Goerz (Salicaceae). MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1602012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Jongsun Park
- InfoBoss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Hong Xi
- InfoBoss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
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Gramlich S, Wagner ND, Hörandl E. RAD-seq reveals genetic structure of the F 2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression. BMC PLANT BIOLOGY 2018; 18:317. [PMID: 30509159 PMCID: PMC6276181 DOI: 10.1186/s12870-018-1552-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/21/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Hybridization of species with porous genomes can eventually lead to introgression via repeated backcrossing. The potential for introgression between species is reflected by the extent of segregation distortion in later generation hybrids. Here we studied a population of hybrids between Salix purpurea and S. helvetica that has emerged within the last 30 years on a glacier forefield in the European Alps due to secondary contact of the parental species. We used 5758 biallelic SNPs produced by RAD sequencing with the aim to ascertain the predominance of backcrosses (F1 hybrid x parent) or F2 hybrids (F1 hybrid x F1 hybrid) among hybrid offspring. Further, the SNPs were used to study segregation distortion in the second hybrid generation. RESULTS The analyses in STRUCTURE and NewHybrids revealed that the population consisted of parents and F1 hybrids, whereas hybrid offspring consisted mainly of backcrosses to either parental species, but also some F2 hybrids. Although there was a clear genetic differentiation between S. purpurea and S. helvetica (FST = 0.24), there was no significant segregation distortion in the backcrosses or the F2 hybrids. Plant height of the backcrosses resembled the respective parental species, whereas F2 hybrids were more similar to the subalpine S. helvetica. CONCLUSIONS The co-occurrence of the parental species and the hybrids on the glacier forefield, the high frequency of backcrossing, and the low resistance to gene flow via backcrossing make a scenario of introgression in this young hybrid population highly likely, potentially leading to the transfer of adaptive traits. We further suggest that this willow hybrid population may serve as a model for the evolutionary processes initiated by recent global warming.
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Affiliation(s)
- Susanne Gramlich
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
| | - Natascha Dorothea Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
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Zhang L, Xi Z, Wang M, Guo X, Ma T. Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows. Ecol Evol 2018; 8:7817-7823. [PMID: 30250665 PMCID: PMC6145263 DOI: 10.1002/ece3.4261] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/27/2018] [Accepted: 05/17/2018] [Indexed: 11/09/2022] Open
Abstract
Phylogenetic relationships and lineage diversification of the family Salicaceae sensu lato (s.l.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, Flacourtia was identified as the most basal and the successive clades comprised both Itoa and Poliothyrsis, Idesia, two genera of the Salicaceae sensu stricto (s.s.) (Populus and Salix). Five major subclades were recovered within the Populus clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the Salix clade. Molecular dating suggested that species diversification of the major subclades in the Populus and Salix clades occurred mainly within the recent Pliocene. In addition, we found that the rpl32 gene was lost and the rps7 gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae s.l. Compared with previous studies, our results provide a well-resolved phylogeny from the perspective of the plastomes.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
| | - Zhenxiang Xi
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
| | - Mingcheng Wang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
| | - Xinyi Guo
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
| | - Tao Ma
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
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Wagner ND, Gramlich S, Hörandl E. RAD sequencing resolved phylogenetic relationships in European shrub willows ( Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs. Ecol Evol 2018; 8:8243-8255. [PMID: 30250699 PMCID: PMC6145212 DOI: 10.1002/ece3.4360] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/15/2018] [Accepted: 06/22/2018] [Indexed: 01/03/2023] Open
Abstract
The large and diverse genus Salix L. is of particular interest for decades of biological research. However, despite the morphological plasticity, the reconstruction of phylogenetic relationships was so far hampered by the lack of informative molecular markers. Infrageneric classification based on morphology separates dwarf shrubs (subg. Chamaetia) and taller shrubs (subg. Vetrix), while previous phylogenetic studies placed species of these two subgenera just in one largely unresolved clade. Here we want to test the utility of genomic RAD sequencing markers for resolving relationships at different levels of divergence in Salix. Based on a sampling of 15 European species representing 13 sections of the two subgenera, we used five different RAD sequencing datasets generated by ipyrad to conduct phylogenetic analyses. Additionally we reconstructed the evolution of growth form and analyzed the genetic composition of the whole clade. The results showed fully resolved trees in both ML and BI analysis with high statistical support. The two subgenera Chamaetia and Vetrix were recognized as nonmonophyletic, which suggests that they should be merged. Within the Vetrix/Chamaetia clade, a division into three major subclades could be observed. All species were confirmed to be monophyletic. Based on our data, arctic-alpine dwarf shrubs evolved four times independently. The structure analysis showed five mainly uniform genetic clusters which are congruent in sister relationships observed in the phylogenies. Our study confirmed RAD sequencing as a useful genomic tool for the reconstruction of relationships on different taxonomic levels in the genus Salix.
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Affiliation(s)
- Natascha Dorothea Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
| | - Susanne Gramlich
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
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Nissinen K, Virjamo V, Mehtätalo L, Lavola A, Valtonen A, Nybakken L, Julkunen-Tiitto R. A Seven-Year Study of Phenolic Concentrations of the Dioecious Salix myrsinifolia. J Chem Ecol 2018; 44:416-430. [DOI: 10.1007/s10886-018-0942-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 02/26/2018] [Accepted: 03/05/2018] [Indexed: 11/25/2022]
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Genetic Diversity and Genetic Relationships of Purple Willow (Salix purpurea L.) from Natural Locations. Int J Mol Sci 2017. [PMID: 29301207 DOI: 10.3390/ijms19010105.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this study, the genetic diversity and structure of 13 natural locations of Salix purpurea were determined with the use of AFLP (amplified length polymorphism), RAPD (randomly amplified polymorphic DNA) and ISSR (inter-simple sequence repeats). The genetic relationships between 91 examined S. purpurea genotypes were evaluated by analyses of molecular variance (AMOVA), principal coordinates analyses (PCoA) and UPGMA (unweighted pair group method with arithmetic mean) dendrograms for both single marker types and a combination of all marker systems. The locations were assigned to distinct regions and the analysis of AMOVA (analysis of molecular variance) revealed a high genetic diversity within locations. The genetic diversity between both regions and locations was relatively low, but typical for many woody plant species. The results noted for the analyzed marker types were generally comparable with few differences in the genetic relationships among S. purpurea locations. A combination of several marker systems could thus be ideally suited to understand genetic diversity patterns of the species. This study makes the first attempt to broaden our knowledge of the genetic parameters of the purple willow (S. purpurea) from natural location for research and several applications, inter alia breeding purposes.
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30
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Sulima P, Prinz K, Przyborowski JA. Genetic Diversity and Genetic Relationships of Purple Willow (Salix purpurea L.) from Natural Locations. Int J Mol Sci 2017; 19:ijms19010105. [PMID: 29301207 PMCID: PMC5796055 DOI: 10.3390/ijms19010105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/12/2017] [Accepted: 12/27/2017] [Indexed: 11/16/2022] Open
Abstract
In this study, the genetic diversity and structure of 13 natural locations of Salix purpurea were determined with the use of AFLP (amplified length polymorphism), RAPD (randomly amplified polymorphic DNA) and ISSR (inter-simple sequence repeats). The genetic relationships between 91 examined S. purpurea genotypes were evaluated by analyses of molecular variance (AMOVA), principal coordinates analyses (PCoA) and UPGMA (unweighted pair group method with arithmetic mean) dendrograms for both single marker types and a combination of all marker systems. The locations were assigned to distinct regions and the analysis of AMOVA (analysis of molecular variance) revealed a high genetic diversity within locations. The genetic diversity between both regions and locations was relatively low, but typical for many woody plant species. The results noted for the analyzed marker types were generally comparable with few differences in the genetic relationships among S. purpurea locations. A combination of several marker systems could thus be ideally suited to understand genetic diversity patterns of the species. This study makes the first attempt to broaden our knowledge of the genetic parameters of the purple willow (S. purpurea) from natural location for research and several applications, inter alia breeding purposes.
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Affiliation(s)
- Paweł Sulima
- Department of Plant Breeding and Seed Production, University of Warmia and Mazury in Olsztyn, 10-724 Olsztyn, Poland.
| | - Kathleen Prinz
- Institute for Systematic Botany, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany.
| | - Jerzy A Przyborowski
- Department of Plant Breeding and Seed Production, University of Warmia and Mazury in Olsztyn, 10-724 Olsztyn, Poland.
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31
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Yanitch A, Brereton NJB, Gonzalez E, Labrecque M, Joly S, Pitre FE. Transcriptomic Response of Purple Willow ( Salix purpurea) to Arsenic Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:1115. [PMID: 28702037 PMCID: PMC5487440 DOI: 10.3389/fpls.2017.01115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/09/2017] [Indexed: 05/25/2023]
Abstract
Arsenic (As) is a toxic element for plants and one of the most common anthropogenic pollutants found at contaminated sites. Despite its severe effects on plant metabolism, several species can accumulate substantial amounts of arsenic and endure the associated stress. However, the genetic mechanisms involved in arsenic tolerance remains obscure in many model plant species used for land decontamination (phytoremediation), including willows. The present study assesses the potential of Salix purpurea cv. 'Fish Creek' for arsenic phytoextraction and reveals the genetic responses behind arsenic tolerance, phytoextraction and metabolism. Four weeks of hydroponic exposure to 0, 5, 30 and 100 mg/L revealed that plants were able to tolerate up to 5 mg/L arsenic. Concentrations of 0 and 5 mg/L of arsenic treatment were then used to compare alterations in gene expression of roots, stems and leaves using RNA sequencing. Differential gene expression revealed transcripts encoding proteins putatively involved in entry of arsenic into the roots, storage in vacuoles and potential transport through the plant as well as primary and secondary (indirect) toxicity tolerance mechanisms. A major role for tannin as a compound used to relieve cellular toxicity is implicated as well as unexpected expression of the cadmium transporter CAX2, providing a potential means for internal arsenic mobility. These insights into the underpinning genetics of a successful phytoremediating species present novel opportunities for selection of dedicated arsenic tolerant crops as well as the potential to integrate such tolerances into a wider Salix ideotype alongside traits including biomass yield, biomass quality, low agricultural inputs and phytochemical production.
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Affiliation(s)
- Aymeric Yanitch
- Institut de Recherche en Biologie Végétale, University of MontrealMontréal, QC, Canada
| | | | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, C3G Montreal Node, McGill University and Genome Quebec Innovation CentreMontréal, QC, Canada
| | - Michel Labrecque
- Institut de Recherche en Biologie Végétale, University of MontrealMontréal, QC, Canada
- Montreal Botanical GardenMontréal, QC, Canada
| | - Simon Joly
- Institut de Recherche en Biologie Végétale, University of MontrealMontréal, QC, Canada
- Montreal Botanical GardenMontréal, QC, Canada
| | - Frederic E. Pitre
- Institut de Recherche en Biologie Végétale, University of MontrealMontréal, QC, Canada
- Montreal Botanical GardenMontréal, QC, Canada
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Braukmann TWA, Kuzmina ML, Sills J, Zakharov EV, Hebert PDN. Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. PLoS One 2017; 12:e0169515. [PMID: 28072819 PMCID: PMC5224991 DOI: 10.1371/journal.pone.0169515] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/18/2016] [Indexed: 01/30/2023] Open
Abstract
Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is highest.
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Affiliation(s)
- Thomas W. A. Braukmann
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Maria L. Kuzmina
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jesse Sills
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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Liu X, Wang Z, Wang D, Zhang J. Phylogeny of Populus-Salix (Salicaceae) and their relative genera using molecular datasets. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Brereton NJB, Gonzalez E, Marleau J, Nissim WG, Labrecque M, Joly S, Pitre FE. Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants. PLANT PHYSIOLOGY 2016; 171:3-24. [PMID: 27002060 PMCID: PMC4854704 DOI: 10.1104/pp.16.00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/20/2016] [Indexed: 05/09/2023]
Abstract
Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/β-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system.
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Affiliation(s)
- Nicholas J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Emmanuel Gonzalez
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Julie Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Werther Guidi Nissim
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Michel Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Simon Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Frederic E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
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Lauron-Moreau A, Pitre FE, Argus GW, Labrecque M, Brouillet L. Correction: Phylogenetic Relationships of American Willows (Salix L., Salicaceae). PLoS One 2015; 10:e0138963. [PMID: 26384334 PMCID: PMC4575191 DOI: 10.1371/journal.pone.0138963] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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