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Martínez-Salazar S, Kramer EM, González F, Pabón-Mora N. Spatio-temporal expression of candidate genes for nectar spur development in Tropaeolum (Tropaeolaceae: Brassicales). Ann Bot 2023; 132:1205-1218. [PMID: 37864498 PMCID: PMC10902891 DOI: 10.1093/aob/mcad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/30/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND AND AIMS Tropaeolaceae (Brassicales) comprise ~100 species native to South and Central America. Tropaeolaceae flowers have a nectar spur, formed by a late expansion and evagination of the fused proximal region of the perianth (i.e. the floral tube). This spur is formed in the domain of the tube oriented towards the inflorescence axis, which corresponds to the adaxial floral region. However, little is known about the molecular mechanisms responsible for the evolution of spurs in Tropaeolaceae. METHODS In this study, we examined the spatio-temporal expression of genes putatively responsible for differential patterns of cell division between the adaxial and abaxial floral regions in Tropaeolaceae. These genes include previously identified TCP and KNOX transcription factors and the cell division marker HISTONE H4 (HIS4). KEY RESULTS We found a TCP4 homologue concomitantly expressed with spur initiation and elaboration. Tropaeolaceae possess two TCP4-like (TCP4L) copies, as a result of a Tropaeolaceae-specific duplication. The two copies (TCP4L1 and TCP4L2) in Tropaeolum longifolium show overlapping expression in the epidermis of reproductive apices (inflorescence meristems) and young floral buds, but only TlTCP4L2 shows differential expression in the floral tube at early stages of spur formation, restricted to the adaxial region. This adaxial expression of TlTCP4L2 overlaps with the expression of TlHIS4. Later in development, only TlTCP4L2 is expressed in the nectariferous tissue of the spur. CONCLUSIONS Based on these results, we hypothesize that Tropaeolaceae TCP4L genes had a plesiomorphic role in epidermal development and that, after gene duplication, TCP4L2 acquired a new function in spur initiation and elaboration. To better understand spur evolution in Tropaeolaceae, it is critical to expand developmental genetic studies to their sister group, the Akaniaceae, which possess simultaneously an independent duplication of TCP4L genes and a spurless floral tube.
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Affiliation(s)
- Sebastián Martínez-Salazar
- Instituto de Biología, Universidad de Antioquia, Medellín 050010, Colombia
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Favio González
- Universidad Nacional de Colombia, Facultad de Ciencias, Instituto de Ciencias Naturales, Sede Bogotá 111321, Colombia
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín 050010, Colombia
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Badenes-Pérez FR. Plant Glucosinolate Content and Host-Plant Preference and Suitability in the Small White Butterfly (Lepidoptera: Pieridae) and Comparison with Another Specialist Lepidopteran. Plants (Basel) 2023; 12:plants12112148. [PMID: 37299126 DOI: 10.3390/plants12112148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]
Abstract
Glucosinolates are used in host-plant recognition by insects specialized on Brassicaceae, such as Pieris rapae L. (Lepidoptera: Pieridae). This research investigated the association between P. rapae oviposition and larval survival and host-plant glucosinolate content using 17 plant species in which glucosinolate content had previously been determined. Two-choice oviposition tests (comparing each plant species to Arabidopsis thaliana L.) and larval survival experiments showed that indolic glucosinolate content had a positive effect on oviposition preference and larval survival in P. rapae. In the host plants tested, the effects of indolic glucosinolates on oviposition preference and of glucosinolate complexity index and aliphatic glucosinolates without sulfur-containing side chains on total oviposition were smaller on P. rapae than on Plutella xylostella L. (Lepidoptera: Plutellidae), another lepidopteran specialized on glucosinolate-containing plants. This study suggests that high indolic glucosinolate content could make crop plants more susceptible to both P. rapae and P. xylostella, but this effect seems to be greater for P. xylostella. Additionally, as some differences in oviposition and larval survival between P. rapae and P. xylostella occurred in some individual plants, it cannot be concluded that bottom-up factors are always similar in these two specialist insects.
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Affiliation(s)
- Francisco Rubén Badenes-Pérez
- Max Planck Institute for Chemical Ecology, Department of Entomology, 07745 Jena, Germany
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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3
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Zenchyzen B, Carey S, Antochi-Crihan G, Hall JC. Developmental and genetic basis of the androgynophore in Gynandropsis gynandra. Am J Bot 2023. [PMID: 37210747 DOI: 10.1002/ajb2.16193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
PREMISE Flowering plants have evolved a vast array of floral features involved in plant-pollinator interactions. A feature that seemingly increases the chance of pollen transfer is the androgynophore; a stalk-like structure that raises the reproductive organs of the flower. However, little is known about the developmental and genetic basis of this structure despite its presence in multiple, distantly related taxa. Here, we address this gap by investigating Gynandropsis gynandra (Cleomaceae), a species with prominent androgynophore. METHODS We combined morphological and anatomical analyses with a comparative transcriptomic study to provide a detailed description of the androgynophore throughout development, examine global gene expression patterns, and identify candidate genes putatively involved in androgynophore elongation. KEY RESULTS The radially symmetric androgynophore of G. gynandra rapidly lengthens primarily via cell elongation. Despite its structural uniformity, androgynophore development is characterized by complex gene expression patterns including differential expression of floral organ identity genes and genes associated with organ development and growth in Arabidopsis thaliana. CONCLUSIONS Our morphological characterizations and high-quality transcriptome for G. gynandra suggest that the androgynophore is a novel structure formed via elaboration of both the receptacle and base of reproductive organs as it is structurally like an elongated internode but expresses the genetic repertoire typically associated with the reproductive organs. The drastic increase in cell length and uniform structure elevates the androgynophore as a potentially powerful model for cell elongation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Brandi Zenchyzen
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, Alberta, Canada
| | - Shane Carey
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, Alberta, Canada
| | | | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, Alberta, Canada
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Freitas AVL, Rosa AHB, Kaminski LA, Silva-Brandão KL. Systematic Position, Immature Stages, and Geographic Distribution of Glennia pylotis (Godart, 1819) (Lepidoptera: Papilionoidea: Pieridae). Neotrop Entomol 2023:10.1007/s13744-023-01044-2. [PMID: 37195558 DOI: 10.1007/s13744-023-01044-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/03/2023] [Indexed: 05/18/2023]
Abstract
The biology, immature stages, geographic distribution, and systematic position of Glennia pylotis (Godart, 1819) are presented. This species is mostly restricted to the southeastern coastal Atlantic Forest, from the States of São Paulo to Bahia, with sparse records in the interior of Brazil, Argentina, and Bolivia (this locality is most probably spurious-see below). Data on immature stages are based on textual descriptions; pupal skins were illustrated and compared with those of other members of the subtribe Pierina. Based on molecular data, G. pylotis was recovered as a member of the "Leptophobia clade," as the sister group of all other genera in this clade except for Leptophobia. The immature stages are similar to, and host plants are the same, of several other related genera within Pierina, especially the "Leptophobia clade." By compiling all available data, searching for unpublished information in museums (including the finding of empty pupal cases) and adding molecular evidence for G. pylotis, not only its systematic position was elucidated, but its true conservation status could also be assessed.
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Affiliation(s)
- André Victor Lucci Freitas
- Departamento de Biologia Animal and Museu de Diversidade Biológica, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
| | - Augusto Henrique Batista Rosa
- Departamento de Biologia Animal and Museu de Diversidade Biológica, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Lucas Augusto Kaminski
- Núcleo de Ecologia e Biodiversidade, Instituto de Ciências Básicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
- Departamento de Zoologia, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
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Tineo D, Bustamante DE, Calderon MS. Analysis of the complete plastidial genome of the newly highland papaya Vasconcellea carvalhoae (Caricaceae) from Peru. Mitochondrial DNA B Resour 2022; 7:1882-1886. [PMID: 36325285 PMCID: PMC9621235 DOI: 10.1080/23802359.2022.2135407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Especially in South American Andean communities, Vasconcellea carvalhoae D. Tineo & D.E. Bustamante 2020 is a significant highland papaya with agronomic promise. High-throughput sequencing of the holotype specimen of V. carvalhoae from Peru (KUELAP227) resulted in the assembly of its complete plastid genome (GenBank accession number ON764441). The plastid genome of this highland papaya is 158,723 bp and contains 130 genes. This plastid genome is similar in length, content, and organization to other members of Caricaceae, except for the absence of the pseudogene infA. Phylogenetic analyses of V. carvalhoae support its sistership to V. pubescens.
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Affiliation(s)
- Daniel Tineo
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru
| | - Danilo E. Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru,Instituto de Investigación en Ingeniería Ambiental (IIIA), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru,CONTACT Danilo E. Bustamante Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Martha S. Calderon
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru,Instituto de Investigación en Ingeniería Ambiental (IIIA), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru
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Wu D, Wei Y, Zhao X, Li B, Zhang H, Xu G, Lv J, Zhang D, Zhang X, Ni M. Ancestral function but divergent epigenetic regulation of HAIKU2 reveals routes of seed developmental evolution. Mol Plant 2022; 15:1575-1589. [PMID: 36071671 DOI: 10.1016/j.molp.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/19/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Evolution is driven by various mechanisms. A directional increase in the embryo to endosperm ratio is an evolutionary trend within the angiosperms. The endosperm constitutes a major portion of the seed volume in Poales and some dicots. However, in other dicots such as Arabidopsis and soybean, the endosperm proliferates early, followed by embryo growth to replace the endosperm. The Arabidopsis leucine-rich repeat receptor protein kinase AtHAIKU2 (AtIKU2) is a key regulator of early endosperm proliferation. In this study, we found that IKU2s from Brachypodium, rice, and soybean can complement the abnormal seed developmental phenotype of Atiku2, while AtIKU2 also rescues the defective endosperm proliferation in the Brachypodium BdIKU2 knockout mutant seeds. AtIKU2 and soybean GmIKU2 are actively expressed a few days after fertilization. Thereafter, expression of AtIKU2 is suppressed by the FIS-PRC2 complex-mediated H3K27me3. The soybean GmIKU2 locus is also enriched with H3K27me3 marks. The histone methyltransferase AtMEA is unique to Brassicaceae, but one GmSWN in soybean plays a similar role in seed development as AtMEA. By contrast, the BdIKU2 and rice OsIKU2 loci are continuously expressed and are devoid of H3K27me3 marks. Taken together, these results suggest that IKU2 genes retain an ancestral function, but the duration of their expression that is controlled by PRC2-mediated epigenetic silencing contributes to silenced or persistent endosperm proliferation in different species. Our study reveals an epigenetic mechanism that drives the development of vastly different seed ontogenies.
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Affiliation(s)
- Di Wu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Yiming Wei
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xiangyu Zhao
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Boka Li
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huankai Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Gang Xu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Juntong Lv
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Dajian Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xiansheng Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China.
| | - Min Ni
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, MN 55108, USA.
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7
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Zuo S, Mandáková T, Kubová M, Lysak MA. Genomes, repeatomes and interphase chromosome organization in the meadowfoam family (Limnanthaceae, Brassicales). Plant J 2022; 110:1462-1475. [PMID: 35352402 DOI: 10.1111/tpj.15750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/17/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The meadowfoam family (Limnanthaceae) is one of the smallest and genomically underexplored families of the Brassicales. The Limnanthaceae harbor about seven species in the genus Limnanthes (meadowfoam) and Floerkea proserpinacoides (false mermaidweed), all native to North America. Because all Limnanthes and Floerkea species have only five chromosome pairs, i.e., a chromosome number rare in Brassicales and shared with Arabidopsis thaliana (Arabidopsis), we examined the Limnanthaceae genomes as a potential model system. Using low-coverage whole-genome sequencing data, we reexamined phylogenetic relationships and characterized the repeatomes of Limnanthaceae genomes. Phylogenies based on complete chloroplast and 35S rDNA sequences corroborated the sister relationship between Floerkea and Limnanthes and two major clades in the latter genus. The genome size of Limnanthaceae species ranges from 1.5 to 2.1 Gb, apparently due to the large increase in DNA repeats, which constitute 60-70% of their genomes. Repeatomes are dominated by long terminal repeat retrotransposons, while tandem repeats represent only less than 0.5% of the genomes. The average chromosome size in Limnanthaceae species (340-420 Mb) is more than 10 times larger than in Arabidopsis (32 Mb). A three-dimensional fluorescence in situ hybridization analysis demonstrated that the five chromosome pairs in interphase nuclei of Limnanthes species adopt the Rabl-like configuration.
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Affiliation(s)
- Sheng Zuo
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Michaela Kubová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
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Julius A. Capparis (Capparaceae) in Peninsular Malaysia, including a new species and two new varieties. PhytoKeys 2022; 189:99-127. [PMID: 35169386 PMCID: PMC8837500 DOI: 10.3897/phytokeys.189.49367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
As part of the Flora of Peninsular Malaysia Project, a species checklist of the genus Capparis in Peninsular Malaysia is presented here with a total of 11 species, two subspecies and four varieties. A new species and two varieties, endemic to Peninsular Malaysia, are described and illustrated: Cappariskenaboiensis, C.scortechiniivar.ruthiae and C.trinerviavar.chungiana. Cappariskenaboiensis is known from a single site in Negeri Sembilan and is assessed as Vulnerable (VU); C.scortechiniivar.ruthiae from Pahang is Vulnerable (VU); and Capparistrinerviavar.chungiana is known from Negeri Sembilan, Pahang and Selangor and its conservation status is assessed as Near Threatened (NT). A checklist and updated key to the genus in Peninsular Malaysia are provided.
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Affiliation(s)
- Avelinah Julius
- Forest Research Institute Malaysia, Kepong, Selangor, 52109, MalaysiaForest Research Institute MalaysiaKepongMalaysia
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9
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Matsunaga T, Reisenman CE, Goldman-Huertas B, Brand P, Miao K, Suzuki HC, Verster KI, Ramírez SR, Whiteman NK. Evolution of olfactory receptors tuned to mustard oils in herbivorous Drosophilidae. Mol Biol Evol 2021; 39:6486429. [PMID: 34963012 PMCID: PMC8826531 DOI: 10.1093/molbev/msab362] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The diversity of herbivorous insects is attributed to their propensity to specialize on toxic plants. In an evolutionary twist, toxins betray the identity of their bearers when herbivores coopt them as cues for host-plant finding, but the evolutionary mechanisms underlying this phenomenon are poorly understood. We focused on Scaptomyza flava, an herbivorous drosophilid specialized on isothiocyanate (ITC)-producing (Brassicales) plants, and identified Or67b paralogs that were triplicated as mustard-specific herbivory evolved. Using in vivo heterologous systems for the expression of olfactory receptors, we found that S. flava Or67bs, but not the homologs from microbe-feeding relatives, responded selectively to ITCs, each paralog detecting different ITC subsets. Consistent with this, S. flava was attracted to ITCs, as was Drosophila melanogaster expressing S. flava Or67b3 in the homologous Or67b olfactory circuit. ITCs were likely coopted as olfactory attractants through gene duplication and functional specialization (neofunctionalization and subfunctionalization) in S. flava, a recently derived herbivore.
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Affiliation(s)
- Teruyuki Matsunaga
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Carolina E Reisenman
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA
| | - Benjamin Goldman-Huertas
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA.,Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
| | - Philipp Brand
- Department of Evolution and Ecology, University of California Davis, Davis, CA
| | - Kevin Miao
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Hiromu C Suzuki
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Kirsten I Verster
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Santiago R Ramírez
- Department of Evolution and Ecology, University of California Davis, Davis, CA
| | - Noah K Whiteman
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA
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Martínez-Salazar S, González F, Alzate JF, Pabón-Mora N. Molecular framework underlying floral bilateral symmetry and nectar spur development in Tropaeolum, an atypical member of the Brassicales. Am J Bot 2021; 108:1315-1330. [PMID: 34458983 DOI: 10.1002/ajb2.1719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Floral spurs are key innovations associated with elaborate pollination mechanisms that have evolved independently several times across angiosperms. Spur formation can shift the floral symmetry from radial to bilateral, as it is the case in Tropaeolum, the only member of the Brassicales with floral nectar spurs. The genetic mechanisms underlying both spur and bilateral symmetry in the family have not yet been investigated. METHODS We studied flower development and morphoanatomy of Tropaeolum longifolium. We also generated a reference transcriptome and isolated all candidate genes involved in adaxial-abaxial differential growth during spur formation. Finally, we evaluated the evolution of the targeted genes across Brassicales and examined their expression in dissected floral parts. RESULTS Five sepals initiate spirally, followed by five petals alternate to the sepals, five antesepalous stamens, three antepetalous stamens, and three carpels. Intercalary growth at the common base of sepals and petals forms a floral tube. The spur is an outgrowth from the adaxial region of the tube, lined up with the medial sepal. We identified Tropaeolum specific duplications in the TCP3/4L and STM gene lineages, which are critical for spur formation in other taxa. In addition, we found that TM6 (MADS-box), RL2 (RAD-like7), and KN2/6L2 and OSH6L (KNOX1 genes), have been lost in core Brassicales but retained in Tropaeolum. CONCLUSIONS Three genes are pivotal during the extreme adaxial-abaxial asymmetry of the floral tube, namely, TlTCP4L2 restricted to the adaxial side where the spur is formed, and TlTCP12 and TlSTM1 to the abaxial side, lacking a spur.
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Affiliation(s)
| | - Favio González
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Instituto de Ciencias Naturales, AA 7495, Bogotá, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, AA 1226, Medellín, Colombia
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Beric A, Mabry ME, Harkess AE, Brose J, Schranz ME, Conant GC, Edger PP, Meyers BC, Pires JC. Comparative phylogenetics of repetitive elements in a diverse order of flowering plants ( Brassicales). G3 (Bethesda) 2021; 11:jkab140. [PMID: 33993297 PMCID: PMC8495927 DOI: 10.1093/g3journal/jkab140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/10/2021] [Indexed: 11/14/2022]
Abstract
Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana-chosen as the model plant system for this reason-as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm the correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.
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Affiliation(s)
- Aleksandra Beric
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Makenzie E Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Alex E Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Julia Brose
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen 6700 AA, The Netherlands
| | - Gavin C Conant
- Bioinformatics Research Center, Program in Genetics and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Department of Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - J Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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Shakour ZT, Shehab NG, Gomaa AS, Wessjohann LA, Farag MA. Metabolic and biotransformation effects on dietary glucosinolates, their bioavailability, catabolism and biological effects in different organisms. Biotechnol Adv 2021; 54:107784. [PMID: 34102260 DOI: 10.1016/j.biotechadv.2021.107784] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/17/2021] [Accepted: 06/04/2021] [Indexed: 12/28/2022]
Abstract
Glucosinolate-producing plants have long been recognized for both their distinctive benefits to human nutrition and their resistance traits against pathogens and herbivores. Despite the accumulation of glucosinolates (GLS) in plants is associated with their resistance to various biotic and abiotic stresses, the defensive and biological activities of GLS are commonly conveyed by their metabolic products. In view of this, metabolism is considered the driving factor upon the interactions of GLS-producing plants with other organisms, also influenced by plant and plant attacking or digesting organism characteristics. Several microbial pathogens and insects have evolved the capacity to detoxify GLS-hydrolysis products or inhibit their formation via different means, highlighting the relevance of their metabolic abilities for the plants' defense system activation and target organism detoxification. Strikingly, some bacteria, fungi and insects can likewise produce their own myrosinase (MYR)-like enzymes in one of the most important adaptation strategies against the GLS-MYR plant defense system. Knowledge of GLS metabolic pathways in herbivores and pathogens can impact plant protection efforts and may be harnessed upon for genetically modified plants that are more resistant to predators. In humans, the interest in the implementation of GLS in diets for the prevention of chronic diseases has grown substantially. However, the efficiency of such approaches is dependent on GLS bioavailability and metabolism, which largely involves the human gut microbiome. Among GLS-hydrolytic products, isothiocyanates (ITC) have shown exceptional properties as chemical plant defense agents against herbivores and pathogens, along with their health-promoting benefits in humans, at least if consumed in reasonable amounts. Deciphering GLS metabolic pathways provides critical information for catalyzing all types of GLS towards the generation of ITCs as the biologically most active metabolites. This review provides an overview on contrasting metabolic pathways in plants, bacteria, fungi, insects and humans towards GLS activation or detoxification. Further, suggestions for the preparation of GLS containing plants with improved health benefits are presented.
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Affiliation(s)
- Zeinab T Shakour
- Laboratory of Phytochemistry, National Organization for Drug Control and Research, Cairo, Egypt
| | - Naglaa G Shehab
- Department of Pharmaceutical Chemistry and Natural Products, Dubai Pharmacy College, Dubai, United Arab Emirates
| | - Ahmed S Gomaa
- Faculty of Graduate Studies for Statistical Research, Cairo University, Cairo, Egypt
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Mohamed A Farag
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt; Chemistry Department, School of Sciences & Engineering, The American University in Cairo, New Cairo, Egypt.
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Kask K, Kaurilind E, Talts E, Kännaste A, Niinemets Ü. Combined Acute Ozone and Water Stress Alters the Quantitative Relationships between O 3 Uptake, Photosynthetic Characteristics and Volatile Emissions in Brassica nigra. Molecules 2021; 26:molecules26113114. [PMID: 34070994 PMCID: PMC8197083 DOI: 10.3390/molecules26113114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Ozone (O3) entry into plant leaves depends on atmospheric O3 concentration, exposure time and openness of stomata. O3 negatively impacts photosynthesis rate (A) and might induce the release of reactive volatile organic compounds (VOCs) that can quench O3, and thereby partly ameliorate O3 stress. Water stress reduces stomatal conductance (gs) and O3 uptake and can affect VOC release and O3 quenching by VOC, but the interactive effects of O3 exposure and water stress, as possibly mediated by VOC, are poorly understood. Well-watered (WW) and water-stressed (WS) Brassica nigra plants were exposed to 250 and 550 ppb O3 for 1 h, and O3 uptake rates, photosynthetic characteristics and VOC emissions were measured through 22 h recovery. The highest O3 uptake was observed in WW plants exposed to 550 ppb O3 with the greatest reduction and poorest recovery of gs and A, and elicitation of lipoxygenase (LOX) pathway volatiles 10 min-1.5 h after exposure indicating cellular damage. Ozone uptake was similar in 250 ppb WW and 550 ppb WS plants and, in both treatments, O3-dependent reduction in photosynthetic characteristics was moderate and fully reversible, and VOC emissions were little affected. Water stress alone did not affect the total amount and composition of VOC emissions. The results indicate that drought ameliorated O3 stress by reducing O3 uptake through stomatal closure and the two stresses operated in an antagonistic manner in B. nigra.
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Affiliation(s)
- Kaia Kask
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (E.K.); (E.T.); (A.K.); (Ü.N.)
- Correspondence:
| | - Eve Kaurilind
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (E.K.); (E.T.); (A.K.); (Ü.N.)
| | - Eero Talts
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (E.K.); (E.T.); (A.K.); (Ü.N.)
| | - Astrid Kännaste
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (E.K.); (E.T.); (A.K.); (Ü.N.)
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (E.K.); (E.T.); (A.K.); (Ü.N.)
- Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia
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14
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Agerbirk N, Hansen CC, Kiefer C, Hauser TP, Ørgaard M, Asmussen Lange CB, Cipollini D, Koch MA. Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps. Phytochemistry 2021; 185:112668. [PMID: 33743499 DOI: 10.1016/j.phytochem.2021.112668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
We review glucosinolate (GSL) diversity and analyze phylogeny in the crucifer tribe Cardamineae as well as selected species from Brassicaceae (tribe Brassiceae) and Resedaceae. Some GSLs occur widely, while there is a scattered distribution of many less common GSLs, tentatively sorted into three classes: ancient, intermediate and more recently evolved. The number of conclusively identified GSLs in the tribe (53 GSLs) constitute 60% of all GSLs known with certainty from any plant (89 GSLs) and apparently unique GSLs in the tribe constitute 10 of those GSLs conclusively identified (19%). Intraspecific, qualitative GSL polymorphism is known from at least four species in the tribe. The most ancient GSL biosynthesis in Brassicales probably involved biosynthesis from Phe, Val, Leu, Ile and possibly Trp, and hydroxylation at the β-position. From a broad comparison of families in Brassicales and tribes in Brassicaceae, we estimate that a common ancestor of the tribe Cardamineae and the family Brassicaceae exhibited GSL biosynthesis from Phe, Val, Ile, Leu, possibly Tyr, Trp and homoPhe (ancient GSLs), as well as homologs of Met and possibly homoIle (intermediate age GSLs). From the comparison of phylogeny and GSL diversity, we also suggest that hydroxylation and subsequent methylation of indole GSLs and usual modifications of Met-derived GSLs (formation of sulfinyls, sulfonyls and alkenyls) occur due to conserved biochemical mechanisms and was present in a common ancestor of the family. Apparent loss of homologs of Met as biosynthetic precursors was deduced in the entire genus Barbarea and was frequent in Cardamine (e.g. C. pratensis, C. diphylla, C. concatenata, possibly C. amara). The loss was often associated with appearance of significant levels of unique or rare GSLs as well as recapitulation of ancient types of GSLs. Biosynthetic traits interpreted as de novo evolution included hydroxylation at rare positions, acylation at the thioglucose and use of dihomoIle and possibly homoIle as biosynthetic precursors. Biochemical aspects of the deduced evolution are discussed and testable hypotheses proposed. Biosyntheses from Val, Leu, Ile, Phe, Trp, homoPhe and homologs of Met are increasingly well understood, while GSL biosynthesis from mono- and dihomoIle is poorly understood. Overall, interpretation of known diversity suggests that evolution of GSL biosynthesis often seems to recapitulate ancient biosynthesis. In contrast, unprecedented GSL biosynthetic innovation seems to be rare.
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Affiliation(s)
- Niels Agerbirk
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| | - Cecilie Cetti Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Christiane Kiefer
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Thure P Hauser
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Marian Ørgaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Conny Bruun Asmussen Lange
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Don Cipollini
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH, 45435, USA
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
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Nguyen VPT, Stewart J, Lopez M, Ioannou I, Allais F. Glucosinolates: Natural Occurrence, Biosynthesis, Accessibility, Isolation, Structures, and Biological Activities. Molecules 2020; 25:E4537. [PMID: 33022970 DOI: 10.3390/molecules25194537] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 12/13/2022] Open
Abstract
Glucosinolates (GSLs) are secondary plant metabolites abundantly found in plant order Brassicales. GSLs are constituted by an S-β-d-glucopyrano unit anomerically connected to O-sulfated (Z)-thiohydroximate moiety. The side-chain of the O-sulfate thiohydroximate moiety, which is derived from a different amino acid, contributes to the diversity of natural GSL, with more than 130 structures identified and validated to this day. Both the structural diversity of GSL and their biological implication in plants have been biochemically studied. Although chemical syntheses of GSL have been devised to give access to these secondary metabolites, direct extraction from biomass remains the conventional method to isolate natural GSL. While intact GSLs are biologically inactive, various products, including isothiocyanates, nitriles, epithionitriles, and cyanides obtained through their hydrolysis of GSLs, exhibit many different biological activities, among which several therapeutic benefits have been suggested. This article reviews natural occurrence, accessibility via chemical, synthetic biochemical pathways of GSL, and the current methodology of extraction, purification, and characterization. Structural information, including the most recent classification of GSL, and their stability and storage conditions will also be discussed. The biological perspective will also be explored to demonstrate the importance of these prominent metabolites.
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Mabry ME, Brose JM, Blischak PD, Sutherland B, Dismukes WT, Bottoms CA, Edger PP, Washburn JD, An H, Hall JC, McKain MR, Al‐Shehbaz I, Barker MS, Schranz ME, Conant GC, Pires JC. Phylogeny and multiple independent whole-genome duplication events in the Brassicales. Am J Bot 2020; 107:1148-1164. [PMID: 32830865 PMCID: PMC7496422 DOI: 10.1002/ajb2.1514] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/05/2020] [Indexed: 05/04/2023]
Abstract
PREMISE Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear. METHODS Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny. RESULTS Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae. CONCLUSIONS Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.
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Affiliation(s)
- Makenzie E. Mabry
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Julia M. Brose
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Paul D. Blischak
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85719USA
| | - Brittany Sutherland
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85719USA
| | - Wade T. Dismukes
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Christopher A. Bottoms
- Informatics Research Core Facility and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Patrick P. Edger
- Department of HorticultureMichigan State UniversityEast LansingMichigan48824USA
| | | | - Hong An
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Jocelyn C. Hall
- Department of Biological SciencesUniversity of AlbertaEdmontonT6G 2E9Canada
| | - Michael R. McKain
- Department of Biological SciencesThe University of AlabamaTuscaloosaAlabama35401USA
| | | | - Michael S. Barker
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85719USA
| | | | - Gavin C. Conant
- Bioinformatics Research CenterProgram in Genetics and Department of Biological SciencesNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - J. Chris Pires
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
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Gomes Pacheco T, Morais da Silva G, de Santana Lopes A, de Oliveira JD, Rogalski JM, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae). Planta 2020; 252:17. [PMID: 32666132 DOI: 10.1007/s00425-020-03427-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Complete plastome sequence of Tropaeolum pentaphyllum revealed molecular markers, hotspots of nucleotide polymorphism, RNA editing sites and phylogenetic aspects Tropaeolaceae Juss. ex DC. comprises approximately 95 species across North and South Americas. Tropaeolum pentaphyllum Lam. is an unconventional and endangered species with occurrence in some countries of South America. Although this species presents nutritional, medicinal and ornamental uses, genetic studies involving natural populations or promising genotypes are practically non-existent. Here, we report the nucleotide sequence of T. pentaphyllum plastome. It represents the first complete plastome sequence of the family Tropaeolaceae to be fully sequenced and analyzed in detail. The sequencing data revealed that the T. pentaphyllum plastome is highly similar to the plastomes of other Brassicales. Notwithstanding, our analyses detected some specific features concerning events of IR expansion and structural changes in some genes such as matK, rpoA, and rpoC2. We also detected 251 SSR loci, nine hotspots of nucleotide polymorphism, and two specific RNA editing sites in the plastome of T. pentaphyllum. Moreover, plastid phylogenomic inference indicated a closed relationship between the families Tropaeolaceae and Akaniaceae, which formed a sister group to Moringaceae-Caricaceae. Finally, our data bring new molecular markers and evolutionary features to be applied in the natural population, germplasm collection, and genotype selection aiming conservation, genetic diversity evaluation, and exploitation of this endangered species.
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Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gleyson Morais da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José Daniel de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Juliana Marcia Rogalski
- Núcleo de Ciências Biológicas e Ambientais, Instituto Federal do Rio Grande do Sul, Distrito Engenheiro Luiz Englert, Sertão, RS, Brazil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Mishra B, Ploch S, Runge F, Schmuker A, Xia X, Gupta DK, Sharma R, Thines M. The Genome of Microthlaspi erraticum (Brassicaceae) Provides Insights Into the Adaptation to Highly Calcareous Soils. Front Plant Sci 2020; 11:943. [PMID: 32719698 PMCID: PMC7350527 DOI: 10.3389/fpls.2020.00943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Microthlaspi erraticum is widely distributed in temperate Eurasia, but restricted to Ca2+-rich habitats, predominantly on white Jurassic limestone, which is made up by calcium carbonate, with little other minerals. Thus, naturally occurring Microthlaspi erraticum individuals are confronted with a high concentration of Ca2+ ions while Mg2+ ion concentration is relatively low. As there is a competitive uptake between these two ions, adaptation to the soil condition can be expected. In this study, it was the aim to explore the genomic consequences of this adaptation by sequencing and analysing the genome of Microthlaspi erraticum. Its genome size is comparable with other diploid Brassicaceae, while more genes were predicted. Two Mg2+ transporters known to be expressed in roots were duplicated and one showed a significant degree of positive selection. It is speculated that this evolved due to the pressure to take up Mg2+ ions efficiently in the presence of an overwhelming amount of Ca2+ ions. Future studies on plants specialized on similar soils and affinity tests of the transporters are needed to provide unequivocal evidence for this hypothesis. If verified, the transporters found in this study might be useful for breeding Brassicaceae crops for higher yield on Ca2+-rich and Mg2+ -poor soils.
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Affiliation(s)
- Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Frankfurt am Main, Germany
| | - Sebastian Ploch
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Fabian Runge
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | | | - Xiaojuan Xia
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Frankfurt am Main, Germany
| | - Deepak K. Gupta
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Frankfurt am Main, Germany
| | - Rahul Sharma
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Frankfurt am Main, Germany
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Murik O, Chandran SA, Nevo-Dinur K, Sultan LD, Best C, Stein Y, Hazan C, Ostersetzer-Biran O. Topologies of N 6 -adenosine methylation (m 6 A) in land plant mitochondria and their putative effects on organellar gene expression. Plant J 2020; 101:1269-1286. [PMID: 31657869 DOI: 10.1111/tpj.14589] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Mitochondria serve as major sites of ATP production and play key roles in many other metabolic processes that are critical to the cell. As relicts of an ancient bacterial endosymbiont, mitochondria contain their own hereditary material (i.e. mtDNA, or mitogenome) and a machinery for protein biosynthesis. The expression of the mtDNA in plants is complex, particularly at the post-transcriptional level. Following transcription, the polycistronic pre-RNAs undergo extensive modifications, including trimming, splicing and editing, before being translated by organellar ribosomes. Our study focuses on N6 -methylation of adenosine ribonucleotides (m6 A-RNA) in plant mitochondria. m6 A is a prevalent modification in nuclear-encoded mRNAs. The biological significance of this dynamic modification is under investigation, but it is widely accepted that m6 A mediates structural switches that affect RNA stability and/or activity. Using m6 A-pulldown/RNA-seq (m6 A-RIP-seq) assays of Arabidopsis and cauliflower mitochondria, we provide information on the m6 A-RNA landscapes in Arabidopsis thaliana and Brassica oleracea mitochondria. The results show that m6 A targets different types of mitochondrial transcripts, including known genes, mtORFs, as well as non-coding (transcribed intergenic) RNA species. While ncRNAs undergo multiple m6 A modifications, N6 -methylation of adenosine residues with mRNAs seem preferably positioned near start codons and may modulate their translatability.
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Affiliation(s)
- Omer Murik
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Sam Aldrin Chandran
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Keren Nevo-Dinur
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Laure D Sultan
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Corinne Best
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Yuval Stein
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Carina Hazan
- Analytical Chemistry Laboratory, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Oren Ostersetzer-Biran
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
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20
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Ouassou M, Mukhaimar M, El Amrani A, Kroymann J, Chauveau O. [Biosynthesis of indole glucosinolates and ecological role of secondary modification pathways]. C R Biol 2019; 342:58-80. [PMID: 31088733 DOI: 10.1016/j.crvi.2019.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/26/2022]
Abstract
Indole glucosinolates are plant secondary metabolites derived from the amino acid tryptophan. They are part of a large group of sulfur-containing molecules almost exclusively found among Brassicales, which include the mustard family (Brassicaceae) with many edible plant species of major nutritional importance. These compounds mediate numerous interactions between these plants and their natural enemies and are therefore of major biological and economical interest. This literature review aims at taking stock of recent advances of our knowledge about the biosynthetic pathways of indole glucosinolates, but also about the defense strategies and ecological processes involving these metabolites.
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Affiliation(s)
- Malika Ouassou
- Unité « Écologie, systématique et évolution », UMR 8079, université Paris-Sud, CNRS, AgroParisTech, université Paris-Saclay, 91405 Orsay, France; Laboratory of Biochemistry and Molecular Genetics, Department of Biology, Faculty of Science and Technics, Abdelmalek Essaadi University, Tangier, Maroc
| | - Maisara Mukhaimar
- National Agricultural Research Center (NARC)-Jenin/Gaza, Ministry of Agriculture, Jenin, Palestine
| | - Amal El Amrani
- Laboratory of Biochemistry and Molecular Genetics, Department of Biology, Faculty of Science and Technics, Abdelmalek Essaadi University, Tangier, Maroc
| | - Juergen Kroymann
- Unité « Écologie, systématique et évolution », UMR 8079, université Paris-Sud, CNRS, AgroParisTech, université Paris-Saclay, 91405 Orsay, France
| | - Olivier Chauveau
- Unité « Écologie, systématique et évolution », UMR 8079, université Paris-Sud, CNRS, AgroParisTech, université Paris-Saclay, 91405 Orsay, France.
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Kask K, Kännaste A, Talts E, Copolovici L, Niinemets Ü. How specialized volatiles respond to chronic and short-term physiological and shock heat stress in Brassica nigra. Plant Cell Environ 2016; 39:2027-42. [PMID: 27287526 PMCID: PMC5798583 DOI: 10.1111/pce.12775] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 05/04/2023]
Abstract
Brassicales release volatile glucosinolate breakdown products upon tissue mechanical damage, but it is unclear how the release of glucosinolate volatiles responds to abiotic stresses such as heat stress. We used three different heat treatments, simulating different dynamic temperature conditions in the field to gain insight into stress-dependent changes in volatile blends and photosynthetic characteristics in the annual herb Brassica nigra (L.) Koch. Heat stress was applied by either heating leaves through temperature response curve measurements from 20 to 40 °C (mild stress), exposing plants for 4 h to temperatures 25-44 °C (long-term stress) or shock-heating leaves to 45-50 °C. Photosynthetic reduction through temperature response curves was associated with decreased stomatal conductance, while the reduction due to long-term stress and collapse of photosynthetic activity after heat shock stress were associated with non-stomatal processes. Mild stress decreased constitutive monoterpene emissions, while long-term stress and shock stress resulted in emissions of the lipoxygenase pathway and glucosinolate volatiles. Glucosinolate volatile release was more strongly elicited by long-term stress and lipoxygenase product released by heat shock. These results demonstrate that glucosinolate volatiles constitute a major part of emission blend in heat-stressed B. nigra plants, especially upon chronic stress that leads to induction responses.
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Affiliation(s)
- Kaia Kask
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia
- Author for correspondence.
| | - Astrid Kännaste
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia
| | - Eero Talts
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia
| | - Lucian Copolovici
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia
- Institute of Technical and Natural Sciences Research-Development of “Aurel Vlaicu” University, 2 Elena Dragoi St., 310330, Arad, Romania
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia
- Elena Dragoi St., 310330, Arad, Romania
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22
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Franzke A, Koch MA, Mummenhoff K. Turnip Time Travels: Age Estimates in Brassicaceae. Trends Plant Sci 2016; 21:554-561. [PMID: 26917156 DOI: 10.1016/j.tplants.2016.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/19/2016] [Accepted: 01/31/2016] [Indexed: 05/07/2023]
Abstract
Results of research in life sciences acquire a deeper meaning if they can also be discussed in temporal contexts of evolution. Despite the importance of the mustard family (Brassicaceae) as a prominent angiosperm model family, a robust, generally accepted hypothesis for a family-wide temporal framework does not yet exist. The main cause for this situation is a poor fossil record of the family. We suggest that the few known fossils require a critical re-evaluation of phylogenetic and temporal assignments as a prerequisite for appropriate molecular dating analyses within the family. In addition, (palaeo)biogeographical calibrations, not explored so far in the family, should be integrated in a synthesis of various dating approaches, with each contributing their specific possibilities and limitations.
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Affiliation(s)
- Andreas Franzke
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany.
| | - Marcus A Koch
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany; Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, German
| | - Klaus Mummenhoff
- Biology Department, Botany, Osnabrück University, D-49069 Osnabrück, Germany
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23
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Rockinger A, Sousa A, Carvalho FA, Renner SS. Chromosome number reduction in the sister clade of Carica papaya with concomitant genome size doubling. Am J Bot 2016; 103:1082-8. [PMID: 27234227 DOI: 10.3732/ajb.1600134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/03/2016] [Indexed: 05/15/2023]
Abstract
PREMISE OF THE STUDY Caricaceae include six genera and 34 species, among them papaya, a model species in plant sex chromosome research. The family was held to have a conserved karyotype with 2n = 18 chromosomes, an assumption based on few counts. We examined the karyotypes and genome size of species from all genera to test for possible cytogenetic variation. METHODS We used fluorescent in situ hybridization using standard telomere, 5S, and 45S rDNA probes. New and published data were combined with a phylogeny, molecular clock dating, and C values (available for ∼50% of the species) to reconstruct genome evolution. KEY RESULTS The African genus Cylicomorpha, which is sister to the remaining Caricaceae (all neotropical), has 2n = 18, as do the species in two other genera. A Mexican clade of five species that includes papaya, however, has 2n = 18 (papaya), 2n = 16 (Horovitzia cnidoscoloides), and 2n = 14 (Jarilla caudata and J. heterophylla; third Jarilla not counted), with the phylogeny indicating that the dysploidy events occurred ∼16.6 and ∼5.5 million years ago and that Jarilla underwent genome size doubling (∼450 to 830-920 Mbp/haploid genome). Pericentromeric interstitial telomere repeats occur in both Jarilla adjacent to 5S rDNA sites, and the variability of 5S rDNA sites across all genera is high. CONCLUSIONS On the basis of outgroup comparison, 2n = 18 is the ancestral number, and repeated chromosomal fusions with simultaneous genome size increase as a result of repetitive elements accumulating near centromeres characterize the papaya clade. These results have implications for ongoing genome assemblies in Caricaceae.
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Affiliation(s)
| | - Aretuza Sousa
- Systematic Botany and Mycology, University of Munich, 80638 Munich, Germany
| | | | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich, 80638 Munich, Germany
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24
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Müller C, van Loon J, Ruschioni S, De Nicola GR, Olsen CE, Iori R, Agerbirk N. Taste detection of the non-volatile isothiocyanate moringin results in deterrence to glucosinolate-adapted insect larvae. Phytochemistry 2015; 118:139-148. [PMID: 26318325 DOI: 10.1016/j.phytochem.2015.08.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 08/11/2015] [Accepted: 08/17/2015] [Indexed: 06/04/2023]
Abstract
Isothiocyanates (ITCs), released from Brassicales plants after hydrolysis of glucosinolates, are known for their negative effects on herbivores but mechanisms have been elusive. The ITCs are initially present in dissolved form at the site of herbivore feeding, but volatile ITCs may subsequently enter the gas phase and all ITCs may react with matrix components. Deterrence to herbivores resulting from topically applied volatile ITCs in artificial feeding assays may hence lead to ambiguous conclusions. In the present study, the non-volatile ITC moringin (4-(α-L-rhamnopyranosyloxy)benzyl ITC) and its glucosinolate precursor glucomoringin were examined for effects on behaviour and taste physiology of specialist insect herbivores of Brassicales. In feeding bioassays, glucomoringin was not deterrent to larvae of Pieris napi (Lepidoptera: Pieridae) and Athalia rosae (Hymenoptera: Tenthredinidae), which are adapted to glucosinolates. Glucomoringin stimulated feeding of larvae of the related Pieris brassicae (Lepidoptera: Pieridae) and also elicited electrophysiological activity from a glucosinolate-sensitive gustatory neuron in the lateral maxillary taste sensilla. In contrast, the ITC moringin was deterrent to P. napi and P. brassicae at high levels and to A. rosae at both high and low levels when topically applied to cabbage leaf discs (either 12, 120 or 1200 nmol moringin per leaf disc of 1cm diameter). Survival of A. rosae was also significantly reduced when larvae were kept on leaves treated with moringin for several days. Furthermore, moringin elicited electrophysiological activity in a deterrent-sensitive neuron in the medial maxillary taste sensillum of P. brassicae, providing a sensory mechanism for the deterrence and the first known ITC taste response of an insect. In simulated feeding assays, recovery of moringin was high, in accordance with its non-volatile nature. Our results demonstrate taste-mediated deterrence of a non-volatile, natural ITC to glucosinolate-adapted insects.
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Affiliation(s)
- Caroline Müller
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Joop van Loon
- Laboratory of Entomology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Sara Ruschioni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Blanche, 60131 Ancona, Italy
| | - Gina Rosalinda De Nicola
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per le colture industriali (CRA-CIN), Via di Corticella 133, 40128 Bologna, Italy
| | - Carl Erik Olsen
- Copenhagen Plant Science Center and Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Renato Iori
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per le colture industriali (CRA-CIN), Via di Corticella 133, 40128 Bologna, Italy
| | - Niels Agerbirk
- Copenhagen Plant Science Center and Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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25
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Riach AC, Perera MVL, Florance HV, Penfield SD, Hill JK. Analysis of plant leaf metabolites reveals no common response to insect herbivory by Pieris rapae in three related host-plant species. J Exp Bot 2015; 66:2547-56. [PMID: 25711707 PMCID: PMC4986865 DOI: 10.1093/jxb/erv045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Studying the biochemical responses of different plant species to insect herbivory may help improve our understanding of the evolution of defensive metabolites found in host plants and their role in plant-herbivore interactions. Untargeted metabolic fingerprints measured as individual mass features were used to compare metabolite reactions in three Brassicales host-plant species (Cleome spinosa, Brassica oleracea, and Lunaria annua) to larval herbivore attack (Pieris rapae; Lepidoptera). Principal component analyses of metabolic fingerprints were able to distinguish among the three plant species and between uneaten control plants and plants that had been eaten. A large number of mass features (1186, 13% of mass features measured in control plants) were common to the three plant species. However, there were few similarities in the mass features that were induced (i.e. changed in abundance) following herbivory. Of the 87 and 68 induced mass features in B. oleracea and C. spinosa, respectively, there were only three that were induced in both plant species. By contrast, L. annua only had one mass feature induced by herbivory, and this was not induced in the other two plant species. The growth of the P. rapae larvae was poorer on the host plant L. annua than on B. oleracea and C. spinosa. The absence of common metabolites among the plants meant these induced responses could not be related to the performance of the herbivore. Thus, the response to herbivory by the same herbivore in these three host plants has evolved to be idiosyncratic in terms of the specific metabolites induced.
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Affiliation(s)
- A C Riach
- Department of Biology, University of York, York YO10 5DD, UK
| | - M V L Perera
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - H V Florance
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - S D Penfield
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - J K Hill
- Department of Biology, University of York, York YO10 5DD, UK
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26
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Grewe F, Edger PP, Keren I, Sultan L, Pires JC, Ostersetzer-Biran O, Mower JP. Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea. Mitochondrion 2014; 19 Pt B:135-43. [PMID: 24907441 DOI: 10.1016/j.mito.2014.05.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 05/21/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
Abstract
To elucidate the evolution of mitochondrial genomic diversity within a single order of angiosperms, we sequenced seven Brassicales genomes and the transcriptome of Brassica oleracea. In the common ancestor of Brassicaceae, several genes of known function were lost and the ccmFN gene was split into two independent genes, which also coincides with a trend of genome reduction towards the smallest sequenced angiosperm genomes of Brassica. For most ORFs of unknown function, the lack of conservation throughout Brassicales and the generally low expression and absence of RNA editing in B. oleracea argue against functionality. However, two chimeric ORFs were expressed and edited in B. oleracea, suggesting a potential role in cytoplasmic male sterility in certain nuclear backgrounds. These results demonstrate how frequent shifts in size, structure, and content of plant mitochondrial genomes can occur over short evolutionary time scales.
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Affiliation(s)
- Felix Grewe
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Ido Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Laure Sultan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
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27
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Goldstein PZ, Metz MA, Solis MA. Phylogenetic systematics of Schacontia Dyar with descriptions of eight new species (Lepidoptera, Crambidae). Zookeys 2013; 291:27-81. [PMID: 23794861 PMCID: PMC3677288 DOI: 10.3897/zookeys.291.3744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 03/08/2013] [Indexed: 11/20/2022] Open
Abstract
The Neotropical genus SchacontiaDyar (1914) is reviewed and revised to include eleven species. Schacontia replica Dyar, 1914, syn. n. and Schacontia pfeifferi Amsel, 1956, syn. n. are synonymized with Schacontia chanesalis (Druce, 1899) and eight new species are described: Schacontia umbra,sp. n., Schacontia speciosa,sp. n., Schacontia themis, sp. n., Schacontia rasa, sp. n., Schacontia nyx,sp. n., Schacontia clotho, sp. n., Schacontia lachesis, sp. n., and Schacontia atropos, sp. n. Three species, Schacontia medalba, Schacontia chanesalis, and Schacontia ysticalis, are re-described. An analysis of 64 characters (56 binary, 8 multistate; 5 head, 13 thoracic, 13 abdominal, 25 male genitalic, and 8 female genitalic) scored for all Schacontia and three outgroup species (Eustixia pupula Hübner, 1823, Glaphyria sesquistrialis Hübner, 1823, and Hellula undalis (Fabricius, 1781)) retrieved 8 equally most parsimonious trees (L=102, CI=71, RI=84) of which the strict consensus is: [[[[medalba + umbra] + chanesalis] + speciosa] + [ysticalis + [rasa + themis + [atropos + lachesis + nyx + clotho]]]]. The relevance of male secondary sexual characters to the diagnosis of Schacontia species is discussed.
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Affiliation(s)
- Paul Z. Goldstein
- Department of Entomology, University of Maryland, College Park, MD USA
- National Museum of Natural History, E-523, P.O. Box 37012, MRC 168, Washington, DC 20013-7012
| | - Mark A. Metz
- Systematic Entomology Laboratory, USDA, National Museum of Natural History, P.O. Box 37012, MRC 168, Washington, DC 20013-7012
| | - M. Alma Solis
- Systematic Entomology Laboratory, USDA, National Museum of Natural History, P.O. Box 37012, MRC 168, Washington, DC 20013-7012
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28
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Hatje K, Kollmar M. A phylogenetic analysis of the brassicales clade based on an alignment-free sequence comparison method. Front Plant Sci 2012; 3:192. [PMID: 22952468 PMCID: PMC3429886 DOI: 10.3389/fpls.2012.00192] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 08/06/2012] [Indexed: 05/06/2023]
Abstract
Phylogenetic analyses reveal the evolutionary derivation of species. A phylogenetic tree can be inferred from multiple sequence alignments of proteins or genes. The alignment of whole genome sequences of higher eukaryotes is a computational intensive and ambitious task as is the computation of phylogenetic trees based on these alignments. To overcome these limitations, we here used an alignment-free method to compare genomes of the Brassicales clade. For each nucleotide sequence a Chaos Game Representation (CGR) can be computed, which represents each nucleotide of the sequence as a point in a square defined by the four nucleotides as vertices. Each CGR is therefore a unique fingerprint of the underlying sequence. If the CGRs are divided by grid lines each grid square denotes the occurrence of oligonucleotides of a specific length in the sequence (Frequency Chaos Game Representation, FCGR). Here, we used distance measures between FCGRs to infer phylogenetic trees of Brassicales species. Three types of data were analyzed because of their different characteristics: (A) Whole genome assemblies as far as available for species belonging to the Malvidae taxon. (B) EST data of species of the Brassicales clade. (C) Mitochondrial genomes of the Rosids branch, a supergroup of the Malvidae. The trees reconstructed based on the Euclidean distance method are in general agreement with single gene trees. The Fitch-Margoliash and Neighbor joining algorithms resulted in similar to identical trees. Here, for the first time we have applied the bootstrap re-sampling concept to trees based on FCGRs to determine the support of the branchings. FCGRs have the advantage that they are fast to calculate, and can be used as additional information to alignment based data and morphological characteristics to improve the phylogenetic classification of species in ambiguous cases.
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Affiliation(s)
- Klas Hatje
- Abteilung NMR-Basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische ChemieGöttingen, Germany
| | - Martin Kollmar
- Abteilung NMR-Basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische ChemieGöttingen, Germany
- *Correspondence: Martin Kollmar, Abteilung NMR-Basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany. e-mail:
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29
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Abstract
Simple sequence repeats (SSRs) are present abundantly in most eukaryotic genomes. They affect several cellular processes like chromatin organization, regulation of gene activity, DNA repair, DNA recombination, etc. Though considerable data exists on using nuclear SSRs to infer phylogenetic relationships, the potential of chloroplast microsatellites (cpSSR), in this regard, remains largely unexplored. In the present study we probe various nucleotide repeat motifs (NRMs) / types of SSRs present in chloroplast genomes (cpDNA) of 12 species belonging to Brassicaceae family. NRMs show a non-random distribution in coding and non-coding compartments of cpDNA. As expected, trinucleotide repeats are more common in coding regions while other repeat motifs are prominent in non-coding DNA. Total numbers of SSRs in coding region show little variation between species while considerable variation is exhibited by SSRs in non-coding regions. Finally, we have designed universal primers that yield polymorphic amplicons from all 12 species. Our analysis also suggests that amplicon length polymorphism shows no significant relationship with sequence based phylogeny of SSRs in cpDNA of Brassicaceae family.
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Affiliation(s)
- Sumit G Gandhi
- Plant Biotechnology Division and Systems Biology Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research),
Canal Road, Jammu ‐ 180 001, India
| | - Praveen Awasthi
- Plant Biotechnology Division and Systems Biology Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research),
Canal Road, Jammu ‐ 180 001, India
| | - Yashbir S Bedi
- Plant Biotechnology Division and Systems Biology Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research),
Canal Road, Jammu ‐ 180 001, India
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30
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Barker MS, Vogel H, Schranz ME. Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. Genome Biol Evol 2009; 1:391-9. [PMID: 20333207 PMCID: PMC2817432 DOI: 10.1093/gbe/evp040] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2009] [Indexed: 11/12/2022] Open
Abstract
The analysis of the Arabidopsis genome revealed evidence of three ancient polyploidy events in the evolution of the Brassicaceae, but the exact phylogenetic placement of these events is still not resolved. The most recent event is called the At-alpha (alpha) or 3R, the intermediate event is referred to as the At-beta (beta) or 2R, and the oldest is the At-gamma (gamma) or 1R. It has recently been established that At-gamma is shared with other Rosids, including papaya (Carica), poplar (Populus), and grape (Vitis), whereas data to date suggest that At-alpha is Brassicaceae specific. To address more precisely when the At-alpha and At-beta events occurred and which plant lineages share these paleopolyploidizations, we sequenced and analyzed over 4,700 normalized expressed sequence tag sequences from the Cleomaceae, the sister family to the Brassicaceae. Analysis of these Cleome data with homologous sequences from other Rosid genomes (Arabidopsis, Carica, Gossypium, Populus, and Vitis) yielded three major findings: 1) confirmation of a Cleome-specific paleopolyploidization (Cs-alpha) that is independent of the Brassicaceae At-alpha paleopolyploidization; 2) Cleome and Arabidopsis share the At-beta duplication, which is lacking from papaya within the Brassicales; and 3) rates of molecular evolution are faster for the herbaceous annual taxa Arabidopsis and Cleome than the other predominantly woody perennial Rosid lineages. These findings contribute to our understanding of the dynamics of genome duplication and evolution within one of the most comprehensively surveyed clades of plants, the Rosids, and clarify the complex history of the At-alpha, At-beta, and At-gamma duplications of Arabidopsis.
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Affiliation(s)
- Michael S Barker
- Department of Botany and The Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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