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Göttlinger T, Pirritano M, Simon M, Fuß J, Lohaus G. Metabolic and transcriptomic analyses of nectaries reveal differences in the mechanism of nectar production between monocots (Ananas comosus) and dicots (Nicotiana tabacum). BMC PLANT BIOLOGY 2024; 24:940. [PMID: 39385091 PMCID: PMC11462711 DOI: 10.1186/s12870-024-05630-3] [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: 06/22/2024] [Accepted: 09/24/2024] [Indexed: 10/11/2024]
Abstract
BACKGROUND Nectar is offered by numerous flowering plants to attract pollinators. To date, the production and secretion of nectar have been analyzed mainly in eudicots, particularly rosids such as Arabidopsis. However, due to the enormous diversity of flowering plants, further research on other plant species, especially monocots, is needed. Ananas comosus (monocot) is an economically important species that is ideal for such analyses because it produces easily accessible nectar in sufficient quantities. In addition, the analyses were also carried out with Nicotiana tabacum (dicot, asterids) for comparison. RESULTS We performed transcriptome sequencing (RNA-Seq) analyses of the nectaries of Ananas comosus and Nicotiana tabacum, to test whether the mechanisms described for nectar production and secretion in Arabidopsis are also present in these plant species. The focus of these analyses is on carbohydrate metabolism and transport (e.g., sucrose-phosphate synthases, invertases, sucrose synthases, SWEETs and further sugar transporters). In addition, the metabolites were analyzed in the nectar, nectaries and leaves of both plant species to address the question of whether concentration gradients for different metabolites exist between the nectaries and nectar The nectar of N. tabacum contains large amounts of glucose, fructose and sucrose, and the sucrose concentration in the nectar appears to be similar to the sucrose concentration in the nectaries. Nectar production and secretion in this species closely resemble corresponding processes in some other dicots, including sucrose synthesis in nectaries and sucrose secretion by SWEET9. The nectar of A. comosus also contains large amounts of glucose, fructose and sucrose and in this species the sucrose concentration in the nectar appears to be higher than the sucrose concentration in the nectaries. Furthermore, orthologs of SWEET9 generally appear to be absent in A. comosus and other monocots. Therefore, sucrose export by SWEETs from nectaries into nectar can be excluded; rather, other mechanisms, such as active sugar export or exocytosis, are more likely. CONCLUSION The mechanisms of nectar production and secretion in N. tabacum appear to be largely similar to those in other dicots, whereas in the monocotyledonous species A. comosus, different synthesis and transport processes are involved.
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Affiliation(s)
- Thomas Göttlinger
- Molecular Plant Science/Plant Biochemistry, University of Wuppertal, Wuppertal, Germany.
| | - Marcello Pirritano
- Molecular Cell Biology and Microbiology, University of Wuppertal, Wuppertal, Germany
| | - Martin Simon
- Molecular Cell Biology and Microbiology, University of Wuppertal, Wuppertal, Germany
| | - Janina Fuß
- Competence Centre for Genomic Analysis, Kiel, Germany
| | - Gertrud Lohaus
- Molecular Plant Science/Plant Biochemistry, University of Wuppertal, Wuppertal, Germany
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Fiesel PD, Kerwin RE, Jones AD, Last RL. Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes. PLANT PHYSIOLOGY 2024; 196:1231-1253. [PMID: 38748602 PMCID: PMC11444299 DOI: 10.1093/plphys/kiae279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/19/2024] [Accepted: 05/01/2024] [Indexed: 05/28/2024]
Abstract
Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by ACYLSUGAR ACYLTRANSFERASE (ASAT) enzymes from sugars and acyl-coenzyme A esters. Published research has revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars have been analyzed across a small fraction of the >1,200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the clade II species brinjal eggplant (Solanum melongena) led to the identification of eight unusual structures with inositol or inositol glycoside cores and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity, with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the brinjal eggplant ASAT 3-LIKE 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.
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Affiliation(s)
- Paul D Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48823, USA
| | - Rachel E Kerwin
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48823, USA
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48823, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48823, USA
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48823, USA
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Pereira L. A tale of sugars' tails-diverse acyl chains decorate sugars in Solanum species' trichomes. PLANT PHYSIOLOGY 2024; 196:686-688. [PMID: 38876086 PMCID: PMC11444274 DOI: 10.1093/plphys/kiae345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Affiliation(s)
- Lara Pereira
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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Frank K, Nagy E, Taller J, Wolf I, Polgár Z. Characterisation of the complete chloroplast genome of Solanum tuberosum cv. White Lady. Biol Futur 2024:10.1007/s42977-024-00240-4. [PMID: 39251554 DOI: 10.1007/s42977-024-00240-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/24/2024] [Indexed: 09/11/2024]
Abstract
Potato (Solanum tuberosum) is considered worldwide as one of the most important non-cereal food crops. As a result of its adaptability and worldwide production area, potato displays a vast phenotypical variability as well as genomic diversity. Chloroplast genomes have long been a core issue in plant molecular evolution and phylogenetic studies, and have an important role in revealing photosynthetic mechanisms, metabolic regulations and the adaptive evolution of plants. We sequenced the complete chloroplast genome of the Hungarian cultivar White Lady, which is 155 549 base pairs (bp) in length and is characterised by the typical quadripartite structure composed of a large- and small single-copy region (85 991 bp and 18 374 bp, respectively) interspersed by two identical inverted repeats (25 592 bp). The genome consists of 127 genes of which 82 are protein-coding, eight are ribosomal RNAs and 37 are transfer RNAs. The overall gene content and distribution of the genes on the White Lady chloroplast was the same as found in other potato chloroplasts. The alignment of S. tuberosum chloroplast genome sequences resulted in a highly resolved tree, with 10 out of the 13 nodes recovered having bootstrap values over 90%. By comparing the White Lady chloroplast genome with available S. tuberosum sequences we found that gene content and synteny are highly conserved. The new chloroplast sequence can support further studies of genetic diversity, resource conservation, evolution and applied agricultural research. The new sequence can support further potato genetic diversity and evolutionary studies, resource conservation, and also applied agricultural research.
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Affiliation(s)
- Krisztián Frank
- Potato Research Centre, MATE Agrárcsoport Kft., Keszthely, Hungary.
| | - Erzsébet Nagy
- Festetics Bioinnovation Group, Institute of Genetics and Biotechnology, Hungarian University of Agricultural and Life Sciences, Keszthely, Hungary
| | - János Taller
- Festetics Bioinnovation Group, Institute of Genetics and Biotechnology, Hungarian University of Agricultural and Life Sciences, Keszthely, Hungary
| | - István Wolf
- Potato Research Centre, MATE Agrárcsoport Kft., Keszthely, Hungary
| | - Zsolt Polgár
- Potato Research Centre, MATE Agrárcsoport Kft., Keszthely, Hungary
- Department of Agronomy, Hungarian University of Agricultural and Life Sciences, Georgikon Campus, Keszthely, Hungary
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Pezzi PH, Wheeler LC, Freitas LB, Smith SD. Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae). Mol Phylogenet Evol 2024; 198:108136. [PMID: 38909873 DOI: 10.1016/j.ympev.2024.108136] [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: 03/27/2024] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.
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Affiliation(s)
- Pedro H Pezzi
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
| | - Lucas C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
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Khatun MS, Islam MSU, Shing P, Zohra FT, Rashid SB, Rahman SM, Sarkar MAR. Genome-wide identification and characterization of FORMIN gene family in potato (Solanum tuberosum L.) and their expression profiles in response to drought stress condition. PLoS One 2024; 19:e0309353. [PMID: 39186738 PMCID: PMC11346945 DOI: 10.1371/journal.pone.0309353] [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: 04/11/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024] Open
Abstract
Formin proteins, characterized by the FH2 domain, are critical in regulating actin-driven cellular processes and cytoskeletal dynamics during abiotic stress. However, no genome-wide analysis of the formin gene family has yet to be conducted in the economically significant plant potato (Solanum tuberosum L.). In this study, 26 formin genes were identified and characterized in the potato genome (named as StFH), each containing the typical FH2 domain and distributed across the ten chromosomes. The StFH was categorized into seven subgroups (A-G) and the gene structure and motif analysis demonstrated higher structural similarities within the subgroups. Besides, the StFH exhibited ancestry and functional similarities with Arabidopsis. The Ka/Ks ratio indicated that StFH gene pairs were evolving through purifying selection, with five gene pairs exhibiting segmental duplications and two pairs exhibiting tandem duplications. Subcellular localization analysis suggested that most of the StFH genes were located in the chloroplast and plasma membrane. Moreover, 54 cis-acting regulatory elements (CAREs) were identified in the promoter regions, some of which were associated with stress responses. According to gene ontology analysis, the majority of the StFH genes were involved in biological processes, with 63 out of 74 GO terms affecting actin polymerization. Six major transcription factor families, including bZIP, C2H2, ERF, GATA, LBD, NAC, and HSF, were identified that were involved in the regulation of StFH genes in various abiotic stresses, including drought. Further, the 60 unique microRNAs targeted 24 StFH by regulating gene expression in response to drought stress were identified. The expression of StFH genes in 14 different tissues, particularly in drought-responsive tissues such as root, stem, shoot apex, and leaf, underscores their significance in managing drought stress. RNA-seq analysis of the drought-resistant Qingshu No. 9 variety revealed the potential role of up-regulated genes, including StFH2, StFH10, StFH19, and StFH25, in alleviating drought stress. Overall, these findings provide crucial insights into the response to drought stress in potatoes and can be utilized in breeding programs to develop potato cultivars with enhanced drought-tolerant traits.
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Affiliation(s)
- Mst. Sumaiya Khatun
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Shohel Ul Islam
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Pollob Shing
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Shuraya Beente Rashid
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Shaikh Mizanur Rahman
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
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Sebastin R, Kim J, Jo IH, Yu JK, Jang W, Han S, Park HS, AlGarawi AM, Hatamleh AA, So YS, Shim D, Chung JW. Comparative chloroplast genome analyses of cultivated and wild Capsicum species shed light on evolution and phylogeny. BMC PLANT BIOLOGY 2024; 24:797. [PMID: 39179978 PMCID: PMC11344449 DOI: 10.1186/s12870-024-05513-7] [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: 05/16/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
The chloroplast (cp.) genome, also known as plastome, plays crucial roles in plant survival, adaptation, and evolution. The stable genetic structure of cp. genomes provides an ideal system for investigating species evolution. We sequenced three complete cp. genome sequences of Capsicum species and analyzed them using sequences of various Capsicum species retrieved from the NCBI database. The cp. genome of Capsicum species maintains a well-preserved quadripartite structure consisting of two inverted repeats (IRs) flanked by a large single copy (LSC) region and a small single copy (SSC) region. The sizes of cp. genome sequences ranged from 156,583 bp (C. lycianthoides) to 157,390 bp (C.pubescens). A total of 127-132 unique genes, including 83-87 protein-coding, 36-37 tRNA, and eight rRNA genes, were predicted. Comparison of cp. genomes of 10 Capsicum species revealed high sequence similarity in genome-wide organization and gene arrangements. Fragments of trnT-UGU/trnL-UAA, ccsA, ndhD, rps12, and ycf1 were identified as variable regions, and nucleotide variability of LSC and SSC was higher than that of IR. Phylogenetic speciation analysis showed that the major domesticated C. annuum species were the most extensively divergent species and closely related to C. tovarii and C. frutescens. Analysis of divergent times suggested that a substantial range of speciation events started occurring ~ 25.79 million years ago (Mya). Overall, comparative analysis of cp. genomes of Capsicum species not only offers new insights into their genetic variation and phylogenetic relationships, but also lays a foundation for evolutionary history, genetic diversity, conservation, and biological breeding of Capsicum species.
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Affiliation(s)
- Raveendar Sebastin
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jaewook Kim
- Department of Biology Education, Korea National University of Education, Cheongju, 28173, Republic of Korea
| | - Ick-Hyun Jo
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ju-Kyung Yu
- Department of Crop Science, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Woojong Jang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, 58245, Republic of Korea
| | - Seahee Han
- Honam National Institute of Biological Resources, Mokpo, 58762, Republic of Korea
| | - Hyun-Seung Park
- Department of Integrative Biological Sciences and Industry, Convergence Research Center for Natural Products, Sejong University, Seoul, 05006, Republic of Korea
| | - Amal Mohamed AlGarawi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Donghwan Shim
- Department of Biological Science, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Hagen ER, Vasconcelos T, Boyko JD, Beaulieu JM. Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multiclade perspective. AMERICAN JOURNAL OF BOTANY 2024; 111:e16356. [PMID: 38867412 DOI: 10.1002/ajb2.16356] [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: 05/06/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
PREMISE The proportion of polyploid plants in a community increases with latitude, and different hypotheses have been proposed about which factors drive this pattern. Here, we aimed to understand the historical causes of the latitudinal polyploidy gradient using a combination of ancestral state reconstruction methods. Specifically, we assessed whether (1) polyploidization enables movement to higher latitudes (i.e., polyploidization precedes occurrences in higher latitudes) or (2) higher latitudes facilitate polyploidization (i.e., occurrence in higher latitudes precedes polyploidization). METHODS We reconstructed the ploidy states and ancestral niches of 1032 angiosperm species at four paleoclimatic time slices ranging from 3.3 million years ago to the present, comprising taxa from four well-represented clades: Onagraceae, Primulaceae, Solanum (Solanaceae), and Pooideae (Poaceae). We used ancestral niche reconstruction models alongside a customized discrete character evolution model to allow reconstruction of states at specific time slices. Patterns of latitudinal movement were reconstructed and compared in relation to inferred ploidy shifts. RESULTS No single hypothesis applied equally well across all analyzed clades. While significant differences in median latitudinal occurrence were detected in the largest clade, Poaceae, no significant differences were detected in latitudinal movement in any clade. CONCLUSIONS Our preliminary study is the first to attempt to connect ploidy changes to continuous latitudinal movement, but we cannot favor one hypothesis over another. Given that patterns seem to be clade-specific, more clades must be analyzed in future studies for generalities to be drawn.
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Affiliation(s)
- Eric R Hagen
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, ON, Canada
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - James D Boyko
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
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Knapp S. A revision of Lycianthes (Solanaceae) in tropical Asia. PHYTOKEYS 2024; 245:1-106. [PMID: 39113755 PMCID: PMC11301032 DOI: 10.3897/phytokeys.245.121988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/31/2024] [Indexed: 08/10/2024]
Abstract
The genus Lycianthes (Dunal) Hassl. (Solanaceae) has in the past been treated as a section of the large genus Solanum L. but is more closely related to Capsicum L. Outside of the Americas, where the highest species diversity occurs, the genus is found in tropical and subtropical habitats from India to Japan and the Philippines, including the islands of Indonesia, New Guinea and the Solomons. The 19 species from Australia, New Guinea and the Pacific were treated in 'PhytoKeys 209'. Here I treat the remaining 10 species occurring across Asia; including two native species, L.biflora (Lour.) Bitter and L.oliveriana (Lauterb. & K.Schum) Bitter, and one cultivated species, L.rantonnetii (Carrière) Bitter that were also included in the earlier work. The Asian species treated here occupy a wide range of forested and disturbed habitats and are diverse in habit, ranging from epiphytic vines to small or medium sized trees, shrubs or creeping herbs. Many of the species are weedy plants of highly disturbed habitats and are best characterised as "ochlospecies", with complex polymorphic variation. Lycianthesrantonnetii, a species native to southern South America, is recorded as cultivated in India and Pakistan, but may be more widespread than collections indicate. The history of taxonomic treatments of Lycianthes in Asia is discussed, along with details of morphology found in all species. All species are treated in full, with complete morphological descriptions, including synonymy, lecto- or neotypifications, discussions of ecology and vernacular names, distribution maps and preliminary conservation assessments (for all except the cultivated L.rantonnetii). Searchable lists of all specimens examined are presented as Suppl. materials 1, 2.
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Affiliation(s)
- Sandra Knapp
- Natural History Museum, Cromwell Road, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
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10
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Messeder JVS, Carlo TA, Zhang G, Tovar JD, Arana C, Huang J, Huang CH, Ma H. A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L. THE NEW PHYTOLOGIST 2024; 243:765-780. [PMID: 38798267 DOI: 10.1111/nph.19849] [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: 12/15/2023] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Mutualisms between plants and fruit-eating animals were key to the radiation of angiosperms. Still, phylogenetic uncertainties limit our understanding of fleshy-fruit evolution, as in the case of Solanum, a genus with remarkable fleshy-fruit diversity, but with unresolved phylogenetic relationships. We used 1786 nuclear genes from 247 species, including 122 newly generated transcriptomes/genomes, to reconstruct the Solanum phylogeny and examine the tempo and mode of the evolution of fruit color and size. Our analysis resolved the backbone phylogeny of Solanum, providing high support for its clades. Our results pushed back the origin of Solanum to 53.1 million years ago (Ma), with most major clades diverging between 35 and 27 Ma. Evolution of Solanum fruit color and size revealed high levels of trait conservatism, where medium-sized berries that remain green when ripe are the likely ancestral form. Our analyses revealed that fruit size and color are evolutionary correlated, where dull-colored fruits are two times larger than black/purple and red fruits. We conclude that the strong phylogenetic conservatism shown in the color and size of Solanum fruits could limit the influences of fruit-eating animals on fleshy-fruit evolution. Our findings highlight the importance of phylogenetic constraints on the diversification of fleshy-fruit functional traits.
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Affiliation(s)
- João Vitor S Messeder
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Graduate Program in Ecology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tomás A Carlo
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Graduate Program in Ecology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Guojin Zhang
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Juan David Tovar
- Programa de Pós-Graduação em Botânica, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, 69060-001, Brazil
| | - César Arana
- Museo de Historia Natural and Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, 15072, Peru
| | - Jie Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia University, Hohhot, 010000, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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11
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Zhang L, Zhang E, Wei Y, Zheng G. Phylogenetic analysis and divergence time estimation of Lycium species in China based on the chloroplast genomes. BMC Genomics 2024; 25:569. [PMID: 38844874 PMCID: PMC11155141 DOI: 10.1186/s12864-024-10487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Lycium is an economically and ecologically important genus of shrubs, consisting of approximately 70 species distributed worldwide, 15 of which are located in China. Despite the economic and ecological importance of Lycium, its phylogeny, interspecific relationships, and evolutionary history remain relatively unknown. In this study, we constructed a phylogeny and estimated divergence time based on the chloroplast genomes (CPGs) of 15 species, including subspecies, of the genus Lycium from China. RESULTS We sequenced and annotated 15 CPGs in this study. Comparative analysis of these genomes from these Lycium species revealed a typical quadripartite structure, with a total sequence length ranging from 154,890 to 155,677 base pairs (bp). The CPGs was highly conserved and moderately differentiated. Through annotation, we identified a total of 128-132 genes. Analysis of the boundaries of inverted repeat (IR) regions showed consistent positioning: the junctions of the IRb/LSC region were located in rps19 in all Lycium species, IRb/SSC between the ycf1 and ndhF genes, and SSC/IRa within the ycf1 gene. Sequence variation in the SSC region exceeded that in the IR region. We did not detect major expansions or contractions in the IR region or rearrangements or insertions in the CPGs of the 15 Lycium species. Comparative analyses revealed five hotspot regions in the CPG: trnR(UCU), atpF-atpH, ycf3-trnS(GGA), trnS(GGA), and trnL-UAG, which could potentially serve as molecular markers. In addition, phylogenetic tree construction based on the CPG indicated that the 15 Lycium species formed a monophyletic group and were divided into two typical subbranches and three minor branches. Molecular dating suggested that Lycium diverged from its sister genus approximately 17.7 million years ago (Mya) and species diversification within the Lycium species of China primarily occurred during the recent Pliocene epoch. CONCLUSION The divergence time estimation presented in this study will facilitate future research on Lycium, aid in species differentiation, and facilitate diverse investigations into this economically and ecologically important genus.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Erdong Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Yuqing Wei
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Guoqi Zheng
- Key Laboratory of the Ministry of Education for Protection and Utilization of Special Biological Resources in the Western, School of Life Science, Ningxia University, Yinchuan, Ningxia, 750021, China.
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12
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Moore CD, Farman DI, Särkinen T, Stevenson PC, Vallejo-Marín M. Floral scent changes in response to pollen removal are rare in buzz-pollinated Solanum. PLANTA 2024; 260:15. [PMID: 38829528 PMCID: PMC11147924 DOI: 10.1007/s00425-024-04403-4] [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: 11/26/2023] [Accepted: 03/30/2024] [Indexed: 06/05/2024]
Abstract
MAIN CONCLUSION One of seven Solanum taxa studied displayed associations between pollen presence and floral scent composition and volume, suggesting buzz-pollinated plants rarely use scent as an honest cue for foraging pollinators. Floral scent influences the recruitment, learning, and behaviour of floral visitors. Variation in floral scent can provide information on the amount of reward available or whether a flower has been visited recently and may be particularly important in species with visually concealed rewards. In many buzz-pollinated flowers, tubular anthers opening via small apical pores (poricidal anthers) visually conceal pollen and appear similar regardless of pollen quantity within the anther. We investigated whether pollen removal changes floral scent composition and emission rate in seven taxa of buzz-pollinated Solanum (Solanaceae). We found that pollen removal reduced both the overall emission of floral scent and the emission of specific compounds (linalool and farnesol) in S. lumholtzianum. Our findings suggest that in six out of seven buzz-pollinated taxa studied here, floral scent could not be used as a signal by visitors as it does not contain information on pollen availability.
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Affiliation(s)
- C Douglas Moore
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK.
| | - Dudley I Farman
- Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, UK
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Philip C Stevenson
- Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, UK
- Royal Botanic Gardens, Kew Green, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Mario Vallejo-Marín
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 752 36, Uppsala, Sweden
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13
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Li Z, Liu J, Liang M, Guo Y, Chen X, Wu H, Jin S. De novo assembly of the complete mitochondrial genome of pepino (Solanum muricatum) using PacBio HiFi sequencing: insights into structure, phylogenetic implications, and RNA editing. BMC PLANT BIOLOGY 2024; 24:361. [PMID: 38702620 PMCID: PMC11069145 DOI: 10.1186/s12870-024-04978-w] [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: 10/29/2023] [Accepted: 04/02/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Solanum muricatum is an emerging horticultural fruit crop with rich nutritional and antioxidant properties. Although the chromosome-scale genome of this species has been sequenced, its mitochondrial genome sequence has not been reported to date. RESULTS PacBio HiFi sequencing was used to assemble the circular mitogenome of S. muricatum, which was 433,466 bp in length. In total, 38 protein-coding, 19 tRNA, and 3 rRNA genes were annotated. The reticulate mitochondrial conformations with multiple junctions were verified by polymerase chain reaction, and codon usage, sequence repeats, and gene migration from chloroplast to mitochondrial genome were determined. A collinearity analysis of eight Solanum mitogenomes revealed high structural variability. Overall, 585 RNA editing sites in protein coding genes were identified based on RNA-seq data. Among them, mttB was the most frequently edited (52 times), followed by ccmB (46 times). A phylogenetic analysis based on the S. muricatum mitogenome and those of 39 other taxa (including 25 Solanaceae species) revealed the evolutionary and taxonomic status of S. muricatum. CONCLUSIONS We provide the first report of the assembled and annotated S. muricatum mitogenome. This information will help to lay the groundwork for future research on the evolutionary biology of Solanaceae species. Furthermore, the results will assist the development of molecular breeding strategies for S. muricatum based on the most beneficial agronomic traits of this species.
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Affiliation(s)
- Ziwei Li
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jiaxun Liu
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Mingtai Liang
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Yanbing Guo
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xia Chen
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Hongzhi Wu
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Shoulin Jin
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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14
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Moonlight PW, Baldaszti L, Cardoso D, Elliott A, Särkinen T, Knapp S. Twenty years of big plant genera. Proc Biol Sci 2024; 291:20240702. [PMID: 38808446 DOI: 10.1098/rspb.2024.0702] [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: 03/24/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
In 2004, David Frodin published a landmark review of the history and concepts of big plant genera. Two decades of taxonomic activity have taken place since, coinciding with a revolution in phylogenetics and taxonomic bioinformatics. Here we use data from the World Flora Online (WFO) to provide an updated list of big (more than 500 species) and megadiverse (more than 1000 species) flowering plant genera and highlight changes since 2004. The number of big genera has increased from 57 to 86; today one of every four plant species is classified as a member of a big genus, with 14% in just 28 megadiverse genera. Most (71%) of the growth in big genera since 2000 is the result of new species description, not generic re-circumscription. More than 15% of all currently accepted flowering plant species described in the last two decades are in big genera, suggesting that groups previously considered intractable are now being actively studied taxonomically. Despite this rapid growth in big genera, they remain a significant yet understudied proportion of plant diversity. They represent a significant proportion of global plant diversity and should remain a priority not only for taxonomy but for understanding global diversity patterns and plant evolution in general.
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Affiliation(s)
- Peter W Moonlight
- Botany Department, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Ludwig Baldaszti
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Domingos Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
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15
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Ames M, Hamernik A, Behling W, Douches DS, Halterman DA, Bethke PC. A survey of the Sli gene in wild and cultivated potato. PLANT DIRECT 2024; 8:e589. [PMID: 38766508 PMCID: PMC11099725 DOI: 10.1002/pld3.589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/27/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Inbred-hybrid breeding of diploid potatoes necessitates breeding lines that are self-compatible. One way of incorporating self-compatibility into incompatible cultivated potato (Solanum tuberosum) germplasm is to introduce the S-locus inhibitor gene (Sli), which functions as a dominant inhibitor of gametophytic self-incompatibility. To learn more about Sli diversity and function in wild species relatives of cultivated potato, we obtained Sli gene sequences that extended from the 5'UTR to the 3'UTR from 133 individuals from 22 wild species relatives of potato and eight diverse cultivated potato clones. DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. DNA sequences in one group contain the 533 bp insertion upstream of the start codon identified previously in self-compatible potato. The second group lacks the insertion. Three diploid and four polyploid individuals of wild species collected from geographically disjointed localities contained Sli with the 533 bp insertion. For most of the wild species clones examined, however, Sli did not have the insertion. Phylogenetic analysis indicated that Sli sequences with the insertion, in wild species and in cultivated clones, trace back to a single origin. Some diploid wild potatoes that have Sli with the insertion were self-incompatible and some wild potatoes that lack the insertion were self-compatible. Although there is evidence of positive selection for some codon positions in Sli, there is no evidence of diversifying selection at the gene level. In silico analysis of Sli protein structure did not support the hypothesis that amino acid changes from wild-type (no insertion) to insertion-type account for changes in protein function. Our study demonstrated that genetic factors besides the Sli gene must be important for conditioning a switch in the mating system from self-incompatible to self-compatible in wild potatoes.
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Affiliation(s)
- Mercedes Ames
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Andy Hamernik
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - William Behling
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - David S. Douches
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Dennis A. Halterman
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Paul C. Bethke
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
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16
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Kerwin RE, Hart JE, Fiesel PD, Lou YR, Fan P, Jones AD, Last RL. Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster. SCIENCE ADVANCES 2024; 10:eadn3991. [PMID: 38657073 PMCID: PMC11094762 DOI: 10.1126/sciadv.adn3991] [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] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Tremendous plant metabolic diversity arises from phylogenetically restricted specialized metabolic pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing in biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and the role of BGCs in pathway evolution remain underappreciated. In this study, we investigated the mechanisms driving acylsugar evolution in the Solanaceae. Previously thought to be restricted to glandular trichomes, acylsugars were recently found in cultivated tomato roots. We demonstrated that acylsugars in cultivated tomato roots and trichomes have different sugar cores, identified root-enriched paralogs of trichome acylsugar pathway genes, and characterized a key paralog required for root acylsugar biosynthesis, SlASAT1-LIKE (SlASAT1-L), which is nested within a previously reported trichome acylsugar BGC. Last, we provided evidence that ASAT1-L arose through duplication of its paralog, ASAT1, and was trichome-expressed before acquiring root-specific expression in the Solanum genus. Our results illuminate the genomic context and molecular mechanisms underpinning metabolic diversity in plants.
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Affiliation(s)
- Rachel E. Kerwin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jaynee E. Hart
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Paul D. Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - A. Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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17
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Fiesel PD, Kerwin RE, Daniel Jones A, Last RL. Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.05.542877. [PMID: 37333341 PMCID: PMC10274652 DOI: 10.1101/2023.06.05.542877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by AcylSugar AcylTransferases from sugars and acyl-coenzyme A esters. Published research revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars were analyzed across a small fraction of the >1200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of the Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the Clade II species Solanum melongena (brinjal eggplant) led to the identification of eight unusual structures with inositol or inositol glycoside cores, and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the S. melongena AcylSugar AcylTransferase 3-Like 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.
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Affiliation(s)
- Paul D. Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
| | - Rachel E. Kerwin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
| | - A. Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823 USA
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18
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de Souza GT, Torquato IHS, Castro CC. Understanding the relations between Solanaceae crops and their pollinators: a global meta-network. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:157-165. [PMID: 38192089 DOI: 10.1111/plb.13616] [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: 07/13/2023] [Accepted: 11/14/2023] [Indexed: 01/10/2024]
Abstract
Crop-pollinator interactions are essential for world food security. Studying crop pollination from a network approach allows identification of target pollinators for conservation and management, and gaps in our knowledge. Solanaceae represents the third highest ranked family based on economic value, and its production is highly improved by animal pollination. This study aimed to integrate global data on solanaceous crop pollination and analyse the interaction patterns using a meta-network approach. Our questions were: (i) how are interactions structured and what are the structuring roles of species; and (ii) what are the main gaps in our knowledge? Data were obtained through a systematic review of the main scientific databases. The network structure was described using connectivity and modularity calculations, and the role of species using centrality metrics. The 251 pollinator species reported were in seven orders, mainly Hymenoptera (84.9%). The generalists Bombus and Apis species were the most common pollinators. The meta-network was modular, and all modules mostly included bees. Most species were peripherals, around 12% were connectors, and there were no module hubs. Apis mellifera was the only network hub (supergeneralist). The most important pollinators are the most managed pollinators worldwide; however, many native species play a role in structuring the meta-network. Main gaps include species of importance to pepper pollination, lack of species-specific identification, and the need for more robust experimental studies evaluating the pollination efficiency of native, manageable bees.
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Affiliation(s)
- G T de Souza
- Programa de Pós-Graduação em Biodiversidade, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
| | - I H S Torquato
- Programa de Pós-Graduação em Biodiversidade, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
| | - C C Castro
- Programa de Pós-Graduação em Biodiversidade, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
- Universidade Federal do Agreste de Pernambuco, Garanhuns, Pernambuco, Brazil
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19
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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20
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Soares LS, Freitas LB. The phylogeographic journey of a plant species from lowland to highlands during the Pleistocene. Sci Rep 2024; 14:3825. [PMID: 38360894 PMCID: PMC10869790 DOI: 10.1038/s41598-024-53414-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
Phylogeographic history refers to how species evolve and diversify in response to historical, ecological, and demographic factors. The climate fluctuation during the Pleistocene period marked a crucial time in shaping many species' distribution and genetic structure, particularly those from southern South American grasslands. This work investigated the phylogeographic history of a highland grassland, Petunia altiplana T. Ando & Hashim. (Solanaceae), its diversity, and geographic distribution using a population genomic approach based on RAD-seq data. Our results indicated that, during the Pleistocene, when the grasslands expanded to highlands, the lowland populations of P. altiplana reached the higher open fields, enlarging their geographic distribution. We found that the P. altiplana genetic diversity followed the geographic division into eastern (E) and western (WE) population groups, with a subtle division in the E group regarding the Pelotas River headwater. The results also showed that isolation by distance was the main divergence pattern, with elevation playing a pivotal role in shaping WE and E groups. Our findings indicated that lowland-adapted populations quickly colonized highlands during the late Pleistocene.
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Affiliation(s)
- Luana Sousa Soares
- Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, Porto Alegre, 91501-970, Brazil
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, Porto Alegre, 91501-970, Brazil.
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21
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Backes A, Turchetto C, Mäder G, Segatto ALA, Bonatto SL, Freitas LB. Shades of white: The Petunia long corolla tube clade evolutionary history. Genet Mol Biol 2024; 47:e20230279. [PMID: 38385448 PMCID: PMC10882218 DOI: 10.1590/1415-4757-gmb-2023-0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 02/23/2024] Open
Abstract
Delimiting species is challenging in recently diverged species, and adaptive radiation is fundamental to understanding the evolutionary processes because it requires multiple ecological opportunities associated with adaptation to biotic and abiotic environments. The young Petunia genus (Solanaceae) is an excellent opportunity to study speciation because of its association with pollinators and unique microenvironments. This study evaluated the phylogenetic relationships among a Petunia clade species with different floral syndromes that inhabit several environments. We based our work on multiple individuals per lineage and employed nuclear and plastid phylogenetic markers and nuclear microsatellites. The phylogenetic tree revealed two main groups regarding the elevation of the distribution range, whereas microsatellites showed high polymorphism-sharing splitting lineages into three clusters. Isolation by distance, migration followed by new environment colonization, and shifts in floral syndrome were the motors for lineage differentiation, including infraspecific structuring, which suggests the need for taxonomic revision in the genus.
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Affiliation(s)
- Alice Backes
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Caroline Turchetto
- Universidade Federal do Rio Grande do Sul, Departamento de Botânica, Porto Alegre, RS, Brazil
| | - Geraldo Mäder
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Ana Lúcia A Segatto
- Universidade Federal de Santa Maria, Departamento de Bioquímica e Biologia Molecular, Santa Maria, RS, Brazil
| | - Sandro L Bonatto
- Pontifícia Universidade Católica do Rio Grande do Sul, A Escola de Ciências da Saúde e da Vida, Porto Alegre, RS, Brazil
| | - Loreta B Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
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22
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Antoniolli HRM, Carvalho TL, Gottschalk MS, Loreto ELS, Robe LJ, Depr M. Systematics and spatio-temporal evolutionary patterns of the flavopilosa group of Drosophila (Diptera, Drosophilidae). Zootaxa 2024; 5399:1-18. [PMID: 38221179 DOI: 10.11646/zootaxa.5399.1.1] [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: 01/09/2024] [Indexed: 01/16/2024]
Abstract
The Drosophila flavopilosa group comprises morphologically cryptic species that are ecologically restricted to feeding, breeding and ovipositing on flowers of Cestrum and Sessea (Solanaceae). Previous studies confirmed the monophyly of the group and the success of DNA barcoding in identifying a subset of its species, but several others remain yet to be evaluated. Furthemore, the taxonomy of the group remains incomplete, with only nine of the 17 species assigned to subgroups. Here, we accessed the phylogenetic relationships and spatio-temporal evolutionary patterns of the flavopilosa group based on a mitochondrial and two nuclear genes, providing the first molecular support to the subdivision of the group and suggesting a new taxonomic scheme for its species. Barcoding proved to be an effective tool, as all species were reciprocally monophyletic and different analyses of species delimitation yielded congruent results. The close relationship of D. flavopilosa with D. cestri and D. cordeiroi was strongly supported, suggesting that the latter should be placed in the flavopilosa subgroup together with the first. Furthermore, D. mariaehelenae was positioned as sister to D. incompta, supporting its inclusion in the nesiota subgroup. Despite new taxonomic assignments, the synapomorphic status of the diagnostic characters proposed for both subgroups was supported. Based on them, each of the remaining species were placed into one of both subgroups. Divergence time estimates suggest that their diversification coincided with the divergence of Sessea and Cestrum, providing an interesting case of coevolution.
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Affiliation(s)
- Henrique R M Antoniolli
- Programa de Ps-Graduao em Biologia Animal; Instituto de Biocincias; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre; RS; Brazil.
| | - Tuane L Carvalho
- Programa de Ps-Graduao em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria; RS; Brazil.
| | - Marco S Gottschalk
- Programa de Ps-Graduao em Gentica e Biologia Molecular; Instituto de Biocincias; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre; RS; Brazil.
| | - Elgion L S Loreto
- Departamento de Ecologia; Zoologia e Gentica; Instituto de Biologia; Universidade Federal de Pelotas (UFPel); Pelotas; RS; Brazil.
| | - Lizandra J Robe
- Programa de Ps-Graduao em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria; RS; Brazil.
| | - Marndia Depr
- Programa de Ps-Graduao em Gentica e Biologia Molecular; Instituto de Biocincias; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre; RS; Brazil.
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23
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Barchi L, Aprea G, Rabanus-Wallace MT, Toppino L, Alonso D, Portis E, Lanteri S, Gaccione L, Omondi E, van Zonneveld M, Schafleitner R, Ferrante P, Börner A, Stein N, Díez MJ, Lefebvre V, Salinier J, Boyaci HF, Finkers R, Brouwer M, Bovy AG, Rotino GL, Prohens J, Giuliano G. Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration-diversification routes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1667-1680. [PMID: 37682777 DOI: 10.1111/tpj.16455] [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: 12/13/2022] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
Abstract
Eggplant (Solanum melongena) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena, similar to what was described for other fruit-bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving 'local' phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P-SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetable.
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Affiliation(s)
- Lorenzo Barchi
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | - Giuseppe Aprea
- ENEA, Casaccia Res Ctr, Via Anguillarese 301, Rome, 00123, Italy
| | - M Timothy Rabanus-Wallace
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
| | - Laura Toppino
- CREA, Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, LO 26836, Italy
| | - David Alonso
- Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | - Ezio Portis
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | - Sergio Lanteri
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | - Luciana Gaccione
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | | | | | | | - Paola Ferrante
- ENEA, Casaccia Res Ctr, Via Anguillarese 301, Rome, 00123, Italy
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University, Von Siebold Str. 8, Göttingen, 37075, Germany
| | - Maria José Díez
- Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | | | - Jérémy Salinier
- INRAE, GAFL, Montfavet, F-84140, France
- CIRAD La Réunion et Mayotte, UMR PVBMT Saint-Pierre, La Réunion, France
| | - Hatice Filiz Boyaci
- Department of Horticulture, Faculty of Agriculture, University of Recep Tayyip Erdogan, Rize, Turkey
| | - Richard Finkers
- Wageningen University & Research WUR, Wageningen, The Netherlands
- GenNovation B.V., Wageningen, The Netherlands
| | - Matthijs Brouwer
- Wageningen University & Research WUR, Wageningen, The Netherlands
| | - Arnaud G Bovy
- Wageningen University & Research WUR, Wageningen, The Netherlands
| | - Giuseppe Leonardo Rotino
- CREA, Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, LO 26836, Italy
| | - Jaime Prohens
- Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
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24
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Turchetto C, Silvério ADC, Waschburger EL, Lacerda MEG, Quintana IV, Turchetto-Zolet AC. Genome-wide identification and evolutionary view of ALOG gene family in Solanaceae. Genet Mol Biol 2023; 46:e20230142. [PMID: 38048778 PMCID: PMC10695626 DOI: 10.1590/1415-4757-gmb-2023-0142] [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: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 12/06/2023] Open
Abstract
The ALOG gene family, which was named after its earliest identified members ( Arabidopsis LSH1 and Oryza G1), encodes a class of transcription factors (TF) characterized by the presence of a highly conserved ALOG domain. These proteins are found in various plant species playing regulatory roles in plant growth, development, and morphological diversification of inflorescence. The functional characterization of these genes in some plant species has demonstrated their involvement in floral architecture. In this study, we used a genome-wide and phylogenetic approach to gain insights into plants' origin, diversification, and functional aspects of the ALOG gene family. In total, 648 ALOG homologous genes were identified in 77 Viridiplantae species, and their evolutionary relationships were inferred using maximum likelihood phylogenetic analyses. Our results suggested that the ALOG gene family underwent several rounds of gene duplication and diversification during angiosperm evolution. Furthermore, we found three functional orthologous groups in Solanaceae species. The study provides insights into the evolutionary history and functional diversification of the ALOG gene family, which could aid in understanding the mechanisms underlying floral architecture in angiosperms.
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Affiliation(s)
- Caroline Turchetto
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica (PPGBOT), Departamento de Botânica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Ariadne de Castro Silvério
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica (PPGBOT), Departamento de Botânica, Porto Alegre, RS, Brazil
| | - Edgar Luis Waschburger
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Maria Eduarda Gonçalves Lacerda
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Isadora Vieira Quintana
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Andreia Carina Turchetto-Zolet
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
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25
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Pezzi PH, Gonçalves LT, Deprá M, Freitas LBD. Evolution and diversification of the O-methyltransferase (OMT) gene family in Solanaceae. Genet Mol Biol 2023; 46:e20230121. [PMID: 37948506 PMCID: PMC10637433 DOI: 10.1590/1678-4685-gmb-2023-0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/30/2023] [Indexed: 11/12/2023] Open
Abstract
O-methyltransferases (OMTs) are a group of enzymes involved in several fundamental biological processes in plants, including lignin biosynthesis, pigmentation, and aroma production. Despite the intensive investigation of the role of OMTs in plant secondary metabolism, the evolution and diversification of this gene family in Solanaceae remain poorly understood. Here, we conducted a genome-wide survey of OMT genes in six Solanaceae species, reconstructing gene phylogenetic trees, predicting the potential involvement in biological processes, and investigating the exon/intron structure and chromosomal location. We identified 57 caffeoyl-CoA OMTs (CCoAOMTs) and 196 caffeic acid OMTs (COMTs) in the studied species. We observed a conserved gene block on chromosome 2 that consisted of tandem duplicated copies of OMT genes. Our results suggest that the expansion of the OMT gene family in Solanaceae was driven by whole genome duplication, segmental duplication, and tandem duplication, with multiple genes being retained by neofunctionalization and subfunctionalization. This study represents an essential first step in unraveling the evolutionary history of OMTs in Solanaceae. Our findings deepen our understanding of the crucial role of OMTs in several biological processes and highlight their significance as potential biotechnological targets.
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Affiliation(s)
- Pedro Henrique Pezzi
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
| | | | - Maríndia Deprá
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
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26
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Boyko JD, Hagen ER, Beaulieu JM, Vasconcelos T. The evolutionary responses of life-history strategies to climatic variability in flowering plants. THE NEW PHYTOLOGIST 2023; 240:1587-1600. [PMID: 37194450 DOI: 10.1111/nph.18971] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 04/17/2023] [Indexed: 05/18/2023]
Abstract
The evolution of annual or perennial strategies in flowering plants likely depends on a broad array of temperature and precipitation variables. Previous documented climate life-history correlations in explicit phylogenetic frameworks have been limited to certain clades and geographic regions. To gain insights which generalize to multiple lineages we employ a multi-clade approach analyzing 32 groups of angiosperms across eight climatic variables. We utilize a recently developed method that accounts for the joint evolution of continuous and discrete traits to evaluate two hypotheses: annuals tend to evolve in highly seasonal regions prone to extreme heat and drought; and annuals tend to have faster rates of climatic niche evolution than perennials. We find that temperature, particularly highest temperature of the warmest month, is the most consistent climatic factor influencing the evolution of annual strategy in flowering plants. Unexpectedly, we do not find significant differences in rates of climatic niche evolution between perennial and annual lineages. We propose that annuals are consistently favored in areas prone to extreme heat due to their ability to escape heat stress as seeds, but they tend to be outcompeted by perennials in regions where extreme heat is uncommon or nonexistent.
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Affiliation(s)
- James D Boyko
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
- Michigan Institute of Data Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eric R Hagen
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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27
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Gramazio P, Alonso D, Arrones A, Villanueva G, Plazas M, Toppino L, Barchi L, Portis E, Ferrante P, Lanteri S, Rotino GL, Giuliano G, Vilanova S, Prohens J. Conventional and new genetic resources for an eggplant breeding revolution. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6285-6305. [PMID: 37419672 DOI: 10.1093/jxb/erad260] [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: 03/16/2023] [Accepted: 07/05/2023] [Indexed: 07/09/2023]
Abstract
Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. It is closely related to over 500 species of Solanum subgenus Leptostemonum that belong to its primary, secondary, and tertiary genepools and exhibit a wide range of characteristics useful for eggplant breeding, including traits adaptive to climate change. Germplasm banks worldwide hold more than 19 000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and for adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in its relatives can greatly contribute to eggplant breeding. The recent creation of new genetic resources such as mutant libraries, core collections, recombinant inbred lines, and sets of introgression lines will be another crucial element and will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change.
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Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Paola Ferrante
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
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Su H, Ding X, Liao B, Zhang D, Huang J, Bai J, Xu S, Zhang J, Xu W, Qiu X, Gong L, Huang Z. Comparative chloroplast genomes provided insights into the evolution and species identification on the Datureae plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1270052. [PMID: 37941675 PMCID: PMC10628451 DOI: 10.3389/fpls.2023.1270052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Generally, chloroplast genomes of angiosperms are always highly conserved but carry a certain number of variation among species. In this study, chloroplast genomes of 13 species from Datureae tribe that are of importance both in ornamental gardening and medicinal usage were studied. In addition, seven chloroplast genomes from Datureae together with two from Solanaceae species retrieved from the National Center for Biotechnology Information (NCBI) were integrated into this study. The chloroplast genomes ranged in size from 154,686 to 155,979 and from 155,497 to 155,919 bp for species of Datura and Brugmansia, respectively. As to Datura and Brugmansia, a total of 128 and 132 genes were identified, in which 83 and 87 protein coding genes were identified, respectively; Furthermore, 37 tRNA genes and 8 rRNA genes were both identified in Datura and Brugmansia. Repeats analysis indicated that the number and type varied among species for Simple sequence repeat (SSR), long repeats, and tandem repeats ranged in number from 53 to 59, 98 to 99, and 22 to 30, respectively. Phylogenetic analysis based on the plastid genomes supported the monophyletic relationship among Datura and Brugmansia and Trompettia, and a refined phylogenic relationships among each individual was resolved. In addition, a species-specific marker was designed based on variation spot that resulted from a comparative analysis of chloroplast genomes and verified as effective maker for identification of D. stramonium and D. stramonium var. inermis. Interestingly, we found that 31 genes were likely to be under positive selection, including genes encoding ATP protein subunits, photosystem protein subunit, ribosome protein subunits, NAD(P)H dehydrogenase complex subunits, and clpP, petB, rbcL, rpoCl, ycf4, and cemA genes. These genes may function as key roles in the adaption to diverse environment during evolution. The diversification of Datureae members was dated back to the late Oligocene periods. These chloroplast genomes are useful genetic resources for taxonomy, phylogeny, and evolution for Datureae.
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Affiliation(s)
- He Su
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaoxia Ding
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Baosheng Liao
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danchun Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Juan Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Junqi Bai
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Subing Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jing Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Wen Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaohui Qiu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Lu Gong
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Zhihai Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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29
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Alisawi O, Richert-Pöggeler KR, Heslop-Harrison J(P, Schwarzacher T. The nature and organization of satellite DNAs in Petunia hybrida, related, and ancestral genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1232588. [PMID: 37868307 PMCID: PMC10587573 DOI: 10.3389/fpls.2023.1232588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/11/2023] [Indexed: 10/24/2023]
Abstract
Introduction The garden petunia, Petunia hybrida (Solanaceae) is a fertile, diploid, annual hybrid species (2n=14) originating from P. axillaris and P. inflata 200 years ago. To understand the recent evolution of the P. hybrida genome, we examined tandemly repeated or satellite sequences using bioinformatic and molecular cytogenetic analysis. Methods Raw reads from available genomic assemblies and survey sequences of P. axillaris N (PaxiN), P. inflata S6, (PinfS6), P. hybrida (PhybR27) and the here sequenced P. parodii S7 (PparS7) were used for graph and k-mer based cluster analysis of TAREAN and RepeatExplorer. Analysis of repeat specific monomer lengths and sequence heterogeneity of the major tandem repeat families with more than 0.01% genome proportion were complemented by fluorescent in situ hybridization (FISH) using consensus sequences as probes to chromosomes of all four species. Results Seven repeat families, PSAT1, PSAT3, PSAT4, PSAT5 PSAT6, PSAT7 and PSAT8, shared high consensus sequence similarity and organisation between the four genomes. Additionally, many degenerate copies were present. FISH in P. hybrida and in the three wild petunias confirmed the bioinformatics data and gave corresponding signals on all or some chromosomes. PSAT1 is located at the ends of all chromosomes except the 45S rDNA bearing short arms of chromosomes II and III, and we classify it as a telomere associated sequence (TAS). It is the most abundant satellite repeat with over 300,000 copies, 0.2% of the genomes. PSAT3 and the variant PSAT7 are located adjacent to the centromere or mid-arm of one to three chromosome pairs. PSAT5 has a strong signal at the end of the short arm of chromosome III in P. axillaris and P.inflata, while in P. hybrida additional interstitial sites were present. PSAT6 is located at the centromeres of chromosomes II and III. PSAT4 and PSAT8 were found with only short arrays. Discussion These results demonstrate that (i) repeat families occupy distinct niches within chromosomes, (ii) they differ in the copy number, cluster organization and homogenization events, and that (iii) the recent genome hybridization in breeding P. hybrida preserved the chromosomal position of repeats but affected the copy number of repetitive DNA.
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Affiliation(s)
- Osamah Alisawi
- Department of Plant Protection, Faculty of Agriculture, University of Kufa, Najaf, Iraq
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
| | - Katja R. Richert-Pöggeler
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - J.S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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30
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Blunt EL, Choi J, Sussman H, Christopherson RC, Keen P, Rahmati Ishka M, Li LY, Idrovo JM, Julkowska MM, Van Eck J, Richards EJ. The nuclear lamina is required for proper development and nuclear shape distortion in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5500-5513. [PMID: 37503569 PMCID: PMC10540737 DOI: 10.1093/jxb/erad294] [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: 03/11/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
The nuclear lamina in plant cells is composed of plant-specific proteins, including nuclear matrix constituent proteins (NMCPs), which have been postulated to be functional analogs of lamin proteins that provide structural integrity to the organelle and help stabilize the three-dimensional organization of the genome. Using genomic editing, we generated alleles for the three genes encoding NMCPs in cultivated tomato (Solanum lycopersicum) to determine if the consequences of perturbing the nuclear lamina in this crop species were similar to or distinct from those observed in the model Arabidopsis thaliana. Loss of the sole NMCP2-class protein was lethal in tomato but is tolerated in Arabidopsis. Moreover, depletion of NMCP1-type nuclear lamina proteins leads to distinct developmental phenotypes in tomato, including leaf morphology defects and reduced root growth rate (in nmcp1b mutants), compared with cognate mutants in Arabidopsis. These findings suggest that the nuclear lamina interfaces with different developmental and signaling pathways in tomato compared with Arabidopsis. At the subcellular level, however, tomato nmcp mutants resembled their Arabidopsis counterparts in displaying smaller and more spherical nuclei in differentiated cells. This result argues that the plant nuclear lamina facilitates nuclear shape distortion in response to forces exerted on the organelle within the cell.
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Affiliation(s)
- Endia L Blunt
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Junsik Choi
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Hayley Sussman
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | | | - Patricia Keen
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | | | - Linda Y Li
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Joanna M Idrovo
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | | | - Joyce Van Eck
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Eric J Richards
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
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31
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Barnett JR, Tieman DM, Caicedo AL. Variation in ripe fruit volatiles across the tomato clade: An evolutionary framework for studying fruit scent diversity in a crop wild relative. AMERICAN JOURNAL OF BOTANY 2023; 110:e16223. [PMID: 37551422 DOI: 10.1002/ajb2.16223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 08/09/2023]
Abstract
PREMISE The scents of volatile organic compounds (VOCs) are an important component of ripe fleshy fruit attractiveness, yet their variation across closely related wild species is poorly understood. Phylogenetic patterns in these compounds and their biosynthetic pathways offer insight into the evolutionary drivers of fruit diversity, including whether scent can communicate an honest signal of nutrient content to animal dispersers. We assessed ripe fruit VOC content across the tomato clade (Solanum sect. Lycopersicon), with implications for crop improvement since these compounds are key components of tomato flavor. METHODS We analyzed ripe fruit volatiles from 13 species of wild tomato grown in a common garden. Interspecific variations in 66 compounds and their biosynthetic pathways were assessed in 32 accessions, and an accession-level phylogeny was constructed to account for relatedness. RESULTS Wild tomato species can be differentiated by their VOCs, with Solanum pennellii notably distinct. Phylogenetic conservatism exists to a limited extent. Major cladewide patterns corresponded to divergence of the five brightly colored-fruited species from the nine green-fruited species, particularly for nitrogen-containing compounds (higher in colored-fruited) and esters (higher in green-fruited), the latter appearing to signal a sugar reward. CONCLUSIONS We established a framework for fruit scent evolution studies in a crop wild relative system, showing that each species in the tomato clade has a unique VOC profile. Differences between color groups align with fruit syndromes that could be driven by selection from frugivores. The evolution of colored fruits was accompanied by changes in biosynthetic pathways for esters and nitrogen-containing compounds, volatiles important to tomato flavor.
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Affiliation(s)
- Jacob R Barnett
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, MA, 01003, USA
| | - Denise M Tieman
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts Amherst, MA, 01003, USA
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32
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Lin X, Jia Y, Heal R, Prokchorchik M, Sindalovskaya M, Olave-Achury A, Makechemu M, Fairhead S, Noureen A, Heo J, Witek K, Smoker M, Taylor J, Shrestha RK, Lee Y, Zhang C, Park SJ, Sohn KH, Huang S, Jones JDG. Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors. Nat Genet 2023; 55:1579-1588. [PMID: 37640880 PMCID: PMC10484786 DOI: 10.1038/s41588-023-01486-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Potato (Solanum tuberosum) and tomato (Solanum lycopersicon) crops suffer severe losses to late blight caused by the oomycete pathogen Phytophthora infestans. Solanum americanum, a relative of potato and tomato, is globally distributed and most accessions are highly blight resistant. We generated high-quality reference genomes of four S. americanum accessions, resequenced 52 accessions, and defined a pan-NLRome of S. americanum immune receptor genes. We further screened for variation in recognition of 315P. infestans RXLR effectors in 52 S. americanum accessions. Using these genomic and phenotypic data, we cloned three NLR-encoding genes, Rpi-amr4, R02860 and R04373, that recognize cognate P. infestans RXLR effectors PITG_22825 (AVRamr4), PITG_02860 and PITG_04373. These genomic resources and methodologies will support efforts to engineer potatoes with durable late blight resistance and can be applied to diseases of other crops.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- Plant Pathology Group, The Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Maria Sindalovskaya
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrea Olave-Achury
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Moffat Makechemu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Azka Noureen
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jung Heo
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Soon Ju Park
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
- Division of Applied Life Sciences and Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea.
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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Knapp S, Särkinen T, Barboza GE. A revision of the South American species of the Morelloid clade ( Solanum L., Solanaceae). PHYTOKEYS 2023; 231:1-342. [PMID: 37680322 PMCID: PMC10481398 DOI: 10.3897/phytokeys.231.100894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 07/13/2023] [Indexed: 09/09/2023]
Abstract
The Morelloid clade, also known as the black nightshades or "Maurella" (Morella), is one of the 10 major clades within the mega-diverse genus Solanum L. The clade is most diverse in the central to southern Andes, but species occur around the tropics and subtropics, some extending well into the temperate zone. Plants of the group vary from herbs to short-lived perennials to perennial shrubs that are distinctly woody at the base, they have small mostly white or purplish white flowers and small juicy berries. Due to the complex morphological variation and weedy nature of these plants, coupled with the large number of published synonyms (especially for European taxa), our understanding of species limits and diversity in the Morelloid clade has lagged behind that of other clades in Solanum. Here we provide the last in a three-part series of monographic treatments of the morelloid solanums (see PhytoKeys Vols. 106, 125), treating the 62 species occurring in South America. This region is by far the most diverse in the clade, both in terms of species number and morphological diversity. We provide complete synonymy, nomenclatural details, including lecto- and neotypifications where needed, common names and uses, morphological descriptions, illustrations to aid identification both in herbaria and in the field, and distribution maps for all native, non-cultivated species. We include a key to all species, a synoptic character list for the species treated here and links to synoptic online keys for all species of the Morelloid clade. Preliminary conservation assessments following IUCN guidelines are also provided for all native species.
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Affiliation(s)
- Sandra Knapp
- Natural History Museum, Cromwell Road, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UKRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Gloria E. Barboza
- Instituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba), Casilla de Correo 495, 5000 Córdoba, ArgentinaInstituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba)CordobaArgentina
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34
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Thomas HR, Gevorgyan A, Frank MH. Anatomical and biophysical basis for graft incompatibility within the Solanaceae. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4461-4470. [PMID: 37103969 PMCID: PMC10687351 DOI: 10.1093/jxb/erad155] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 04/26/2023] [Indexed: 06/19/2023]
Abstract
Interspecies grafting is an economically relevant technique that allows beneficial shoot and root combinations from separate species to be combined. One hypothesis for the basis of graft compatibility revolves around taxonomic relatedness. To test how phylogenetic distance affects interspecific graft compatibility within the economically important Solanaceae subfamily, Solanoideae, we characterized the anatomical and biophysical integrity of graft junctions between four species: tomato (Solanum lycopersicum), eggplant (Solanum melongena), pepper (Capsicum annuum), and groundcherry (Physalis pubescens). We analyzed the survival, growth, integrity, and cellular composition of the graft junctions. Utilizing various techniques, we were able to quantitatively assess compatibility among the interspecific grafts. Even though most of our graft combinations could survive, we show that only intrageneric combinations between tomato and eggplant are compatible. Unlike incompatible grafts, the formation of substantial vascular reconnections between tomato and eggplant in the intrageneric heterografts likely contributed to biophysically stable grafts. Furthermore, we identified 10 graft combinations that show delayed incompatibility, providing a useful system to pursue deeper work into graft compatibility. This work provides new evidence that graft compatibility may be limited to intrageneric combinations within the Solanoideae subfamily. Further research amongst additional Solanaceous species can be used to test the extent to which our hypothesis applies to this family.
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Affiliation(s)
- Hannah R Thomas
- Cornell University, School of Integrative Plant Science, Ithaca, NY 14850, USA
| | - Alice Gevorgyan
- Cornell University, School of Integrative Plant Science, Ithaca, NY 14850, USA
| | - Margaret H Frank
- Cornell University, School of Integrative Plant Science, Ithaca, NY 14850, USA
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35
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Tiley GP, Flouri T, Jiao X, Poelstra JW, Xu B, Zhu T, Rannala B, Yoder AD, Yang Z. Estimation of species divergence times in presence of cross-species gene flow. Syst Biol 2023; 72:820-836. [PMID: 36961245 PMCID: PMC10405360 DOI: 10.1093/sysbio/syad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1000 transcriptome loci from 14 species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling. [divergence time; gene flow; hybridization; introgression; MSci model; multispecies coalescent].
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Affiliation(s)
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Xiyun Jiao
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Department of Statistics and Data Science, China Southern University of Science and Technology, Shenzhen, Guangdong, China
| | | | - Bo Xu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianqi Zhu
- National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, China
- Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, China
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
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36
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Wang S, Gao J, Li Z, Chen K, Pu W, Feng C. Phylotranscriptomics supports numerous polyploidization events and phylogenetic relationships in Nicotiana. FRONTIERS IN PLANT SCIENCE 2023; 14:1205683. [PMID: 37575947 PMCID: PMC10421670 DOI: 10.3389/fpls.2023.1205683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
Introduction Nicotiana L. (Solanaceae) is of great scientific and economic importance, and polyploidization has been pivotal in shaping this genus. Despite many previous studies on the Nicotiana phylogenetic relationship and hybridization, evidence from whole genome data is still lacking. Methods In this study, we obtained 995 low-copy genes and plastid transcript fragments from the transcriptome datasets of 26 Nicotiana species, including all sections. We reconstructed the phylogenetic relationship and phylogenetic network of diploid species. Results The incongruence among gene trees showed that the formation of N. sylvestris involved incomplete lineage sorting. The nuclear-plastid discordance and nuclear introgression absence indicated that organelle capture from section Trigonophyllae was involved in forming section Petunioides. Furthermore, we analyzed the evolutionary origin of polyploid species and dated the time of hybridization events based on the analysis of PhyloNet, sequence similarity search, and phylogeny of subgenome approaches. Our results highly evidenced the hybrid origins of five polyploid sections, including sections Nicotiana, Repandae, Rusticae, Polydicliae, and Suaveolentes. Notably, we provide novel insights into the hybridization event of section Polydicliae and Suaveolentes. The section Polydicliae formed from a single hybridization event between maternal progenitor N. attenuata and paternal progenitor N. undulata; the N. sylvestris (paternal progenitor) and the N. glauca (maternal progenitor) were involved in the formation of section Suaveolentes. Discussion This study represents the first exploration of Nicotiana polyploidization events and phylogenetic relationships using the high-throughput RNA-seq approach. It will provide guidance for further studies in molecular systematics, population genetics, and ecological adaption studies in Nicotiana and other related species.
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Affiliation(s)
- Shuaibin Wang
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Junping Gao
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Zhaowu Li
- Puai Medical College, Shaoyang University, Shaoyang, China
| | - Kai Chen
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Wenxuan Pu
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Chen Feng
- Jiangxi Provincial Key Laboratory of ex-situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
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37
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Zeng S, Lin S, Wang Z, Zong Y, Wang Y. The health-promoting anthocyanin petanin in Lycium ruthenicum fruit: a promising natural colorant. Crit Rev Food Sci Nutr 2023; 64:10484-10497. [PMID: 37351558 DOI: 10.1080/10408398.2023.2225192] [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] [Indexed: 06/24/2023]
Abstract
Acylated anthocyanins derived from dietary sources have gained significant attention due to their health-promoting properties and potential as natural colorants with high stability. However, exploration of the functional food products using acylated anthocyanins enriched in fruits and vegetables remains largely delayed in food industries. The black goji (Lycium ruthencium) fruit (LRF) is a functional food that is extensively used due to its exceptionally high levels of acylated anthocyanins, including petanin. This review provides a comprehensive summary of the functional properties and anthocyanin components of LRF. The stability, bioaccessibility, bioavailability, and bioactivities of petanin, the major anthocyanin component, are compared with those of LRF anthocyanin extracts and other food sources. Furthermore, the biosynthetic pathway and regulatory network of petanin in LRF are proposed and constructed, respectively. The key genes that could be potentially used for metabolic engineering to produce petanin are predicted. Finally, the potential application of petanin derivatives in the food industry is also discussed. This review presents comprehensive and systematic information about the dual-function of petanin as a bioactive component and a promising natural colorant for future food industrial applications.
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Affiliation(s)
- Shaohua Zeng
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Digital Botanical Garden and Popular Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuang Lin
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Digital Botanical Garden and Popular Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhiqiang Wang
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Digital Botanical Garden and Popular Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Zong
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai, Xining, China
| | - Ying Wang
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Digital Botanical Garden and Popular Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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38
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Cantley JT, Jordon-Thaden IE, Roche MD, Hayes D, Kate S, Martine CT. A Foundational Population Genetics Investigation of the Sexual Systems of Solanum (Solanaceae) in the Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit from Increased Genetic Admixture via Obligate Outcrossing. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112200. [PMID: 37299179 DOI: 10.3390/plants12112200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Solanum section Leptostemonum is an ideal lineage to test the theoretical framework regarding proposed evolutionary benefits of outcrossing sexual systems in comparison to cosexuality. Theoretically, non-cosexual taxa should support more genetic diversity within populations, experience less inbreeding, and have less genetic structure due to a restricted ability to self-fertilize. However, many confounding factors present challenges for a confident inference that inherent differences in sexual systems influence observed genetic patterns among populations. This study provides a foundational baseline of the population genetics of several species of different sexual systems with the aim of generating hypotheses of any factor-including sexual system-that influences genetic patterns. Importantly, results indicate that dioecious S. asymmetriphyllum maintains less genetic structure and greater admixture among populations than cosexual S. raphiotes at the same three locations where they co-occur. This suggests that when certain conditions are met, the evolution of dioecy may have proceeded as a means to avoid genetic consequences of self-compatibility and may support hypotheses of benefits gained through differential resource allocation partitioned across sexes. Arguably, the most significant finding of this study is that all taxa are strongly inbred, possibly reflective of a shared response to recent climate shifts, such as the increased frequency and intensity of the region's fire regime.
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Affiliation(s)
- Jason T Cantley
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA
| | - Ingrid E Jordon-Thaden
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA
- Department of Botany, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Morgan D Roche
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniel Hayes
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA
| | - Stephanie Kate
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
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Deanna R, Martínez C, Manchester S, Wilf P, Campos A, Knapp S, Chiarini FE, Barboza GE, Bernardello G, Sauquet H, Dean E, Orejuela A, Smith SD. Fossil berries reveal global radiation of the nightshade family by the early Cenozoic. THE NEW PHYTOLOGIST 2023; 238:2685-2697. [PMID: 36960534 DOI: 10.1111/nph.18904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 03/14/2023] [Indexed: 05/19/2023]
Abstract
Fossil discoveries can transform our understanding of plant diversification over time and space. Recently described fossils in many plant families have pushed their known records farther back in time, pointing to alternative scenarios for their origin and spread. Here, we describe two new Eocene fossil berries of the nightshade family (Solanaceae) from the Esmeraldas Formation in Colombia and the Green River Formation in Colorado (USA). The placement of the fossils was assessed using clustering and parsimony analyses based on 10 discrete and five continuous characters, which were also scored in 291 extant taxa. The Colombian fossil grouped with members of the tomatillo subtribe, and the Coloradan fossil aligned with the chili pepper tribe. Along with two previously reported early Eocene fossils from the tomatillo genus, these findings indicate that Solanaceae were distributed at least from southern South America to northwestern North America by the early Eocene. Together with two other recently discovered Eocene berries, these fossils demonstrate that the diverse berry clade and, in turn, the entire nightshade family, is much older and was much more widespread in the past than previously thought.
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Affiliation(s)
- Rocío Deanna
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, CO, 80309-0334, USA
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), Vélez Sarsfield 299, Córdoba, 5000, Argentina
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Medina Allende y Haya de la Torre, Córdoba, 5000, Argentina
| | - Camila Martínez
- Biological Science Department, Universidad EAFIT, Carrera 49, Cl. 7 Sur #50, Medellín, 050022, Antioquia, Colombia
- Center for Tropical Paleoecology and Archaeology, Smithsonian Tropical Research Institute, Luis Clement Avenue, Bldg. 401 Tupper Balboa Ancon, Panama City, 0843-03092, Panama
| | - Steven Manchester
- Florida Museum of Natural History, University of Florida, 3215 Hull Rd, Gainesville, FL, 32611, USA
| | - Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, State College, 201 Old Main, University Park, PA, 16802, USA
| | - Abel Campos
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, CO, 80309-0334, USA
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Franco E Chiarini
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Gloria E Barboza
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Gabriel Bernardello
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW, 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, High St Kensington, Sydney, NSW, 2052, Australia
| | - Ellen Dean
- Center for Plant Diversity, Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Andrés Orejuela
- Grupo de Investigación en Recursos Naturales Amazónicos - GRAM, Facultad de Ingenierías y Ciencias Básicas, Instituto Tecnológico del Putumayo - ITP, Calle 17, Carrera 17, Mocoa, Putumayo, Colombia
- Subdirección científica, Jardín Botánico de Bogotá José Celestino Mutis, Calle 63 #68-95, Bogotá, DC, Colombia
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, CO, 80309-0334, USA
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Li N, He Q, Wang J, Wang B, Zhao J, Huang S, Yang T, Tang Y, Yang S, Aisimutuola P, Xu R, Hu J, Jia C, Ma K, Li Z, Jiang F, Gao J, Lan H, Zhou Y, Zhang X, Huang S, Fei Z, Wang H, Li H, Yu Q. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat Genet 2023; 55:852-860. [PMID: 37024581 PMCID: PMC10181942 DOI: 10.1038/s41588-023-01340-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop.
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Grants
- the National Natural Science Foundation of China (31860555, 32260763 and 31991180), Key projects for crop traits formation and cutting-edge technologies in biological breeding (xjnkywdzc-2022001), Key Research and development task special project of Xinjiang (2022B02002), Special Incubation Project of Science & Technology Renovation of Xinjiang Academy of Agricultural Sciences (xjkcpy-2021001), China Agriculture Research System of MOF and MARA (CARS-23-G24), Guangdong Major Project of Basic and Applied Basic Research (2021B0301030004), the National Key Research and Development Program of China (2019YFA0906200 and 2021YFF1000100), Shenzhen Science and Technology Program (Grant No. KQTD2016113010482651), Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District (Grand No. RC201901-05), Shenzhen Outstanding Talents Training Fund and the US National Science Foundation (IOS-1855585).
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Affiliation(s)
- Ning Li
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Wang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Baike Wang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Jiantao Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shaoyong Huang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yaping Tang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Shengbao Yang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Patiguli Aisimutuola
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ruiqiang Xu
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Jiahui Hu
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Chunping Jia
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Kai Ma
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumqi, China
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jie Gao
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Haiyan Lan
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinyan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Qinghui Yu
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
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Wu Y, Li D, Hu Y, Li H, Ramstein GP, Zhou S, Zhang X, Bao Z, Zhang Y, Song B, Zhou Y, Zhou Y, Gagnon E, Särkinen T, Knapp S, Zhang C, Städler T, Buckler ES, Huang S. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 2023; 186:2313-2328.e15. [PMID: 37146612 DOI: 10.1016/j.cell.2023.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/20/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.
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Affiliation(s)
- Yaoyao Wu
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Dawei Li
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yong Hu
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China; The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Hongbo Li
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China
| | - Guillaume P Ramstein
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus 8000, Denmark
| | - Shaoqun Zhou
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China
| | - Xinyan Zhang
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China
| | - Zhigui Bao
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Yu Zhang
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China; School of Agriculture, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
| | - Yao Zhou
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China; Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100094, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China
| | - Edeline Gagnon
- Technische Universität München, TUM School of Life Sciences, Emil-Ramann-Strasse 2, 85354 Freising, Germany
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Chunzhi Zhang
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China
| | - Thomas Städler
- Institute of Integrative Biology and Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; USDA-ARS, Ithaca, NY 14853, USA
| | - Sanwen Huang
- State Key Laboratory of Tropical Crop Breeding, 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, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
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42
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Sapkota M, Pereira L, Wang Y, Zhang L, Topcu Y, Tieman D, van der Knaap E. Structural variation underlies functional diversity at methyl salicylate loci in tomato. PLoS Genet 2023; 19:e1010751. [PMID: 37141297 PMCID: PMC10187894 DOI: 10.1371/journal.pgen.1010751] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/16/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023] Open
Abstract
Methyl salicylate is an important inter- and intra-plant signaling molecule, but is deemed undesirable by humans when it accumulates to high levels in ripe fruits. Balancing the tradeoff between consumer satisfaction and overall plant health is challenging as the mechanisms regulating volatile levels have not yet been fully elucidated. In this study, we investigated the accumulation of methyl salicylate in ripe fruits of tomatoes that belong to the red-fruited clade. We determine the genetic diversity and the interaction of four known loci controlling methyl salicylate levels in ripe fruits. In addition to Non-Smoky Glucosyl Transferase 1 (NSGT1), we uncovered extensive genome structural variation (SV) at the Methylesterase (MES) locus. This locus contains four tandemly duplicated Methylesterase genes and genome sequence investigations at the locus identified nine distinct haplotypes. Based on gene expression and results from biparental crosses, functional and non-functional haplotypes for MES were identified. The combination of the non-functional MES haplotype 2 and the non-functional NSGT1 haplotype IV or V in a GWAS panel showed high methyl salicylate levels in ripe fruits, particularly in accessions from Ecuador, demonstrating a strong interaction between these two loci and suggesting an ecological advantage. The genetic variation at the other two known loci, Salicylic Acid Methyl Transferase 1 (SAMT1) and tomato UDP Glycosyl Transferase 5 (SlUGT5), did not explain volatile variation in the red-fruited tomato germplasm, suggesting a minor role in methyl salicylate production in red-fruited tomato. Lastly, we found that most heirloom and modern tomato accessions carried a functional MES and a non-functional NSGT1 haplotype, ensuring acceptable levels of methyl salicylate in fruits. Yet, future selection of the functional NSGT1 allele could potentially improve flavor in the modern germplasm.
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Affiliation(s)
- Manoj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Lara Pereira
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Yanbing Wang
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Lei Zhang
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Yasin Topcu
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Denise Tieman
- Horticultural Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Esther van der Knaap
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
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43
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Yang Q, Li Y, Cai L, Gan G, Wang P, Li W, Li W, Jiang Y, Li D, Wang M, Xiong C, Chen R, Wang Y. Characteristics, Comparative Analysis, and Phylogenetic Relationships of Chloroplast Genomes of Cultivars and Wild Relatives of Eggplant (Solanum melongena). Curr Issues Mol Biol 2023; 45:2832-2846. [PMID: 37185709 PMCID: PMC10136506 DOI: 10.3390/cimb45040185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/22/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
The eggplant (Solanum melongena) is a popular vegetable around the world. However, the origin and evolution of eggplant has long been considered complex and unclear, which has become the barrier to improvements in eggplant breeding. Sequencing and comparative analyses of 13 complete chloroplast (cp) genomes of seven Solanum species were performed. Genome sizes were between 154,942 and 156,004 bp, the smallest genome was from S. torvum and the largest from S. macrocapon. Thirteen cp genomes showed highly conserved sequences and GC contents, particularly at the subgenus level. All genes in the 13 genomes were annotated. The cp genomes in this study comprised 130 genes (i.e., 80 protein-coding genes, 8 rRNA genes, and 42 tRNA genes), apart from S. sisymbriifolium, which had 129 (79 protein-coding genes, 8 rRNA genes, and 42 tRNA genes.). The rps16 was absent from the cp genome of S. sisymbriifolium, resulting in a nonsense mutation. Twelve hotspot regions of the cp genome were identified, which showed a series of sequence variations and differed significantly in the inverted repeat/single-copy boundary regions. Furthermore, phylogenetic analysis was conducted using 46 cp genomic sequences to determine interspecific genetic and phylogenetic relationships in Solanum species. All species formed two branches, one of which contained all cultivars of the subgenus Leptostemonum. The cp genome data and phylogenetic analysis provides molecular evidence revealing the origin and evolutionary relationships of S. melongena and its wild relatives. Our findings suggest precise intra- and interspecies relatedness within the subgenus Leptostemonum, which has positive implications for work on improvements in eggplant breeding, particularly in producing heterosis, expanding the source of species variation, and breeding new varieties.
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Affiliation(s)
- Qihong Yang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Ye Li
- Habin Academy of Agricultural Sciences, Harbin 150008, China
| | - Liangyu Cai
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Guiyun Gan
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Peng Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Weiliu Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Wenjia Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Yaqin Jiang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Dandan Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Mila Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Xiong
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
| | - Riyuan Chen
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530003, China
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44
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Huang J, Xu W, Zhai J, Hu Y, Guo J, Zhang C, Zhao Y, Zhang L, Martine C, Ma H, Huang CH. Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants. PLANT COMMUNICATIONS 2023:100595. [PMID: 36966360 PMCID: PMC10363554 DOI: 10.1016/j.xplc.2023.100595] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/02/2023] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.
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Affiliation(s)
- Jie Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Weibin Xu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Junwen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | | | - Hong Ma
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA.
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
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45
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Strazzer P, Verbree B, Bliek M, Koes R, Quattrocchio FM. The Amsterdam petunia germplasm collection: A tool in plant science. FRONTIERS IN PLANT SCIENCE 2023; 14:1129724. [PMID: 37025133 PMCID: PMC10070740 DOI: 10.3389/fpls.2023.1129724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
Petunia hybrida is a plant model system used by many researchers to investigate a broad range of biological questions. One of the reasons for the success of this organism as a lab model is the existence of numerous mutants, involved in a wide range of processes, and the ever-increasing size of this collection owing to a highly active and efficient transposon system. We report here on the origin of petunia-based research and describe the collection of petunia lines housed in the University of Amsterdam, where many of the existing genotypes are maintained.
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46
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Coughlan JM. The role of hybrid seed inviability in angiosperm speciation. AMERICAN JOURNAL OF BOTANY 2023; 110:1-14. [PMID: 36801827 DOI: 10.1002/ajb2.16135] [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: 08/27/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
Understanding which reproductive barriers contribute to speciation is essential to understanding the diversity of life on earth. Several contemporary examples of strong hybrid seed inviability (HSI) between recently diverged species suggest that HSI may play a fundamental role in plant speciation. Yet, a broader synthesis of HSI is needed to clarify its role in diversification. Here, I review the incidence and evolution of HSI. Hybrid seed inviability is common and evolves rapidly, suggesting that it may play an important role early in speciation. The developmental mechanisms that underlie HSI involve similar developmental trajectories in endosperm, even between evolutionarily deeply diverged incidents of HSI. In hybrid endosperm, HSI is often accompanied by whole-scale gene misexpression, including misexpression of imprinted genes which have a key role in endosperm development. I explore how an evolutionary perspective can clarify the repeated and rapid evolution of HSI. In particular, I evaluate the evidence for conflict between maternal and paternal interests in resource allocation to offspring (i.e., parental conflict). I highlight that parental conflict theory generates explicit predictions regarding the expected hybrid phenotypes and genes responsible for HSI. While much phenotypic evidence supports a role of parental conflict in the evolution of HSI, an understanding of the underlying molecular mechanisms of this barrier is essential to test parental conflict theory. Lastly, I explore what factors may influence the strength of parental conflict in natural plant populations as an explanation for why rates of HSI may differ between plant groups and the consequences of strong HSI in secondary contact.
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Affiliation(s)
- Jenn M Coughlan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
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Sun L, Cao S, Zheng N, Kao TH. Analyses of Cullin1 homologs reveal functional redundancy in S-RNase-based self-incompatibility and evolutionary relationships in eudicots. THE PLANT CELL 2023; 35:673-699. [PMID: 36478090 PMCID: PMC9940881 DOI: 10.1093/plcell/koac357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In Petunia (Solanaceae family), self-incompatibility (SI) is regulated by the polymorphic S-locus, which contains the pistil-specific S-RNase and multiple pollen-specific S-Locus F-box (SLF) genes. SLFs assemble into E3 ubiquitin ligase complexes known as Skp1-Cullin1-F-box complexes (SCFSLF). In pollen tubes, these complexes collectively mediate ubiquitination and degradation of all nonself S-RNases, but not self S-RNase, resulting in cross-compatible, but self-incompatible, pollination. Using Petunia inflata, we show that two pollen-expressed Cullin1 (CUL1) proteins, PiCUL1-P and PiCUL1-B, function redundantly in SI. This redundancy is lost in Petunia hybrida, not because of the inability of PhCUL1-B to interact with SSK1, but due to a reduction in the PhCUL1-B transcript level. This is possibly caused by the presence of a DNA transposon in the PhCUL1-B promoter region, which was inherited from Petunia axillaris, one of the parental species of Pe. hybrida. Phylogenetic and syntenic analyses of Cullin genes in various eudicots show that three Solanaceae-specific CUL1 genes share a common origin, with CUL1-P dedicated to S-RNase-related reproductive processes. However, CUL1-B is a dispersed duplicate of CUL1-P present only in Petunia, and not in the other species of the Solanaceae family examined. We suggest that the CUL1s involved (or potentially involved) in the SI response in eudicots share a common origin.
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Affiliation(s)
- Linhan Sun
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Shiyun Cao
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Teh-hui Kao
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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48
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Jose J, Éva C, Bozsó Z, Hamow KÁ, Fekete Z, Fábián A, Bánfalvi Z, Sági L. Global transcriptome and targeted metabolite analyses of roots reveal different defence mechanisms against Ralstonia solanacearum infection in two resistant potato cultivars. FRONTIERS IN PLANT SCIENCE 2023; 13:1065419. [PMID: 36733596 PMCID: PMC9889091 DOI: 10.3389/fpls.2022.1065419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Ralstonia solanacearum (Rs), the causal agent of bacterial wilt disease in an unusually wide range of host plants, including potato (Solanum tuberosum), is one of the most destructive phytopathogens that seriously reduces crop yields worldwide. Identification of defence mechanisms underlying bacterial wilt resistance is a prerequisite for biotechnological approaches to resistance breeding. Resistance to Rs has been reported only in a few potato landraces and cultivars. Our in vitro inoculation bioassays confirmed that the cultivars 'Calalo Gaspar' (CG) and 'Cruza 148' (CR) are resistant to Rs infection. Comparative transcriptome analyses of CG and CR roots, as well as of the roots of an Rs-susceptible cultivar, 'Désirée' (DES), were carried out two days after Rs infection, in parallel with their respective noninfected controls. In CR and DES, the upregulation of chitin interactions and cell wall-related genes was detected. The phenylpropanoid biosynthesis and glutathione metabolism pathways were induced only in CR, as confirmed by high levels of lignification over the whole stele in CR roots six days after Rs infection. At the same time, Rs infection greatly increased the concentrations of chlorogenic acid and quercetin derivatives in CG roots as it was detected using ultra-performance liquid chromatography - tandem mass spectrometry. Characteristic increases in the expression of MAP kinase signalling pathway genes and in the concentrations of jasmonic, salicylic, abscisic and indoleacetic acid were measured in DES roots. These results indicate different Rs defence mechanisms in the two resistant potato cultivars and a different response to Rs infection in the susceptible cultivar.
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Affiliation(s)
- Jeny Jose
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Csaba Éva
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Zoltán Bozsó
- Plant Protection Institute, Centre for Agricultural Research, Budapest, Hungary
| | - Kamirán Áron Hamow
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Zsófia Fekete
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Attila Fábián
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Zsófia Bánfalvi
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - László Sági
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
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49
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He J, Alonge M, Ramakrishnan S, Benoit M, Soyk S, Reem NT, Hendelman A, Van Eck J, Schatz MC, Lippman ZB. Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. THE PLANT CELL 2023; 35:351-368. [PMID: 36268892 PMCID: PMC9806562 DOI: 10.1093/plcell/koac305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative Physalis pruinosa and use these resources to study natural and engineered variations in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9-targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system and establish a paradigm in the search for factors driving ICS.
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Affiliation(s)
- Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Matthias Benoit
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sebastian Soyk
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nathan T Reem
- Boyce Thompson Institute, Ithaca, New York 14853, USA
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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50
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Williams TM, Hayes J, McDonnell AJ, Cantley JT, Jobson P, Martine CT. Solanumscalarium (Solanaceae), a newly-described dioecious bush tomato from Judbarra/Gregory National Park, Northern Territory, Australia. PHYTOKEYS 2022; 216:103-116. [PMID: 36761892 PMCID: PMC9836722 DOI: 10.3897/phytokeys.216.85972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/15/2022] [Indexed: 06/12/2023]
Abstract
A new species of functionally dioecious bush tomato of SolanumsubgenusLeptostemonum is described. Solanumscalarium Martine & T.M.Williams, sp. nov., is a member of the taxonomically challenging "Kimberley dioecious clade" in Australia and differs from other species in the group in its spreading decumbent habit and conspicuously prickly male floral rachis. The species is so far known from one site in Judbarra/Gregory National Park in the Northern Territory. Ex situ crosses and confirmation of inaperturate pollen grains produced in morphologically cosexual flowers indicate that these flowers are functionally female and the species is functionally dioecious. The scientific name reflects the ladder-like appearance of the inflorescence rachis armature of male individuals, the stone staircase that provides access to the type locality at the Escarpment Lookout Walk, and the importance of maintaining equitable and safe access to outdoor spaces. The common name Garrarnawun Bush Tomato is proposed in recognition of the lookout point at this site, a traditional meeting place of the Wardaman and Nungali-Ngaliwurru peoples whose lands overlap in this area.
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Affiliation(s)
- Tanisha M. Williams
- Department of Biology, Bucknell University, 1 Dent Drive, Lewisburg, PA, USABucknell UniversityLewisburgUnited States of America
| | - Jonathan Hayes
- Department of Biology, Bucknell University, 1 Dent Drive, Lewisburg, PA, USABucknell UniversityLewisburgUnited States of America
| | - Angela J. McDonnell
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL 60022, USANegaunee Institute for Plant Conservation Science and Action, Chicago Botanic GardenGlencoeUnited States of America
| | - Jason T. Cantley
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 96132, USASan Francisco State UniversitySan FranciscoUnited States of America
| | - Peter Jobson
- Northern Territory Herbarium, Alice Springs, Department of Environment, Parks and Water Security, Alice Springs, Northern Territory, 0870, AustraliaNorthern Territory HerbariumAlice SpringsAustralia
| | - Christopher T. Martine
- Department of Biology, Bucknell University, 1 Dent Drive, Lewisburg, PA, USABucknell UniversityLewisburgUnited States of America
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