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More GK, Meddows-Taylor S, Prinsloo G. Metabolomic Profiling of Antioxidant Compounds in Five Vachellia Species. Molecules 2021; 26:molecules26206214. [PMID: 34684798 PMCID: PMC8539452 DOI: 10.3390/molecules26206214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
The genus Vachellia, previously known as Acacia, belongs to the family Fabaceae, subfamily Leguminosae, which are flowering plants, commonly known as thorn trees. They are traditionally used medicinally in various countries including South Africa for the treatment of ailments such as fever, sore throat, Tuberculosis, convulsions and as sedatives. The aim of this study was to determine biochemical variations in five Vachellia species and correlate their metabolite profiles to antioxidant activity using a chemometric approach. The antioxidant activity of five Vachellia aqueous-methanolic extracts were analyzed using three methods: 2,2-di-phenyl-1-picrylhydrazyl (DPPH) radical scavenging assay, 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS+) analysis and the ferric reducing antioxidant power (FRAP) assay by means of serial dilution and bioautography with the thin-layer chromatography (TLC) method. Amongst the Vachellia extracts tested, V. karroo, V. kosiensis and V. xanthophloea demonstrated the highest DPPH, ABTS+ and FRAP inhibitory activity. The antioxidant activities of DPPH were higher than those obtained by ABTS+, although these values varied among the Vachellia species. Proton nuclear magnetic resonance (1H NMR), coupled with multivariate statistical modeling tools such as principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA), were performed to profile metabolites responsible for the observed activity. The OPLS-DA categorized the five Vachellia species, separating them into two groups, with V. karroo, V. kosiensis and V. xanthophloea demonstrating significantly higher radical scavenging activity than V. tortilis and V. sieberiana, which clustered together to form another group with lower radical scavenging activity. Annotation of metabolites was carried out using the ultra-high-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UHPLC-qTOF-MS), and it tentatively identified 23 metabolites of significance, including epigallocatechin (m/z = 305.0659), methyl gallate (m/z = 183.0294) and quercetin (m/z = 301.0358), amongst others. These results elucidated the metabolites that separated the Vachellia species from each other and demonstrated their possible free radical scavenging activities.
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Affiliation(s)
- Garland Kgosi More
- College of Agriculture and Environmental Sciences Laboratories, University of South Africa, Florida, Johannesburg 1710, South Africa
- Correspondence:
| | - Stephen Meddows-Taylor
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, Johannesburg 1710, South Africa;
| | - Gerhard Prinsloo
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Florida, Johannesburg 1710, South Africa;
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Usai M, Marchetti M, Melis RA, Porqueddu C. Volatolomics of Sardinian and Spanish Bituminaria: Characterization of Different Accessions Using Chemometrics. Molecules 2021; 26:molecules26175247. [PMID: 34500681 PMCID: PMC8434016 DOI: 10.3390/molecules26175247] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
The present study aims to determine the volatile compositions of 15 different accessions of native Sardinian populations of Bituminaria morisiana (Pignatti & Metlesics) Greuter, Bituminaria bituminosa (L.) C. H. Stirt. (B. b.), and Spanish native accessions of B. bituminosa. Furthermore, we particularly focused on the essential oil characterization of these accessions and discriminated within populations with low furocoumarin content useful for fodder production in Mediterranean environments or furocoumarin extraction for pharmaceutical utilization. The plant extracts were analyzed by GC/MS, showing great variability in the content and composition. No differences were found in Bituminaria bituminosa (L.) C.H. Stirt. var. bituminosa essential oils, while the varieties Bituminaria bituminosa (L.) C.H. Stirt. var. crassiuscula P. Méndez, Fern. Galván & A. Santos and Bituminaria bituminosa (L.) C.H. Stirt. var. albomarginata P. Méndez, Fern. Galván & A. Santos are characterized by the presence of a high concentration of long-chain alcohols and of salicylic acid benzylic ester. In B. bituminosa var. albomarginata, we observed a different profile with predominance of a large concentration of alcohols as dodecanol and tetradecanol. The endemic B. morisiana can be identified for the predominant presence of farnesene. In methanolic fractions, we detected the presence of maltol, methyl citrate, methyl cumarate, santonin, and methyl linoleate. B. morisiana showed a low content of psoralens, and the accession of B. morisiana, from Siliqua indicated the presence of apocynin.
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Affiliation(s)
- Marianna Usai
- Department of Chemistry and Pharmacy, University of Sassari, via Muroni 23/a, 07100 Sassari, Italy
- Correspondence: ; Tel.: +39-079228751
| | - Mauro Marchetti
- Institute of Biomolecular Chemistry, National Research Council (CNR), Trav. La Crucca 3, 07100 Sassari, Italy;
| | - Rita A.M. Melis
- Institute for the Animal Production System in the Mediterranean Environment (CNR), Traversa La Crucca 3, 07040 Sassari, Italy; (R.A.M.M.); (C.P.)
| | - Claudio Porqueddu
- Institute for the Animal Production System in the Mediterranean Environment (CNR), Traversa La Crucca 3, 07040 Sassari, Italy; (R.A.M.M.); (C.P.)
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Lee C, Choi IS, Cardoso D, de Lima HC, de Queiroz LP, Wojciechowski MF, Jansen RK, Ruhlman TA. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. Plant J 2021; 107:861-875. [PMID: 34021942 DOI: 10.1111/tpj.15351] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 02/04/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non-papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in the progression of plastome change is discussed.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal de Bahia (UFBA), Rua Barão de Jeremoabo, s.n., Ondina, Salvador, Bahia, 40170-115, Brazil
| | - Haroldo C de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, Rio de Janeiro, 915 22460-030, Brazil
| | - Luciano P de Queiroz
- Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, Feira de Santana, Bahia, 44036-900, Brazil
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Kitaeva AB, Gorshkov AP, Kirichek EA, Kusakin PG, Tsyganova AV, Tsyganov VE. General Patterns and Species-Specific Differences in the Organization of the Tubulin Cytoskeleton in Indeterminate Nodules of Three Legumes. Cells 2021; 10:cells10051012. [PMID: 33923032 PMCID: PMC8146709 DOI: 10.3390/cells10051012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 01/28/2023] Open
Abstract
The tubulin cytoskeleton plays an important role in establishing legume–rhizobial symbiosis at all stages of its development. Previously, tubulin cytoskeleton organization was studied in detail in the indeterminate nodules of two legume species, Pisum sativum and Medicago truncatula. General as well as species-specific patterns were revealed. To further the understanding of the formation of general and species-specific microtubule patterns in indeterminate nodules, the tubulin cytoskeleton organization was studied in three legume species (Vicia sativa, Galega orientalis, and Cicer arietinum). It is shown that these species differ in the shape and size of rhizobial cells (bacteroids). Immunolocalization of microtubules revealed the universality of cortical and endoplasmic microtubule organization in the meristematic cells, infected cells of the infection zone, and uninfected cells in nodules of the three species. However, there are differences in the endoplasmic microtubule organization in nitrogen-fixing cells among the species, as confirmed by quantitative analysis. It appears that the differences are linked to bacteroid morphology (both shape and size).
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Quilbé J, Lamy L, Brottier L, Leleux P, Fardoux J, Rivallan R, Benichou T, Guyonnet R, Becana M, Villar I, Garsmeur O, Hufnagel B, Delteil A, Gully D, Chaintreuil C, Pervent M, Cartieaux F, Bourge M, Valentin N, Martin G, Fontaine L, Droc G, Dereeper A, Farmer A, Libourel C, Nouwen N, Gressent F, Mournet P, D'Hont A, Giraud E, Klopp C, Arrighi JF. Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium-legume symbiosis. Nat Commun 2021; 12:829. [PMID: 33547303 PMCID: PMC7864950 DOI: 10.1038/s41467-021-21094-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conduct genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiates singular mechanisms in the early and late nodulation steps. A forward genetic screen also shows that AeCRK, coding a receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2, and AeNIN are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel mechanisms underlying the rhizobium-legume symbiosis.
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Affiliation(s)
- Johan Quilbé
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Léo Lamy
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Philippe Leleux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Thomas Benichou
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Rémi Guyonnet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Irene Villar
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Bárbara Hufnagel
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Amandine Delteil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Marjorie Pervent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Mickaël Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nicolas Valentin
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Loïc Fontaine
- BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34398, Montpellier, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, France
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Cyril Libourel
- LRSV, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Frédéric Gressent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Christophe Klopp
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France.
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Abstract
A pangenome is a collection of genomic sequences found in the entire species rather than a single individual. It allows for comprehensive, species-wide characterization of genetic variations and mining of variable genes which may play important roles in phenotypes of interest. Recent advances in sequencing technologies have facilitated draft genome sequence construction and have made pangenome constructions feasible. Here, we present a reference genome-based iterative mapping and assembly method to construct a pangenome for a legume species.
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Affiliation(s)
- Haifei Hu
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Yuxuan Yuan
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Cassandria T Fernandez
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Armin Scheben
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia.
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Dai X, Zhuang Z, Boschiero C, Dong Y, Zhao PX. LegumeIP V3: from models to crops-an integrative gene discovery platform for translational genomics in legumes. Nucleic Acids Res 2021; 49:D1472-D1479. [PMID: 33166388 PMCID: PMC7778993 DOI: 10.1093/nar/gkaa976] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 11/30/2022] Open
Abstract
Legumes have contributed to human health, sustainable food and feed production worldwide for centuries. The study of model legumes has played vital roles in deciphering key genes, pathways, and networks regulating biological mechanisms and agronomic traits. Along with emerging breeding technology such as genome editing, translation of the knowledge gained from model plants to crops is in high demand. The updated database (V3) was redesigned for translational genomics targeting the discovery of novel key genes in less-studied non-model legume crops by referring to the knowledge gained in model legumes. The database contains genomic data for all 22 included species, and transcriptomic data covering thousands of RNA-seq samples mostly from model species. The rich biological data and analytic tools for gene expression and pathway analyses can be used to decipher critical genes, pathways, and networks in model legumes. The integrated comparative genomic functions further facilitate the translation of this knowledge to legume crops. Therefore, the database will be a valuable resource to identify important genes regulating specific biological mechanisms or agronomic traits in the non-model yet economically significant legume crops. LegumeIP V3 is available free to the public at https://plantgrn.noble.org/LegumeIP. Access to the database does not require login, registration, or password.
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Affiliation(s)
- Xinbin Dai
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Zhaohong Zhuang
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Clarissa Boschiero
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Yibo Dong
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Patrick X Zhao
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
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8
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Tor-Roca A, Garcia-Aloy M, Mattivi F, Llorach R, Andres-Lacueva C, Urpi-Sarda M. Phytochemicals in Legumes: A Qualitative Reviewed Analysis. J Agric Food Chem 2020; 68:13486-13496. [PMID: 33169614 DOI: 10.1021/acs.jafc.0c04387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Legumes are an excellent source of nutrients and phytochemicals. They have been recognized for their contributions to health, sustainability, and the economy. Although legumes comprise several species and varieties, little is known about the differences in their phytochemical composition and the magnitude of these. Therefore, the aim of this review is to describe and compare the qualitative profile of phytochemicals contained in legumes and identified through LC-MS and GC-MS methods. Among the 478 phytochemicals reported in 52 varieties of legumes, phenolic compounds were by far the most frequently described (n = 405, 85%). Metabolomics data analysis tools were used to visualize the qualitative differences, showing beans to be the most widely analyzed legumes and those with the highest number of discriminant phytochemicals (n = 180, 38%). A Venn diagram showed that lentils, beans, soybeans, and chickpeas shared only 7% of their compounds. This work highlighted the huge chemical diversity among legumes and identified the need for further research in this field and the use of metabolomics as a promising tool to achieve it.
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Affiliation(s)
- Alba Tor-Roca
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Science and Gastronomy, Food Technology Reference Net (XaRTA), Institute for Research on Nutrition and Food Safety (INSA-UB), Food and Nutrition Torribera Campus, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Mar Garcia-Aloy
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Science and Gastronomy, Food Technology Reference Net (XaRTA), Institute for Research on Nutrition and Food Safety (INSA-UB), Food and Nutrition Torribera Campus, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red (CIBER) on Frailty and Healthy Ageing (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach (FEM), 38010 San Michele all'Adige, Italy
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach (FEM), 38010 San Michele all'Adige, Italy
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Povo, Italy
| | - Rafael Llorach
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Science and Gastronomy, Food Technology Reference Net (XaRTA), Institute for Research on Nutrition and Food Safety (INSA-UB), Food and Nutrition Torribera Campus, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red (CIBER) on Frailty and Healthy Ageing (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - Cristina Andres-Lacueva
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Science and Gastronomy, Food Technology Reference Net (XaRTA), Institute for Research on Nutrition and Food Safety (INSA-UB), Food and Nutrition Torribera Campus, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red (CIBER) on Frailty and Healthy Ageing (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - Mireia Urpi-Sarda
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Science and Gastronomy, Food Technology Reference Net (XaRTA), Institute for Research on Nutrition and Food Safety (INSA-UB), Food and Nutrition Torribera Campus, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red (CIBER) on Frailty and Healthy Ageing (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
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9
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Amal TC, Thottathil AT, Veerakumari KP, Rakkiyappan R, Vasanth K. Morphological traits of drought tolerant horse gram germplasm: classification through machine learning. J Sci Food Agric 2020; 100:4959-4967. [PMID: 32484245 DOI: 10.1002/jsfa.10559] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/21/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Horse gram (Macrotyloma uniflorum (Lam.) Verdc.) is an underutilized pulse crop with good drought resistance traits. It is a rich source of protein. Conventional breeding methods for high yielding and abiotic stress tolerant germplasm are hampered by the scarcity of morphological data sets. Thus, horse gram cultivars considered for this study is classified based on prevailing growth factors showing homogenous genotype in various agro ecological zones. Nowadays, several machine learning (ML) methods are used in the field of plant phenotyping. RESULTS We adopted unsupervised learning techniques from the K-means clustering algorithm to analyze important morphological traits: plant shoot length, total plant height, flowering percentage, number of pods per plant, pod length, number of seeds per plant, and seed length variants between germplasm. Unsupervised clustering revealed that 20 germplasm accessions were grouped in four clusters in which high-yielding traits were predominantly observed in cluster 2. CONCLUSION These findings could guide ML-based classification to characterize suitable germplasms on the basis of high-yielding varieties for different agro-ecological zones. © 2020 Society of Chemical Industry.
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Affiliation(s)
| | - Asif T Thottathil
- Department of Statistics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - Rajan Rakkiyappan
- Department of Mathematics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Krishnan Vasanth
- Department of Botany, Bharathiar University, Coimbatore, Tamil Nadu, India
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10
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Zhang R, Wang YH, Jin JJ, Stull GW, Bruneau A, Cardoso D, De Queiroz LP, Moore MJ, Zhang SD, Chen SY, Wang J, Li DZ, Yi TS. Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae. Syst Biol 2020; 69:613-622. [PMID: 32065640 PMCID: PMC7302050 DOI: 10.1093/sysbio/syaa013] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 02/02/2020] [Accepted: 02/07/2020] [Indexed: 01/02/2023] Open
Abstract
Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding data sets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone. [Leguminosae; maximum likelihood; phylogenetic conflict; plastome; recalcitrant relationships; stochasticity; systematic error.].
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Affiliation(s)
- Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yin-Huan Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- School of Primary Education, Chongqing Normal University, Chongqing 400700, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Department of Botany, Smithsonian Institution, Washington, DC 20013, USA
| | - Anne Bruneau
- Institut de recherche en biologie végétale & Département de Sciences biologiques, Université de Montréal, Montréal, QC H1X 2B2, Canada
| | - Domingos Cardoso
- Diversity, Biogeography and Systematics Laboratory, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil
| | - Luciano Paganucci De Queiroz
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
| | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA
| | - Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Si-Yun Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jian Wang
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Mt Coot-tha Road, Brisbane 4066, Australia
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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11
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Romero N, Areche C, Cubides-Cárdenas J, Escobar N, García-Beltrán O, Simirgiotis MJ, Céspedes Á. In Vitro Anthelmintic Evaluation of Gliricidia sepium, Leucaena leucocephala, and Pithecellobium dulce: Fingerprint Analysis of Extracts by UHPLC-Orbitrap Mass Spectrometry. Molecules 2020; 25:molecules25133002. [PMID: 32630065 PMCID: PMC7412154 DOI: 10.3390/molecules25133002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/17/2020] [Accepted: 05/20/2020] [Indexed: 02/03/2023] Open
Abstract
In the present work, the anthelmintic activity (AA) of ethanolic extracts obtained from Gliricidia sepium, Leucaena leucocephala, and Pithecellobium dulce was evaluated using the third-stage-larval (L3) exsheathment inhibition test (LEIT) and egg hatch test (EHT) on Haemonchus contortus. Extracts were tested at concentrations of 0.3, 0.6, 1.2, 2.5, 5.0, 10, 20, and 40 mg/mL. The larval exsheathment inhibition (LEI) results showed that G. sepium achieved the highest average inhibition of 91.2%, compared with 44.6% for P. dulce and 41.0% for L. leucocephala at a concentration of 40 mg/mL; the corresponding IC50 values were 22.4, 41.7, and 43.3 mg/mL, respectively. The rates of egg hatching inhibition (EHI) at a concentration of 5 mg/mL were 99.5% for G. sepium, 64.2% for P. dulce, and 54% for L. leucocephala; the corresponding IC50 values were 1.9 mg/mL for G. sepium, 3.9 mg/mL for P. dulce, and 4.3 mg/mL for L. leucocephala. The species extracts studied here were also analyzed by ultra-high performance liquid chromatography and Orbitrap high resolution mass spectrometry (UHPLC-Q/Orbitrap/MS/MS), resulting in the compounds' identification associated with AA. Glycosylated flavonoids and methoxyphenols were observed in all three species: fatty acids in G. sepium and P. dulce; phenylpropanoids, anthraquinone glycosides, amino acids and glycosylated phenolic acids in G. sepium; and flavonoids in L. leucocephala. Comparatively, G. sepium presented a greater diversity of compounds potentially active against the control of gastrointestinal nematodes, which was associated with the results obtained in the applied tests.
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Affiliation(s)
- Néstor Romero
- Departamento de Sanidad Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad del Tolima, Ibagué 730001, Colombia;
- Correspondence:
| | - Carlos Areche
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Nuñoa, Santiago 7800024, Chile;
| | - Jaime Cubides-Cárdenas
- Grupo de Investigación e Innovación en Salud y Bienestar Animal, Laboratorio de Salud Animal, Centro de Investigación Tibaitatá, Agrosavia, Mosquera 250047, Colombia;
| | - Natalia Escobar
- Facultad de Ciencias Agropecuarias, Universidad de Cundinamarca, Fusagasugá 252212, Colombia;
| | - Olimpo García-Beltrán
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, Ibagué 730002, Colombia;
| | | | - Ángel Céspedes
- Departamento de Sanidad Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad del Tolima, Ibagué 730001, Colombia;
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12
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Santos ES, Luís Â, Gonçalves J, Rosado T, Pereira L, Gallardo E, Duarte AP. Julbernardia paniculata and Pterocarpus angolensis: From Ethnobotanical Surveys to Phytochemical Characterization and Bioactivities Evaluation. Molecules 2020; 25:molecules25081828. [PMID: 32316213 PMCID: PMC7221604 DOI: 10.3390/molecules25081828] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/13/2020] [Indexed: 12/26/2022] Open
Abstract
Julbernardia paniculata and Pterocarpus angolensis are two plant species with important application in African traditional medicine, particularly in Angola, in the treatment of several diseases. However, scientific studies concerning these species are scarce. The goal of this work was to know better which medicinal approaches are used by the Huíla population in Angola by means of ethnobotanical surveys. Furthermore, extracts of both plants were phytochemically characterized. Antioxidant, anti-inflammatory, wound-healing activities, and potential cytotoxicity were also studied. With this study it was possible to verify that 67% of the individuals that use medicinal plants are women, and their main therapeutic uses are the treatment of problems of the digestive system and skin disorders. Barks of J. paniculata and leaves of P. angolensis are the most often used plant parts. Through high-performance liquid chromatography coupled to diode-array detector (HPLC-DAD) and GC-MS it was possible to characterize the chemical composition of the two species, which are rich in phenolic compounds, terpenes, terpenoids, sesquiterpenoids and fatty acids. Both plants showed to possess antioxidant, anti-inflammatory proprieties, and wound-healing activity. To the best of our knowledge, this is the most comprehensive study of these two species and the first ethnobotanical and ethnopharmacological study of medicinal plants from this region of Angola.
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Affiliation(s)
- Eugénia Solange Santos
- Centro de Investigação em Ciências da Saúde (CICS-UBI), Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (E.S.S.); (Â.L.); (J.G.); (T.R.); (E.G.)
- Instituto Superior Politécnico da Huíla, Universidade Mandume Ya Ndemufayo, Bairro Comercial, Avenida Hoji Ya Henda N. 30, Caixa Postal N. 201, Lubango, Huíla, Angola
| | - Ângelo Luís
- Centro de Investigação em Ciências da Saúde (CICS-UBI), Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (E.S.S.); (Â.L.); (J.G.); (T.R.); (E.G.)
- Laboratório de Fármaco-Toxicologia, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Joana Gonçalves
- Centro de Investigação em Ciências da Saúde (CICS-UBI), Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (E.S.S.); (Â.L.); (J.G.); (T.R.); (E.G.)
- Laboratório de Fármaco-Toxicologia, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Tiago Rosado
- Centro de Investigação em Ciências da Saúde (CICS-UBI), Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (E.S.S.); (Â.L.); (J.G.); (T.R.); (E.G.)
- Laboratório de Fármaco-Toxicologia, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
- C4-Cloud Computing Competence Centre, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Luísa Pereira
- Centro de Matemática e Aplicações (CMA-UBI), Universidade da Beira Interior, Rua Marquês d’Ávila e Bolama, 6201-001 Covilhã, Portugal;
| | - Eugenia Gallardo
- Centro de Investigação em Ciências da Saúde (CICS-UBI), Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (E.S.S.); (Â.L.); (J.G.); (T.R.); (E.G.)
- Laboratório de Fármaco-Toxicologia, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Ana Paula Duarte
- Centro de Investigação em Ciências da Saúde (CICS-UBI), Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (E.S.S.); (Â.L.); (J.G.); (T.R.); (E.G.)
- Laboratório de Fármaco-Toxicologia, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
- Correspondence: ; Tel.: +351-275-329-099
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13
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Koenen EJM, Ojeda DI, Steeves R, Migliore J, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Bruneau A, Hughes CE. Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies. New Phytol 2020; 225:1355-1369. [PMID: 31665814 PMCID: PMC6972672 DOI: 10.1111/nph.16290] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [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: 06/28/2019] [Accepted: 09/14/2019] [Indexed: 05/02/2023]
Abstract
Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear-encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as 'basal' or 'early-diverging' with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.
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Affiliation(s)
- Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107CH‐8008ZurichSwitzerland
| | - Dario I. Ojeda
- Service Évolution Biologique et ÉcologieFaculté des SciencesUniversité Libre de BruxellesAvenue Franklin Roosevelt 501050BrusselsBelgium
- Norwegian Institute of Bioeconomy ResearchHøgskoleveien 81433ÅsNorway
| | - Royce Steeves
- Institut de Recherche en Biologie Végétale and Département de Sciences BiologiquesUniversité de Montréal4101 Sherbrooke St EMontrealQCH1X 2B2Canada
- Fisheries & Oceans CanadaGulf Fisheries Center343 Université AveMonctonNBE1C 5K4Canada
| | - Jérémy Migliore
- Service Évolution Biologique et ÉcologieFaculté des SciencesUniversité Libre de BruxellesAvenue Franklin Roosevelt 501050BrusselsBelgium
| | - Freek T. Bakker
- Biosystematics GroupWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Jan J. Wieringa
- Naturalis Biodiversity Center, LeidenDarwinweg 22333 CRLeidenthe Netherlands
| | - Catherine Kidner
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- School of Biological SciencesUniversity of EdinburghKing's Buildings, Mayfield RdEdinburghEH9 3JUUK
| | - Olivier J. Hardy
- Service Évolution Biologique et ÉcologieFaculté des SciencesUniversité Libre de BruxellesAvenue Franklin Roosevelt 501050BrusselsBelgium
| | - R. Toby Pennington
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- GeographyUniversity of ExeterAmory Building, Rennes DriveExeterEX4 4RJUK
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences BiologiquesUniversité de Montréal4101 Sherbrooke St EMontrealQCH1X 2B2Canada
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107CH‐8008ZurichSwitzerland
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14
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Asaf S, Khan A, Khan AL, Al-Harrasi A, Al-Rawahi A. Complete Chloroplast Genomes of Vachellia nilotica and Senegalia senegal: Comparative Genomics and Phylogenomic Placement in a New Generic System. PLoS One 2019; 14:e0225469. [PMID: 31765416 PMCID: PMC6876885 DOI: 10.1371/journal.pone.0225469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/05/2019] [Indexed: 12/15/2022] Open
Abstract
Vachellia and Senegalia are the most important genera in the subfamily Mimosoideae (Fabaceae). Recently, species from both genera were separated from the long-characterized Acacia due to their macro-morphological characteristics. However, this morpho-taxonomic differentiation struggles to discriminate some species, for example, Vachellia nilotica and Senegalia senegal. Therefore, sequencing the chloroplast (cp) genomes of these species and determining their phylogenetic placement via conserved genes may help to validate the taxonomy. Hence, we sequenced the cp genomes of V. nilotica and S. senegal, and the results showed that the sizes of the genomes are 165.3 and 162.7 kb, respectively. The cp genomes of both species comprised large single-copy regions (93,849~91,791 bp) and pairs of inverted repeats (IR; 26,093~26,008 bp). The total numbers of genes found in the V. nilotica and S. senegal cp genomes were 135 and 132, respectively. Approximately 123:130 repeats and 290:281 simple sequence repeats were found in the S. senegal and V. nilotica cp genomes, respectively. Genomic characterization was undertaken by comparing these genomes with those of 17 species belonging to related genera in Fabaceae. A phylogenetic analysis of the whole genome dataset and 56 shared genes was undertaken by generating cladograms with the same topologies and placing both species in a new generic system. These results support the likelihood of identifying segregate genera from Acacia with phylogenomic disposition of both V. nilotica and S. senegal in the subfamily Mimosoideae. The current study is the first to obtain complete genomic information on both species and may help to elucidate the genome architecture of these species and evaluate the genetic diversity among species.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Arif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodo, Norway
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- * E-mail: (ALK); (AAH)
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- * E-mail: (ALK); (AAH)
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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15
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Kreplak J, Madoui MA, Cápal P, Novák P, Labadie K, Aubert G, Bayer PE, Gali KK, Syme RA, Main D, Klein A, Bérard A, Vrbová I, Fournier C, d'Agata L, Belser C, Berrabah W, Toegelová H, Milec Z, Vrána J, Lee H, Kougbeadjo A, Térézol M, Huneau C, Turo CJ, Mohellibi N, Neumann P, Falque M, Gallardo K, McGee R, Tar'an B, Bendahmane A, Aury JM, Batley J, Le Paslier MC, Ellis N, Warkentin TD, Coyne CJ, Salse J, Edwards D, Lichtenzveig J, Macas J, Doležel J, Wincker P, Burstin J. A reference genome for pea provides insight into legume genome evolution. Nat Genet 2019; 51:1411-1422. [PMID: 31477930 DOI: 10.1038/s41588-019-0480-1] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/10/2019] [Indexed: 02/03/2023]
Abstract
We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.
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Affiliation(s)
- Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Petr Cápal
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Krishna K Gali
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Robert A Syme
- Centre for Crop and Disease Management, Curtin University, Bentley, Western Australia, Australia
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Anthony Klein
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Aurélie Bérard
- Etude du Polymorphisme des Génomes Végétaux, INRA, Université Paris-Saclay, Evry, France
| | - Iva Vrbová
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Cyril Fournier
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Leo d'Agata
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Wahiba Berrabah
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Zbyněk Milec
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - HueyTyng Lee
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Ayité Kougbeadjo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Morgane Térézol
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Cécile Huneau
- UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Chala J Turo
- Centre for Crop and Disease Management, School of Molecular and Life Science, Curtin University, Bentley, Western Australia, Australia
| | | | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Matthieu Falque
- GQE-Le Moulon, INRA, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Rebecca McGee
- USDA Agricultural Research Service, Pullman, WA, USA
| | - Bunyamin Tar'an
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, University of Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Orsay, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | | | - Noel Ellis
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Thomas D Warkentin
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Jérome Salse
- UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Judith Lichtenzveig
- School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.
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16
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Morales M, Oakley L, Sartori ALB, Mogni VY, Atahuachi M, Vanni RO, Fortunato RH, Prado DE. Diversity and conservation of legumes in the Gran Chaco and biogeograpical inferences. PLoS One 2019; 14:e0220151. [PMID: 31412055 PMCID: PMC6693842 DOI: 10.1371/journal.pone.0220151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/09/2019] [Indexed: 11/18/2022] Open
Abstract
The Gran Chaco is a wide ecologic-geographic region comprising northern Argentina, western Paraguay, southern Bolivia and the southwestern extreme of Brazil. This region exhibits extreme temperatures, annually regular frosts, and sedimentary soils; it has been dramatically threatened by agriculture expansion in recent decades. Therefore, increasing knowledge of plant diversity is critical for conservation purposes. We present a Legume checklist of the Gran Chaco ecoregion including conservation status of its endemic species. Leguminosae is the third most diverse plant family in the Neotropics. Assuming a rigorous spatial definition of the Gran Chaco, we recorded 98 genera, 362 species, and 404 specific and infraspecific taxa. Endemic/typical taxa were 17%, comparable to adjacent tropical plant formations, and they were found in higher percentages in Caesalpinioideae (24%) and Cercidoideae (33%) than Papilionoideae (11%) subfamily. We also analyzed the plant diversity comparing lineages and subregions. The Gran Chaco Legumes are predominantly widespread generalists, or they belong to either Chaco sensu stricto or Neotropical Seasonally Dry Tropical Forest (SDTF) lineages. Though the Humid Chaco registered the highest species richness, Dry Chaco and Sierra Chaco, the most threatrened subregions, exhibited the highest percentages of exclusive and proper Chaco-lineage species. These results suggest that diversification of Legumes has been most relevant in Dry Chaco and Sierra Chaco, probably by their more demanding and harsh environmental conditions limiting the dispersion of generalists or intrusive-invading species. This study is paramount to reach an improved delimitation of the Gran Chaco ecoregion in transitional areas with the SDTF and Cerrado formations. Conservation status is critical in genera of high economic interest, such as Arachis, Mimosa and Prosopis. At least one third of endemic taxa exhibit a critical status of conservation or are endangered, many of them being relevant to inbreeding program or exhibiting multiple economic uses.
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Affiliation(s)
- Matías Morales
- Instituto de Recursos Biológicos (CIRN–CNIA, INTA). Las Cabañas y Los Reseros s.n. Hurlingham (1686), Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Buenos Aires. Argentina
- Facultad de Agronomía y Cs. Agroalimentarias, Universidad de Morón, Cabildo, Morón, Argentina
- * E-mail: ,
| | - Luis Oakley
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario. Campo Experimental Villarino, CC Nº 14, S2125ZAA, Zavalla, Santa Fe, Argentina
- Red List Authority Coordinator for the Temperate South American Plant Specialist Groups -International Union for Conservation of Nature (IUCN), Cambridge, United Kingdom
| | - Angela L. B. Sartori
- Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório de Sistemática Vegetal, Cidade Universitária, s/n, C.P. 549, CEP, Campo Grande, Mato Grosso do Sul, Brasil
| | - Virginia Y. Mogni
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario. Campo Experimental Villarino, CC Nº 14, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Margoth Atahuachi
- Herbario Forestal Nacional M. Cárdenas, Centro de Biodiversidad y Genética, Universidad Mayor de San Simón, Final Jordan este, Casilla, Cochabamba, Bolivia
| | - Ricardo O. Vanni
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Buenos Aires. Argentina
- Instituto de Botánica del Nordeste (IBONE), Casilla de Correo, Corrientes, Argentina
| | - Renée H. Fortunato
- Instituto de Recursos Biológicos (CIRN–CNIA, INTA). Las Cabañas y Los Reseros s.n. Hurlingham (1686), Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Buenos Aires. Argentina
- Facultad de Agronomía y Cs. Agroalimentarias, Universidad de Morón, Cabildo, Morón, Argentina
| | - Darién E. Prado
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Buenos Aires. Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario. Campo Experimental Villarino, CC Nº 14, S2125ZAA, Zavalla, Santa Fe, Argentina
- Instituto de Investigaciones en Ciencias Agrarias IICAR (UNR-CONICET), Zavalla, Santa Fe, Argentina
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17
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Abstract
Recent plastid genome (plastome) studies of legumes (family Fabaceae) have shown that this family has undergone multiple atypical plastome evolutions from each of the major clades. The tribe Desmodieae belongs to the Phaseoloids, an important but systematically puzzling clade within Fabaceae. In this study, we investigated the plastome evolution of Desmodieae and analyzed its phylogenetic signaling. We sequenced six complete plastomes from representative members of Desmodieae and from its putative sister Phaseoloid genus Mucuna. Those genomes contain 128 genes and range in size from 148,450 to 153,826 bp. Analyses of gene and intron content revealed similar characters among the members of Desmodieae and Mucuna. However, there were also several distinct characters identified. The loss of the rpl2 intron was a feature shared between Desmodieae and Mucuna, whereas the loss of the rps12 intron was specific to Desmodieae. Likewise, gene loss of rps16 was observed in Mucuna but not in Desmodieae. Substantial sequence variation of ycf4 was detected from all the sequenced plastomes, but pseudogenization was restricted to the genus Desmodium. Comparative analysis of gene order revealed a distinct plastome conformation of Desmodieae compared with other Phaseoloid legumes, i.e., an inversion of an approximately 1.5-kb gene cluster (trnD-GUC, trnY-GUA, and trnE-UUC). The inversion breakpoint suggests that this event was mediated by the recombination of an 11-bp repeat motif. A phylogenetic analysis based on the plastome-scale data set found the tribe Desmodieae is a highly supported monophyletic group nested within the paraphyletic Phaseoleae, as has been found in previous phylogenetic studies. Two subtribes (Desmodiinae and Lespedezinae) of Desmodieae were also supported as monophyletic groups. Within the subtribe Lespedezinae, Lespedeza is closer to Kummerowia than Campylotropis.
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Affiliation(s)
- Dong-Pil Jin
- Department of Biological Sciences, Inha University, Michuhol-gu, Incheon, Republic of Korea
| | - In-Su Choi
- Department of Biological Sciences, Inha University, Michuhol-gu, Incheon, Republic of Korea
| | - Byoung-Hee Choi
- Department of Biological Sciences, Inha University, Michuhol-gu, Incheon, Republic of Korea
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18
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Vanier NL, de Oliveira JP, Bruni GP, El Halal SLM, Villanova FA, Zavareze EDR, Dias ARG, Bassinello PZ. Characteristics of starch from different bean genotypes and its effect on biodegradable films. J Sci Food Agric 2019; 99:1207-1214. [PMID: 30058215 DOI: 10.1002/jsfa.9292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 01/02/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Starches from four common bean genotypes were characterized and used in the production of biodegradable films. Starches were characterized by their swelling power, solubility, amylose content, granule morphology, relative crystallinity, thermal and pasting properties, and susceptibility to α-amylase hydrolysis. Films were characterized according to their morphology, mechanical and water vapor barrier properties, whiteness and opacity. RESULT Depending on the common bean genotype, a great variation on starch properties was found, which, in turn, clearly impacted on the characteristics of the starch-based films. Starches from BRS Pitanga and BRS Pérola genotypes exhibited the highest amylose content and the lowest swelling capabilities. Bean starch from the IPR Uirapuru genotype presented granules with an irregular surface and shape. Starches from IPR Uirapuru and BRS Estilo genotypes provided well-structured biodegradable films, without the occurrence of fissures or cracks. Moreover, starch films containing starch from BRS Estilo genotype exhibited the highest flexibility, permeability and solubility. CONCLUSION The morphological, mechanical and water vapor barrier properties of films elaborated with common bean starch vary greatly as a function of the bean genotype used for starch production. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Nathan Levien Vanier
- Department of Agroindustrial Science and Technology, Federal University of Pelotas, Capão do Leão, RS, Brazil
| | - Jean Paulo de Oliveira
- Department of Agroindustrial Science and Technology, Federal University of Pelotas, Capão do Leão, RS, Brazil
| | - Graziella Pinheiro Bruni
- Department of Agroindustrial Science and Technology, Federal University of Pelotas, Capão do Leão, RS, Brazil
| | | | - Franciene Almeida Villanova
- Department of Agroindustrial Science and Technology, Federal University of Pelotas, Capão do Leão, RS, Brazil
| | - Elessandra da Rosa Zavareze
- Department of Agroindustrial Science and Technology, Federal University of Pelotas, Capão do Leão, RS, Brazil
| | - Alvaro Renato Guerra Dias
- Department of Agroindustrial Science and Technology, Federal University of Pelotas, Capão do Leão, RS, Brazil
| | - Priscila Zaczuk Bassinello
- Grains and By-Products Laboratory, Embrapa - National Rice and Bean Research Center, Santo Antônio de Goiás, GO, Brazil
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19
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Ricci L, Umiltà E, Righetti MC, Messina T, Zurlini C, Montanari A, Bronco S, Bertoldo M. On the thermal behavior of protein isolated from different legumes investigated by DSC and TGA. J Sci Food Agric 2018; 98:5368-5377. [PMID: 29660127 DOI: 10.1002/jsfa.9078] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 01/05/2018] [Revised: 03/22/2018] [Accepted: 04/07/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Pea, lentil, faba bean, chickpea and bean proteins are potentially renewable raw materials for bioplastic production that can be obtained from agricultural waste. Plastics are usually processed under heating, and thus thermal stability is a mandatory requirement for the application. In this study, the thermal behavior of several legume protein isolates at different purity degrees was investigated. RESULTS The thermal stability of proteins extracted from legumes was maximum for chickpeas and minimum for beans and decreased with decreasing protein purity in the range 30-88%. A similar dependence on purity was observed for the glass transition temperature. On the contrary, the denaturation temperature was found not to depend on sample purity and origin and was lower than the degradation temperature only in the case of protein samples with purity higher than 60%. CONCLUSION Proteins from legumes are suitable to produce thermoplastic biopolymeric materials if isolated at purity higher than 60%. In fact, under this circumstance, they can be denaturized without degrading and thus are suitable for extrusion processing. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Lucia Ricci
- Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Consiglio Nazionale delle Ricerche, CNR-IPCF, Area della Ricerca, Pisa, Italy
| | - Eleonora Umiltà
- Stazione Sperimentale per l'Industria delle Conserve Alimentari - SSICA, Parma, Italy
| | - Maria C Righetti
- Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Consiglio Nazionale delle Ricerche, CNR-IPCF, Area della Ricerca, Pisa, Italy
| | - Tiziana Messina
- Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Consiglio Nazionale delle Ricerche, CNR-IPCF, Area della Ricerca, Pisa, Italy
| | - Chiara Zurlini
- Stazione Sperimentale per l'Industria delle Conserve Alimentari - SSICA, Parma, Italy
| | - Angela Montanari
- Stazione Sperimentale per l'Industria delle Conserve Alimentari - SSICA, Parma, Italy
| | - Simona Bronco
- Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Consiglio Nazionale delle Ricerche, CNR-IPCF, Area della Ricerca, Pisa, Italy
| | - Monica Bertoldo
- Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Consiglio Nazionale delle Ricerche, CNR-IPCF, Area della Ricerca, Pisa, Italy
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20
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Ricardo LM, Dias BM, Mügge FLB, Leite VV, Brandão MGL. Evidence of traditionality of Brazilian medicinal plants: The case studies of Stryphnodendron adstringens (Mart.) Coville (barbatimão) barks and Copaifera spp. (copaíba) oleoresin in wound healing. J Ethnopharmacol 2018; 219:319-336. [PMID: 29501844 DOI: 10.1016/j.jep.2018.02.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 03/20/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The World Health Organization (WHO) recognizes the potential of plants used in secular traditional medicine and considers this an important source of evidence to assess their effectiveness and safety. Brazil is rich in biodiversity and traditional uses based on the Amerindian culture. However, many processes started with the arrival of the Portuguese in the year 1500. The successive economic cycles, for example, led to destruction of native vegetation and an intense cultural erosion. As a consequence, the information about the use of plants in the past centuries are dispersed and without interpretation. In this study a methodology to evidence the traditionality of Brazilian plants was demonstrated using data about barbatimão barks (Stryphnodendron adstringens (Mart.) Coville - Fabaceae) and Copaiba oleoresin (Copaifera spp. - Fabaceae) in wound healing, was established. MATERIAL AND METHODS Data about use of the plants were recovered from bibliography published between 1576 and 2011. The books (101) were classified using weights, considering the date of publication and the source of Information. Older books that describe primary information received weight 10, while books written more recently and with secondary information received weight 0.4. A score for each category of medicinal use was calculated based on the books weights and the frequency of citation. A review about the current use of both plants was also performed from ethnobotanical studies published in journals. RESULTS AND DISCUSSION The traditional secular use of barks of barbatimão and oleoresin of copaiba to treat wounds was confirmed based on the historic bibliographic research. The most frequent use of barbatimão in a timeline of 500 years of Brazil's history, was as astringent, whereas for copaíba was as healing of skin and mucosal lesions. The continuous and current use of these plants to treat wounds, confirmed by recent ethnobotanical studies, is an indicative of the resilience of these remedies and their effectiveness. CONCLUSION The use of preparations containing barbatimão barks and copaiba oleoresin can be considered effective in the treatment of wounds. Nonetheless, it is necessary to improve the quality of the formulas as established by WHO.
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Affiliation(s)
- Letícia M Ricardo
- Centro Especializado em Plantas Aromáticas, Medicinais e Tóxicas (CEPLAMT), Museu de História Natural e Jardim Botânico, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Programa de Pós-Graduação em Medicamentos e Assistência Farmacêutica, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Departamento de Assistência Farmacêutica e Insumos Estratégicos, Secretaria de Ciência, Tecnologia e Insumos Estratégicos, Ministério da Saúde, Brasília, DF, Brazil
| | - Bianca M Dias
- Centro Especializado em Plantas Aromáticas, Medicinais e Tóxicas (CEPLAMT), Museu de História Natural e Jardim Botânico, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fernanda L B Mügge
- Centro Especializado em Plantas Aromáticas, Medicinais e Tóxicas (CEPLAMT), Museu de História Natural e Jardim Botânico, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Viviane V Leite
- Centro Especializado em Plantas Aromáticas, Medicinais e Tóxicas (CEPLAMT), Museu de História Natural e Jardim Botânico, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Hospital Publico Regional de Betim, Prefeitura Municipal de Betim, MG, Brazil
| | - Maria G L Brandão
- Centro Especializado em Plantas Aromáticas, Medicinais e Tóxicas (CEPLAMT), Museu de História Natural e Jardim Botânico, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Programa de Pós-Graduação em Medicamentos e Assistência Farmacêutica, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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21
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Yang S, Grall A, Chapman MA. Origin and diversification of winged bean (Psophocarpus tetragonolobus (L.) DC.), a multipurpose underutilized legume. Am J Bot 2018; 105:888-897. [PMID: 29874397 DOI: 10.1002/ajb2.1093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 12/18/2017] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY For many crops, research into the origin and partitioning of genetic variation is limited and this can slow or prevent crop improvement programs. Many of these underutilized crops have traits that could be of benefit in a changing climate due to stress tolerance or nutritional properties. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one such crop. All parts of the plant can be eaten, from the roots to the seeds, and is high in protein as well as other micronutrients. The goal of our study was to identify the wild progenitor and analyze the partitioning of genetic variation in the crop. METHODS We used molecular phylogenetic analyses (cpDNA and nuclear ITS sequencing) to resolve relationships between all species in the genus, and population genetics (utilizing microsatellites) to identify genetic clusters of winged bean accessions and compare this to geography. KEY RESULTS We find that winged bean is genetically distinct from all other members of the genus. We also provide support for four groups of species in the genus, largely, but not completely, corresponding to the results of previous morphological analyses. Within winged bean, population genetic analysis using 10 polymorphic microsatellite markers suggests four genetic groups; however, there is little correspondence between the genetic variation and the geography of the accessions. CONCLUSIONS The true wild progenitor of winged bean remains unknown (or is extinct). There has likely been large-scale cross-breeding, trade, and transport of winged bean and/or multiple origins of the crop.
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Affiliation(s)
- Shuyi Yang
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
| | - Aurélie Grall
- Africa & Madagascar Team, Identification & Naming Department, Royal Botanic Gardens, Kew, TW9 3AE, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
- Centre for Underutilised Crops, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
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22
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Liu W, Kong H, Zhou J, Fritsch PW, Hao G, Gong W. Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae. Int J Mol Sci 2018; 19:E1286. [PMID: 29693617 PMCID: PMC5983592 DOI: 10.3390/ijms19051286] [Citation(s) in RCA: 22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 11/17/2022] Open
Abstract
The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.
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Affiliation(s)
- Wanzhen Liu
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Juan Zhou
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107, USA.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Wei Gong
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
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23
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Endara MJ, Coley PD, Wiggins NL, Forrister DL, Younkin GC, Nicholls JA, Pennington RT, Dexter KG, Kidner CA, Stone GN, Kursar TA. Chemocoding as an identification tool where morphological- and DNA-based methods fall short: Inga as a case study. New Phytol 2018; 218:847-858. [PMID: 29436716 DOI: 10.1111/nph.15020] [Citation(s) in RCA: 5] [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: 08/04/2017] [Accepted: 01/04/2018] [Indexed: 05/12/2023]
Abstract
The need for species identification and taxonomic discovery has led to the development of innovative technologies for large-scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species-rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or 'chemocoding', has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species-level fingerprints, which we define as chemocoding. We evaluated the utility of chemocoding with species that were defined morphologically and subject to next-generation DNA sequencing in the diverse and recently radiated neotropical genus Inga (Leguminosae), both at single study sites and across broad geographic scales. Our results show that chemocoding is a robust method for distinguishing morphologically similar species at a single site and for identifying widespread species across continental-scale ranges. Given that species are the fundamental unit of analysis for conservation and biodiversity research, the development of accurate identification methods is essential. We suggest that chemocoding will be a valuable additional source of data for a quick identification of plants, especially for groups where other methods fall short.
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Affiliation(s)
- María-José Endara
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, EC170103, Ecuador
| | - Phyllis D Coley
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancón, Republic of Panamá
| | - Natasha L Wiggins
- School of Biological Sciences, University of Tasmania, Sandy Bay, TAS, 7001, Australia
| | - Dale L Forrister
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - Gordon C Younkin
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - James A Nicholls
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JY, UK
| | | | - Kyle G Dexter
- Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Catherine A Kidner
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JY, UK
- Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
| | - Graham N Stone
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JY, UK
| | - Thomas A Kursar
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancón, Republic of Panamá
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Grosse Brinkhaus A, Bee G, Schwarm A, Kreuzer M, Dohme-Meier F, Zeitz JO. Rumen microbial protein synthesis and nitrogen efficiency as affected by tanniferous and non-tanniferous forage legumes incubated individually or together in Rumen Simulation Technique. J Sci Food Agric 2018; 98:1712-1718. [PMID: 28853148 DOI: 10.1002/jsfa.8643] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 02/24/2017] [Revised: 08/09/2017] [Accepted: 08/23/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND A limited availability of microbial protein can impair productivity in ruminants. Ruminal nitrogen efficiency might be optimised by combining high-quality forage legumes such as red clover (RC), which has unfavourably high ruminal protein degradability, with tanniferous legumes like sainfoin (SF) and birdsfoot trefoil (BT). Silages from SF and from BT cultivars [Bull (BB) and Polom (BP)] were incubated singly or in combination with RC using the Rumen Simulation Technique (n = 6). RESULTS The tanniferous legumes, when compared to RC, changed the total short-chain fatty acid profile by increasing propionate proportions at the expense of butyrate. Silage from SF contained the most condensed tannins (CTs) (136 g CT kg-1 dry matter) and clearly differed in various traits from the BT and RC silages. The apparent nutrient degradability (small with SF), microbial protein synthesis, and calculated content of potentially utilisable crude protein (large with SF) indicated that SF had the greatest efficiency in ruminal protein synthesis. The effects of combining SF with RC were mostly linear. CONCLUSION The potential of sainfoin to improve protein supply, demonstrated either individually or in combination with a high-performance forage legume, indicates its potential usefulness in complementing protein-deficient ruminant diets and high-quality forages rich in rumen-degradable protein. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Anja Grosse Brinkhaus
- Agroscope, Posieux, Switzerland
- ETH Zurich, Institute of Agricultural Sciences, Zurich, Switzerland
| | | | - Angela Schwarm
- ETH Zurich, Institute of Agricultural Sciences, Zurich, Switzerland
| | - Michael Kreuzer
- ETH Zurich, Institute of Agricultural Sciences, Zurich, Switzerland
| | | | - Johanna O Zeitz
- Justus-Liebig-University Giessen, Institute for Animal Nutrition and Nutritional Physiology, Giessen, Germany
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Natabirwa H, Muyonga JH, Nakimbugwe D, Lungaho M. Physico-chemical properties and extrusion behaviour of selected common bean varieties. J Sci Food Agric 2018; 98:1492-1501. [PMID: 28799654 DOI: 10.1002/jsfa.8618] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 05/19/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Extrusion processing offers the possibility of processing common beans industrially into highly nutritious and functional products. However, there is limited information on properties of extrudates from different bean varieties and their association with raw material characteristics and extrusion conditions. In this study, physico-chemical properties of raw and extruded Bishaz, K131, NABE19, Roba1 and RWR2245 common beans were determined. The relationships between bean characteristics and extrusion conditions on the extrudate properties were analysed. RESULTS Extrudate physico-chemical and pasting properties varied significantly (P < 0.05) among bean varieties. Expansion ratio and water solubility decreased, while bulk density, water absorption, peak and breakdown viscosities increased as feed moisture increased. Protein exhibited significant positive correlation (P < 0.05) with water solubility index, and negative correlations (P < 0.05) with water absorption, bulk density and pasting viscosities. Iron and dietary fibre showed positive correlation while total ash exhibited negative correlation with peak viscosity, final viscosity and setback. Similar trends were observed in principal component analysis. CONCLUSION Extrudate physico-chemical properties were found to be associated with beans protein, starch, iron, zinc and fibre contents. Therefore, bean chemical composition may serve as an indicator for beans extrusion behaviour and could be useful in selection of beans for extrusion. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Hedwig Natabirwa
- School of Food Technology Nutrition & Bioengineering, Makerere University, Kampala, Uganda
- National Agricultural Research Laboratories, National Agricultural Research Organization, Kampala, Uganda
| | - John H Muyonga
- School of Food Technology Nutrition & Bioengineering, Makerere University, Kampala, Uganda
| | - Dorothy Nakimbugwe
- School of Food Technology Nutrition & Bioengineering, Makerere University, Kampala, Uganda
| | - Mercy Lungaho
- Center for International Tropical Agriculture, Kampala, Uganda
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Winham DM, Hutchins AM, Thompson SV, Dougherty MK. Arizona Registered Dietitians Show Gaps in Knowledge of Bean Health Benefits. Nutrients 2018; 10:E52. [PMID: 29316699 PMCID: PMC5793280 DOI: 10.3390/nu10010052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 12/21/2022] Open
Abstract
Registered Dietitians (RDs) promote nutrition practices and policies and can influence food consumption patterns to include nutrient dense foods such as beans. Although many evidence-based health benefits of bean consumption (e.g., cholesterol reduction, glycemic control) have been demonstrated, there is limited research on the knowledge, attitudes, and perceptions of RDs regarding the inclusion of beans in a healthy diet. To fill this existing research gap, this cross-sectional survey explored the perceptions, knowledge, and attitudes of 296 RDs in Arizona, USA, toward beans. The RDs largely held positive attitudes toward the healthfulness of beans and were aware of many health benefits. Some gaps in awareness were evident, including effect on cancer risk, intestinal health benefits, folate content, and application with celiac disease patients. RDs with greater personal bean consumption had significantly higher bean health benefit knowledge. Twenty-nine percent of the RDs did not know the meaning of 'legume', and over two-thirds could not define the term 'pulse'. It is essential that RDs have up-to-date, evidence-based information regarding bean benefits to provide appropriate education to patients, clients, and the public.
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Affiliation(s)
- Donna M Winham
- Department of Food Science & Human Nutrition, Iowa State University, Ames, IA 50011, USA.
| | - Andrea M Hutchins
- Department of Health Sciences, University of Colorado, Colorado Springs, CO 80918, USA.
| | - Sharon V Thompson
- Division of Nutritional Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA.
| | - Mariah K Dougherty
- Department of Pharmaceutical & Nutrition Care, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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Rashid N, Zafar M, Ahmad M, Malik K, Haq IU, Shah SN, Mateen A, Ahmed T. Intraspecific variation in seed morphology of tribe vicieae (Papilionoidae) using scanning electron microscopy techniques. Microsc Res Tech 2017; 81:298-307. [PMID: 29280232 DOI: 10.1002/jemt.22979] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 11/30/2017] [Accepted: 12/09/2017] [Indexed: 11/07/2022]
Abstract
Seed micromorphology of 12 species of tribe Vicieae (Papilionoidae) representing five genera were examined using Scanning Electron Microscope (SEM). The different seed types were described, illustrated, compared, and their taxonomic importance is discussed. Seeds exhibit great diversity in ultrastructure and a variety of novel morphological features have been determined among and within genera of the tribe. Seeds were characterized by oval to round shape, ovate to oblong outline and striate to papillate ornamentation. Radiate and wavy cell pattern has been observed as a characteristic exomorphological feature. In Vicia sativa, testa cells superficially seem to form peltate hairs. As a result, seed micromorphology with few exceptions showed variation and its taxonomic value was significant in distinguishing taxa at species level. The disparity in shape and density of papillae or protuberances and alignment of testa cells, may possibly give further insight at intraspecific level within tribe. The findings also illustrated that the use of SEM in seed morphology can reveal hidden morphological affinities among species and showed potential in delimitation of Vicieae members generally at tribe, genus, and particularly at species level.
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Affiliation(s)
- Neelam Rashid
- Department of Plant Sciences, Quaid- i- Azam University Islamabad, 45320, Pakistan
| | - Muhammad Zafar
- Department of Plant Sciences, Quaid- i- Azam University Islamabad, 45320, Pakistan
| | - Mushtaq Ahmad
- Department of Plant Sciences, Quaid- i- Azam University Islamabad, 45320, Pakistan
| | - Khafsa Malik
- Department of Plant Sciences, Quaid- i- Azam University Islamabad, 45320, Pakistan
| | - Ihsan-Ul Haq
- Department of Pharmacy, Quaid-i-Azam University Islamabad, 45320, Pakistan
| | - Syed Nasar Shah
- Department of Plant Sciences, Quaid- i- Azam University Islamabad, 45320, Pakistan
| | - Abdul Mateen
- Department of Materials Science and Engineering, Institute of Space Technology, Islamabad, 44000, Pakistan
| | - Tauseef Ahmed
- Department of Materials Science and Engineering, Institute of Space Technology, Islamabad, 44000, Pakistan
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Deklerck V, Finch K, Gasson P, Van den Bulcke J, Van Acker J, Beeckman H, Espinoza E. Comparison of species classification models of mass spectrometry data: Kernel Discriminant Analysis vs Random Forest; A case study of Afrormosia (Pericopsis elata (Harms) Meeuwen). Rapid Commun Mass Spectrom 2017; 31:1582-1588. [PMID: 28700098 DOI: 10.1002/rcm.7939] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE The genus Pericopsis includes four tree species of which only Pericopsis elata (Harms) Meeuwen is of commercial interest. Enforcement officers might have difficulties discerning this CITES-listed species from some other tropical African timber species. Therefore, we tested several methods to separate and identify these species rapidly in order to enable customs officials to uncover illegal trade. In this study, two classification methods using Direct Analysis in Real Time (DART™) ionization coupled with Time-of-Flight Mass Spectrometry (DART-TOFMS) data to discern between several species are presented. METHODS Metabolome profiles were collected using DART™ ionization coupled with TOFMS analysis of heartwood specimens of all four Pericopsis species and Haplormosia monophylla (Harms) Harms, Dalbergia melanoxylon Guill. & Perr. Harms, and Milicia excelsa (Welw.) C.C. Berg. In total, 95 specimens were analysed and the spectra evaluated. Kernel Discriminant Analysis (KDA) and Random Forest classification were used to discern the species. RESULTS DART-TOFMS spectra obtained from wood slivers and post-processing analysis using KDA and Random Forest classification separated Pericopsis elata from the other Pericopsis taxa and its lookalike timbers Haplormosia monophylla, Milicia excelsa, and Dalbergia melanoxylon. Only 50 ions were needed to achieve the highest accuracy. CONCLUSIONS DART-TOFMS spectra of the taxa were reproducible and the results of the chemometric analysis provided comparable accuracy. Haplormosia monophylla was visually distinguished based on the heatmap and was excluded from further analysis. Both classification methods, KDA and Random Forest, were capable of distinguishing Pericopsis elata from the other Pericopsis taxa, Milicia excelsa, and Dalbergia melanoxylon, timbers that are commonly traded.
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Affiliation(s)
- V Deklerck
- Woodlab-UGent, Ghent University, Laboratory of Wood Technology, Department of Forest and Water Management, Coupure Links 653, B-9000, Ghent, Belgium
- Wood Biology Service, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, 3080, Tervuren, Belgium
| | - K Finch
- Department of Botany and Plant Pathology, Oregon State University, Cordley Hall, 2701 SW Campus Way, Corvalis, OR, USA
| | - P Gasson
- Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - J Van den Bulcke
- Woodlab-UGent, Ghent University, Laboratory of Wood Technology, Department of Forest and Water Management, Coupure Links 653, B-9000, Ghent, Belgium
| | - J Van Acker
- Woodlab-UGent, Ghent University, Laboratory of Wood Technology, Department of Forest and Water Management, Coupure Links 653, B-9000, Ghent, Belgium
| | - H Beeckman
- Wood Biology Service, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, 3080, Tervuren, Belgium
| | - E Espinoza
- U.S. National Fish and Wildlife Forensic Laboratory, 1490 East Main Street, Ashland, OR, USA
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Nawaz MA, Rehman HM, Imtiaz M, Baloch FS, Lee JD, Yang SH, Lee SI, Chung G. Systems Identification and Characterization of Cell Wall Reassembly and Degradation Related Genes in Glycine max (L.) Merill, a Bioenergy Legume. Sci Rep 2017; 7:10862. [PMID: 28883533 PMCID: PMC5589831 DOI: 10.1038/s41598-017-11495-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/24/2017] [Indexed: 12/22/2022] Open
Abstract
Soybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510275, China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, 14280, Bolu, Turkey
| | - Jeong Dong Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Soo In Lee
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), Jeonju, 54874, Republic of Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
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Ahmed S, Zafar Mahmood SB, Hasan MM, Mahmood ZA. Essential minerals and phytic acid in legumes with reference to their nutritive and medicinal properties. Pak J Pharm Sci 2017; 30:1733-1742. [PMID: 29084696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Three commonly used legumes, Macrotyloma uniflorum (Lam.) Verdc., Phaseolus lunatus Linn., and Phaseolus vulgaris Linn., were subjected to determine their minerals and phytic acid contents to correlate their nutritional and medicinal properties. To quantify essential minerals, atomic absorption spectroscopic method, while for phytic acid estimation, spectrophotometric method was used. Presence of Fe, Mg, Mn, P and Zn were recorded in good quantities, Ca and Cu in moderate, while K in small quantity in the seed flours of all the three tested legumes. Maximum Fe and Zn content (0.38 and 0.40 mg/g) were recorded in P. vulgaris, while M. uniflorum delivered high content of Mg, Mn, P and Ca (0.21, 0.20, 77.94 and 0.04 mg/g) and 0.04 mg/g Cu was recorded in P. lunatus. The highest level of phytic acid (37.00 mg/g) was recorded in M. uniflorum at 519 nm. The estimated quantities of minerals and phytic acid provide a good opportunity to draw a conclusion that all the three tested legumes could potentially be used as food to achieve nutritional and health related functional benefits.
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Affiliation(s)
- Salman Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, University of Karachi, Karachi, Pakistan
| | | | - Muhammad Mohtasheemul Hasan
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, University of Karachi, Karachi, Pakistan
| | - Zafar Alam Mahmood
- Colorcon Limited UK, Flagship House, Victory Way, Crossways, Dartford, Kent, DA26 QD, England
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31
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Epihov DZ, Batterman SA, Hedin LO, Leake JR, Smith LM, Beerling DJ. N 2-fixing tropical legume evolution: a contributor to enhanced weathering through the Cenozoic? Proc Biol Sci 2017; 284:20170370. [PMID: 28814651 PMCID: PMC5563791 DOI: 10.1098/rspb.2017.0370] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/12/2017] [Indexed: 11/30/2022] Open
Abstract
Fossil and phylogenetic evidence indicates legume-rich modern tropical forests replaced Late Cretaceous palm-dominated tropical forests across four continents during the early Cenozoic (58-42 Ma). Tropical legume trees can transform ecosystems via their ability to fix dinitrogen (N2) and higher leaf N compared with non-legumes (35-65%), but it is unclear how their evolutionary rise contributed to silicate weathering, the long-term sink for atmospheric carbon dioxide (CO2). Here we hypothesize that the increasing abundance of N2-fixing legumes in tropical forests amplified silicate weathering rates by increased input of fixed nitrogen (N) to terrestrial ecosystems via interrelated mechanisms including increasing microbial respiration and soil acidification, and stimulating forest net primary productivity. We suggest the high CO2 early Cenozoic atmosphere further amplified legume weathering. Evolution of legumes with high weathering rates was probably driven by their high demand for phosphorus and micronutrients required for N2-fixation and nodule formation.
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Affiliation(s)
- Dimitar Z Epihov
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Sarah A Batterman
- School of Geography and Priestley International Centre for Climate, University of Leeds, Leeds LS2 9JT, UK
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
| | - Lars O Hedin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan R Leake
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Lisa M Smith
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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Sprent JI, Ardley J, James EK. Biogeography of nodulated legumes and their nitrogen-fixing symbionts. New Phytol 2017; 215:40-56. [PMID: 28211601 DOI: 10.1111/nph.14474] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [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: 07/18/2016] [Accepted: 12/22/2016] [Indexed: 05/21/2023]
Abstract
Contents 40 I. 40 II. 41 III. 44 IV. 48 V. 49 VI. 49 VII. 52 VIII. 53 53 References 53 SUMMARY: In the last decade, analyses of both molecular and morphological characters, including nodulation, have led to major changes in our understanding of legume taxonomy. In parallel there has been an explosion in the number of genera and species of rhizobia known to nodulate legumes. No attempt has been made to link these two sets of data or to consider them in a biogeographical context. This review aims to do this by relating the data to the evolution of the two partners: it highlights both longitudinal and latitudinal trends and considers these in relation to the location of major land masses over geological time. Australia is identified as being a special case and latitudes north of the equator as being pivotal in the evolution of highly specialized systems in which the differentiated rhizobia effectively become ammonia factories. However, there are still many gaps to be filled before legume nodulation is sufficiently understood to be managed for the benefit of a world in which climate change is rife.
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Affiliation(s)
- Janet I Sprent
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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Victor MM, David JM, Sakukuma MCK, Costa-Lotufo LV, Moura AF, Araújo AJ. Terpene Esters from Natural Products: Synthesis and Evaluation of Cytotoxic Activity. AN ACAD BRAS CIENC 2017; 89:1369-1379. [PMID: 28813102 DOI: 10.1590/0001-3765201720160780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/22/2017] [Indexed: 01/27/2023] Open
Abstract
Natural steroids and triterpenes such as b-sitosterol, stigmasterol, lupeol, ursolic and betulinic acids were transformed into its hexanoic and oleic esters, to evaluate the influence of chemical modification towards the cytotoxic activities against tumor cells. The derivatives were evaluated against five tumor cell lines [OVCAR-8 (ovarian carcinoma); SF-295 (glioblastoma); HCT-116 (colon adenocarcinoma); HL-60 (leukemia); and PC-3 (prostate carcinoma)] and the results showed only betulinic acid hexyl ester exhibits cytotoxic potential activity.
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Affiliation(s)
- Mauricio M Victor
- Instituto de Química, Universidade Federal da Bahia, Depto de Química Orgânica, Rua Barão do Jeremoabo, s/n, Campus de Ondina, Ondina, 40170-115 Salvador, BA, Brazil
- Instituto Nacional de Ciência e Tecnologia/INCT de Energia e Ambiente,Universidade Federal da Bahia/UFBA, Rua Barão de Geremoabo, 147, Campus de Ondina, 40170-290 Salvador, BA, Brazil
| | - Jorge M David
- Instituto de Química, Universidade Federal da Bahia, Depto de Química Orgânica, Rua Barão do Jeremoabo, s/n, Campus de Ondina, Ondina, 40170-115 Salvador, BA, Brazil
- Instituto Nacional de Ciência e Tecnologia/INCT de Energia e Ambiente,Universidade Federal da Bahia/UFBA, Rua Barão de Geremoabo, 147, Campus de Ondina, 40170-290 Salvador, BA, Brazil
| | - Maria C K Sakukuma
- Instituto de Química, Universidade Federal da Bahia, Depto de Química Orgânica, Rua Barão do Jeremoabo, s/n, Campus de Ondina, Ondina, 40170-115 Salvador, BA, Brazil
- Instituto Nacional de Ciência e Tecnologia/INCT de Energia e Ambiente,Universidade Federal da Bahia/UFBA, Rua Barão de Geremoabo, 147, Campus de Ondina, 40170-290 Salvador, BA, Brazil
| | - Letícia V Costa-Lotufo
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Centro de Ciências da Saúde, Av. Coronel Nunes de Melo, 1127, Rodolfo Teófilo, 60430-270 Fortaleza, CE, Brazil
- Departamento de Farmacologia, Universidade de São Paulo, Av. Professor Lineu Prestes, 1524, Cidade Universitária, Butantã, 05508-900 São Paulo, SP, Brazil
| | - Andrea F Moura
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Centro de Ciências da Saúde, Av. Coronel Nunes de Melo, 1127, Rodolfo Teófilo, 60430-270 Fortaleza, CE, Brazil
| | - Ana J Araújo
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Centro de Ciências da Saúde, Av. Coronel Nunes de Melo, 1127, Rodolfo Teófilo, 60430-270 Fortaleza, CE, Brazil
- Universidade Federal do Piauí, Av. São Sebastião, 2819, São Benedito, Campus Ministro Reis Velloso, 64202-020 Parnaíba, PB, Brazil
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Chozas S, Chefaoui RM, Correia O, Bonal R, Hortal J. Environmental niche divergence among three dune shrub sister species with parapatric distributions. Ann Bot 2017; 119:1157-1167. [PMID: 28334085 PMCID: PMC5604598 DOI: 10.1093/aob/mcx004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 12/02/2016] [Accepted: 01/10/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND AND AIMS The geographical distributions of species are constrained by their ecological requirements. The aim of this work was to analyse the effects of environmental conditions, historical events and biogeographical constraints on the diversification of the three species of the western Mediterranean shrub genus Stauracanthus , which have a parapatric distribution in the Iberian Peninsula. METHODS Ecological niche factor analysis and generalized linear models were used to measure the response of all Stauracanthus species to the environmental gradients and map their potential distributions in the Iberian Peninsula. The bioclimatic niche overlap between the three species was determined by using Schoener's index. The genetic differentiation of the Iberian and northern African populations of Stauracanthus species was characterized with GenalEx. The effects on genetic distances of the most important environmental drivers were assessed through Mantel tests and non-metric multidimensional scaling. KEY RESULTS The three Stauracanthus species show remarkably similar responses to climatic conditions. This supports the idea that all members of this recently diversified clade retain common adaptations to climate and consequently high levels of climatic niche overlap. This contrasts with the diverse edaphic requirements of Stauracanthus species. The populations of the S. genistoides-spectabilis clade grow on Miocene and Pliocene fine-textured sedimentary soils, whereas S. boivinii , the more genetically distant species, occurs on older and more coarse-textured sedimentary substrates. These patterns of diversification are largely consistent with a stochastic process of geographical range expansion and fragmentation coupled with niche evolution in the context of spatially complex environmental fluctuations. CONCLUSIONS : The combined analysis of the distribution, realized environmental niche and phylogeographical relationships of parapatric species proposed in this work allows integration of the biogeographical, ecological and evolutionary processes driving the evolution of species adaptations and how they determine their current geographical ranges.
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Affiliation(s)
- Sergio Chozas
- cE3c, Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, Piso 5, 1749-016 Lisboa, Portugal
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales (MNCN-CSIC), C/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Rosa M. Chefaoui
- CCMAR, Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Otília Correia
- cE3c, Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, Piso 5, 1749-016 Lisboa, Portugal
| | - Raúl Bonal
- Forest Research Group, INDEHESA, Universidad de Extremadura, Avda Virgen del Puerto 2, 10600 Plasencia, Spain
- DITEG Research Group, University of Castilla-La Mancha, Toledo, Spain
| | - Joaquín Hortal
- cE3c, Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, Piso 5, 1749-016 Lisboa, Portugal
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales (MNCN-CSIC), C/José Gutiérrez Abascal 2, 28006 Madrid, Spain
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35
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Wallace LE, Wheeler GL, McGlaughlin ME, Bresowar G, Helenurm K. Phylogeography and genetic structure of endemic Acmispon argophyllus and A. dendroideus (Fabaceae) across the California Channel Islands. Am J Bot 2017; 104:743-756. [PMID: 28526725 DOI: 10.3732/ajb.1600429] [Citation(s) in RCA: 2] [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] [Received: 12/07/2016] [Accepted: 04/06/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular Acmispon argophyllus and A. dendroideus to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands. METHODS DNA sequences were collected from nuclear (ADH) and plastid genomes (rpL16, ndhA, psbD-trnT) from >450 samples on the Channel Islands and California. We estimated population genetic diversity and structure, phylogenetic patterns among populations, and migration rates, and tested for population growth. KEY RESULTS Populations of northern island A. argophyllus var. niveus are genetically distinct from conspecific populations on southern islands. On the southern islands, A. argophyllus var. argenteus populations on Santa Catalina are phylogenetically distinct from populations of var. argenteus and var. adsurgens on the other southern islands. For A. dendroideus, we found the varieties to be monophyletic. Populations of A. dendroideus var. traskiae on San Clemente are genetically differentiated from other conspecific populations, whereas populations on the northern islands and Santa Catalina show varying degrees of gene flow. Evidence of population growth was found in both species. CONCLUSIONS Oceanic barriers between islands have had a strong influence on population genetic structure in both Acmispon species, although the species have differing phylogeographic patterns. This study provides a contrasting pattern of dispersal on a near island system that does not follow a strict stepping-stone model, commonly found on isolated island systems.
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Affiliation(s)
- Lisa E Wallace
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Gregory L Wheeler
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Mitchell E McGlaughlin
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Gerald Bresowar
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Kaius Helenurm
- Department of Biology, University of South Dakota, Vermillion, South Dakota 57069, USA
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36
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Wang J, Sun P, Li Y, Liu Y, Yu J, Ma X, Sun S, Yang N, Xia R, Lei T, Liu X, Jiao B, Xing Y, Ge W, Wang L, Wang Z, Song X, Yuan M, Guo D, Zhang L, Zhang J, Jin D, Chen W, Pan Y, Liu T, Jin L, Sun J, Yu J, Cheng R, Duan X, Shen S, Qin J, Zhang MC, Paterson AH, Wang X. Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform. Plant Physiol 2017; 174:284-300. [PMID: 28325848 PMCID: PMC5411148 DOI: 10.1104/pp.16.01981] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/19/2017] [Indexed: 05/18/2023]
Abstract
Mainly due to their economic importance, genomes of 10 legumes, including soybean (Glycine max), wild peanut (Arachis duranensis and Arachis ipaensis), and barrel medic (Medicago truncatula), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape (Vitis vinifera) and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by widespread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported the likely autopolyploidy nature of its tetraploid ancestor. Moreover, although most gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to the copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes and, by performing synonymous nucleotide substitutions at synonymous sites correction, redated major evolutionary events during their expansion. This effort laid a solid foundation for further genomics exploration in the legume research community and beyond. We describe only a tiny fraction of legume comparative genomics analysis that we performed; more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org).
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Affiliation(s)
- Jinpeng Wang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Pengchuan Sun
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Yuxian Li
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Yinzhe Liu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jigao Yu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xuelian Ma
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Sangrong Sun
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Nanshan Yang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Ruiyan Xia
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Tianyu Lei
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xiaojian Liu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Beibei Jiao
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Yue Xing
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Weina Ge
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Li Wang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Zhenyi Wang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xiaoming Song
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Min Yuan
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Di Guo
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Lan Zhang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jiaqi Zhang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Dianchuan Jin
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Wei Chen
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Yuxin Pan
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Tao Liu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Ling Jin
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jinshuai Sun
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jiaxiang Yu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Rui Cheng
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xueqian Duan
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Shaoqi Shen
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jun Qin
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Meng-Chen Zhang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Andrew H Paterson
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xiyin Wang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
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37
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Abstract
BACKGROUND Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and they have been discovered in a variety of organisms ranging from viruses and microbes to eukaryotic organisms. The computational detection of pre-miRNAs is of great interest, and such approaches usually employ machine learning to discriminate between miRNAs and other sequences. Many features have been proposed describing pre-miRNAs, and we have previously introduced the use of sequence motifs and k-mers as useful ones. There have been reports of xeno-miRNAs detected via next generation sequencing. However, they may be contaminations and to aid that important decision-making process, we aimed to establish a means to differentiate pre-miRNAs from different species. RESULTS To achieve distinction into species, we used one species' pre-miRNAs as the positive and another species' pre-miRNAs as the negative training and test data for the establishment of machine learned models based on sequence motifs and k-mers as features. This approach resulted in higher accuracy values between distantly related species while species with closer relation produced lower accuracy values. CONCLUSIONS We were able to differentiate among species with increasing success when the evolutionary distance increases. This conclusion is supported by previous reports of fast evolutionary changes in miRNAs since even in relatively closely related species a fairly good discrimination was possible.
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Affiliation(s)
- Malik Yousef
- Community Information Systems, Zefat Academic College, Zefat, 13206 Israel
| | - Waleed Khalifa
- Computer Science, The College of Sakhnin, Sakhnin, 30810 Israel
| | - İlhan Erkin Acar
- Biotechnology, Izmir Institute of Technology, 35430 Urla, Izmir Turkey
| | - Jens Allmer
- Molecular Biology and Genetics, Izmir Institute of Technology, 35430 Urla, Izmir Turkey
- Bionia Incorporated, IZTEKGEB A8, 35430 Urla, Izmir Turkey
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De Barros TC, Pedersoli GD, Paulino JV, Teixeira SP. In the interface of caesalpinioids and mimosoids: Comparative floral development elucidates shared characters in Dimorphandra mollis and Pentaclethra macroloba (Leguminosae). Am J Bot 2017; 104:218-232. [PMID: 28202455 DOI: 10.3732/ajb.1600308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 08/19/2016] [Accepted: 01/13/2017] [Indexed: 05/26/2023]
Abstract
PREMISE OF THE STUDY Pentaclethra and Dimorphandra (Leguminosae) have long been considered a possible enigmatic link between caesalpinioids and mimosoids because they both have an imbricate calyx and heteromorphic androecium, floral features that are rare among mimosoids but common among caesalpinioids. This study compared the developing flowers of Dimorphandra mollis and Pentaclethra macroloba to determine whether the shared floral conditions also have the same ontogenetic origin. METHODS Buds of different sizes and flowers were processed for surface (scanning electron microscopy) and histological (light microscopy) examination. KEY RESULTS The floral meristem initiates five sepal primordia in a modified helical order in both species. The median sagittal sepal is adaxial. The overlap of the sepals during elongation culminates with the formation of the imbricate calyx. Heteromorphic androecia arise in the intermediate stages of development. In P. macroloba, the fertile pollen-bearing stamens are antesepalous, robust and short, and the anthers carry a robust apical gland; the staminodes are long and white with a vestigial apical gland. In contrast, in D. mollis the fertile pollen-bearing stamens are antepetalous without glands and as long as the staminodes. The staminodes are thinner with an expanded apical region. CONCLUSIONS The imbricate calyx and the heteromorphic androecium in the studied species originated via distinct pathways, favoring the hypothesis of homoplasy of these conditions. The pathways observed in P. macroloba are more similar to those observed in caesalpinioids than to those observed in mimosoids, indicating that although the floral development differs between the species studied, it supports the basal placement of Pentaclethra among mimosoids.
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Affiliation(s)
- Thais C De Barros
- Programa de Pós-Graduação em Biologia Comparada, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14040-901, Brazil
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Avenida do Café, s/n., Ribeirão Preto, SP 14040-903, Brazil
| | - Giseli D Pedersoli
- Programa de Pós-Graduação em Biologia Comparada, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14040-901, Brazil
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Avenida do Café, s/n., Ribeirão Preto, SP 14040-903, Brazil
| | - Juliana V Paulino
- Universidade Federal do Rio de Janeiro, Faculdade de Farmácia, Centro de Ciências da Saúde, Departamento de Produtos Naturais e Alimentos, Av. Prof Paulo Rocco s/n-Bl A 2°, Ilha do Fundão, Rio de Janeiro, RJ 21941-902, Brazil
| | - Simone P Teixeira
- Programa de Pós-Graduação em Biologia Comparada, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, SP 14040-901, Brazil
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Avenida do Café, s/n., Ribeirão Preto, SP 14040-903, Brazil
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39
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Abstract
MLO proteins are highly conserved proteins with seven trans-membrane domains. Specific MLO genes have been linked to plant disease susceptibility. Others are involved in plant reproduction and in root thigmomorphogenesis. Functions of the remaining MLOs are still unknown. Here we performed a genome-wide survey of the MLO family in eight legume species from different clades of the Papillionoideae sub-family. A total of 118 MLO sequences were identified and characterized. Their deduced protein sequences shared the characteristics of MLO proteins. The total number of MLO genes per legume species varied from 13 to 20 depending on the species. Legume MLOs were evenly distributed over their genomes and tended to localize within syntenic blocks conserved across legume genomes. Phylogenetic analysis indicated that these sequences clustered in seven well-defined clades. Comparison of MLO protein sequences revealed 34 clade-specific motifs in the variable regions of the proteins. Comparative analyses of the MLO family between legume species also uncovered several evolutionary differences between the tropical legume species from the Phaseoloid clades and the other legume species. Altogether, this study provides interesting new features on the evolution of the MLO family. It also provides valuable clues to identify additional MLO genes from non-sequenced species.
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Affiliation(s)
- Nicolas Rispail
- Institute for Sustainable Agriculture, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
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40
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Kholina AB, Kozyrenko MM, Artyukova EV, Sandanov DV, Andrianova EA. [Phylogenetic relationships of the species of Oxytropis DC. subg. Oxytropis and Phacoxytropis (Fabaceae) from Asian Russia inferred from the nucleotide sequence analysis of the intergenic spacers of the chloroplast genome]. Genetika 2016; 52:895-909. [PMID: 29368883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The nucleotide sequence analysis of trnH–psbA, trnL–trnF, and trnS–trnG intergenic spacer regions of chloroplast DNA performed in the representatives of the genus Oxytropis from Asian Russia provided clarification of the phylogenetic relationships of some species and sections in the subgenera Oxytropis and Phacoxytropis and in the genus Oxytropis as a whole. Only the section Mesogaea corresponds to the subgenus Phacoxytropis, while the section Janthina of the same subgenus groups together with the sections of the subgenus Oxytropis. The sections Chrysantha and Ortholoma of the subgenus Oxytropis are not only closely related to each other, but together with the section Mesogaea, they are grouped into the subgenus Phacoxytropis. It seems likely that the sections Chrysantha and Ortholoma should be assigned to the subgenus Phacoxytropis, and the section Janthina should be assigned to the subgenus Oxytropis. The molecular differences were identified between O. coerulea and O. mandshurica from the section Janthina that were indicative of considerable divergence of their chloroplast genomes and the species independence of the taxa. The species independence of O. czukotica belonging to the section Arctobia was also confirmed.
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41
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Lam HK, Ross JJ, McAdam EL, McAdam SAM. The single evolutionary origin of chlorinated auxin provides a phylogenetically informative trait in the Fabaceae. Plant Signal Behav 2016; 11:e1197467. [PMID: 27302610 PMCID: PMC4991336 DOI: 10.1080/15592324.2016.1197467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 05/11/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 06/01/2023]
Abstract
Chlorinated auxin (4-chloroindole-3-acetic acid, 4-Cl-IAA), a highly potent plant hormone, was once thought to be restricted to species of the tribe Fabeae within the Fabaceae, until we recently detected this hormone in the seeds of Medicago, Melilotus and Trifolium species. The absence of 4-Cl-IAA in the seeds of the cultivated species Cicer aeritinum from the Cicerae tribe, immediately basal to the Fabeae and Trifolieae tribes, suggested a single evolutionary origin of 4-Cl-IAA. Here, we provide a more robust phylogenetic placement of the ability to produce chlorinated auxin by screening key species spanning this evolutionary transition. We report no detectable level of 4-Cl-IAA in Cicer echinospermum (a wild relative of C. aeritinum) and 4 species (Galega officinalis, Parochetus communis, Astragalus propinquus and A. sinicus) from tribes or clades more basal or sister to the Cicerae tribe. We did detect 4-Cl-IAA in the dry seeds of 4 species from the genus Ononis that are either basal to the genera Medicago, Melilotus and Trigonella or basal to, but still within, the Fabeae and Trifolieae (ex. Parochetus) clades. We conclude that the single evolutionary origin of this hormone in seeds can be used as a phylogenetically informative trait within the Fabaceae.
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Affiliation(s)
- Hong Kiat Lam
- School of Biological Sciences, University of Tasmania, Hobart, TAS, Australia
| | - John J. Ross
- School of Biological Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Erin L. McAdam
- School of Biological Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Scott A. M. McAdam
- School of Biological Sciences, University of Tasmania, Hobart, TAS, Australia
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42
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Zvyagina NS, Dorogina OV, Krasnikov AA. Genetic differentiation and karyotype variation in Hedysarum chaiyrakanicum, an endemic species of Tuva Republic, Russia. Indian J Exp Biol 2016; 54:338-344. [PMID: 27319053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Overgrazing and mining affect vegetation, particularly in mountains. At times, it goes to such an extent that the plant species become vulnerable and slowly extinct from its habitat. Such endemic species need to be protected. One such endemic species Hedysarum chaiyrakanicum Kurbatsky, a vulnerable steppe vegetation of Tuva Republic, Russia was evaluated for its genetic diversity and taxonomic definition using molecular technique and chromosome number adjustment. The genetic differentiation among H. chaiyrakanicum, H. setigerum Turcz. and H. gmelinii Ledeb. genotypes was determined using five inter-simple sequence repeat (ISSR) markers and then examined with Nei's genetic distance coefficient (D) and Shannon's information index (H). A total of 134 reproducible bands were detected with polymorphism percentage of 98%. The genetic diversity of H. chaiyrakanicum was found to be 0.343 while the Shannon index H(sp) was determined as 8 06. The chromosome number 2n = 16 is newly observed within the H. chaiyrakanicum. The genetic relationship based on ISSR data supported the taxonomic distinction of H. chaiyrakanicum from H. setigerum and H. gmelinii. We recommend both in situ and ex situ conservation strategies, specially germplasm sampling, to save this endemic species.
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Takahashi Y, Somta P, Muto C, Iseki K, Naito K, Pandiyan M, Natesan S, Tomooka N. Novel Genetic Resources in the Genus Vigna Unveiled from Gene Bank Accessions. PLoS One 2016; 11:e0147568. [PMID: 26800459 PMCID: PMC4723357 DOI: 10.1371/journal.pone.0147568] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/05/2016] [Indexed: 11/30/2022] Open
Abstract
The genus Vigna (Fabaceae) consists of five subgenera, and includes more than 100 wild species. In Vigna, 10 crops have been domesticated from three subgenera, Vigna, Plectrotropis, and Ceratotropis. The habitats of wild Vigna species are so diverse that their genomes could harbor various genes responsible for environmental stress adaptation, which could lead to innovations in agriculture. Since some of the gene bank Vigna accessions were unidentified and they seemed to be novel genetic resources, these accessions were identified based on morphological traits. The phylogenetic positions were estimated based on the DNA sequences of nuclear rDNA-ITS and chloroplast atpB-rbcL spacer regions. Based on the results, the potential usefulness of the recently described species V. indica and V. sahyadriana, and some wild Vigna species, i.e., V. aconitifolia, V. dalzelliana, V. khandalensis, V. marina var. oblonga, and V. vexillata, was discussed.
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Affiliation(s)
- Yu Takahashi
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand
| | - Chiaki Muto
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Kohtaro Iseki
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Ken Naito
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | | | | | - Norihiko Tomooka
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
- * E-mail:
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Wang Z, Cheng K, Wan L, Yan L, Jiang H, Liu S, Lei Y, Liao B. Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes. BMC Genomics 2015; 16:1053. [PMID: 26651343 PMCID: PMC4676100 DOI: 10.1186/s12864-015-2258-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/30/2015] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. They have been shown to be diverse transcriptional regulators, playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of six completely sequenced legume genomes, a comprehensive investigation of bZIP family members in legumes has yet to be presented. RESULTS In this study, we identified 428 bZIP genes encoding 585 distinct proteins in six legumes, Glycine max, Medicago truncatula, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Lotus japonicus. The legume bZIP genes were categorized into 11 groups according to their phylogenetic relationships with genes from Arabidopsis. Four kinds of intron patterns (a-d) within the basic and hinge regions were defined and additional conserved motifs were identified, both presenting high group specificity and supporting the group classification. We predicted the DNA-binding patterns and the dimerization properties, based on the characteristic features in the basic and hinge regions and the Leu zipper, respectively, which indicated that some highly conserved amino acid residues existed across each major group. The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. We also detected several key legume bZIP genes involved in drought- and salt-responses by comparing fold changes of expression values in drought-stressed or salt-stressed roots and leaves. CONCLUSIONS In summary, this genome-wide identification, characterization and expression analysis of legume bZIP genes provides valuable information for understanding the molecular functions and evolution of the legume bZIP transcription factor family, and highlights potential legume bZIP genes involved in regulating tissue development and abiotic stress responses.
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Affiliation(s)
- Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Ke Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Liyun Wan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
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Zou CM, Wang YQ, Cao WD, Liu Y, Zhang XH, Tang S. [Response of photosynthesis and growth to weak light regime in different Adzuki bean (Vigna angularis) varieties]. Ying Yong Sheng Tai Xue Bao 2015; 26:3687-3692. [PMID: 27112006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In order to determine the adaptability of Adzuki beans as the interplanting crops in fruit yards, field and pot experimental treatments with full natural light and weak light (48% of full natural light) regimes were conducted to test the shade tolerance and physiological responses of three Adzuki bean varieties including Funan green Vigna angularis (FGVA), early-mature black V. angularis (EBVA) and late-mature black V. angularis (LBVA). The leaf photosynthetic characteristic parameters, photosynthetic pigment contents and the activity of RuBPCase were measured during the first bloom stage. The response of growth to weak light was likewise studied. The results showed that the photosynthetic characteristic parameters, i.e., the maximum net photosynthetic rate, light saturation point and light compensation point of the three Adzuki bean varieties under the weak light stress changed differently. The weak light stress induced the reduction of net photosynthetic rate, water use efficiency and RuBPCase activity of the three Adzuki bean varieties significantly. The contents of chlorophyll a and chlorophyll b in leaves of FGVA increased significantly, while Chl a/b and carotenoid content in the leaves decreased significantly after shading. But the other two varieties did not change obviously in photosynthetic pigments content after shading. The weak light changed the growth of the three Adzuki bean varieties, such as decreasing dry matter yield and dry matter accumulation efficiency, reducing root nodule and root-shoot ratio, debasing leaves quantity and leaf area index. The first bloom stage and maturing stage of FGVA advanced, while that of EBVA delayed under weak light. However, flowers were not strong enough to seed for LBVA under the weak light. In conclusion, according to the photosynthetic characteristics changes after shading, as well as the growth status, we concluded that the shade tolerance of the three Adzuki beans was ranked as FGVA>EBVA>LBVA.
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Macas J, Novák P, Pellicer J, Čížková J, Koblížková A, Neumann P, Fuková I, Doležel J, Kelly LJ, Leitch IJ. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae. PLoS One 2015; 10:e0143424. [PMID: 26606051 PMCID: PMC4659654 DOI: 10.1371/journal.pone.0143424] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/04/2015] [Indexed: 01/30/2023] Open
Abstract
The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55–83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.
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Affiliation(s)
- Jiří Macas
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
- * E-mail:
| | - Petr Novák
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Jana Čížková
- Institute of Experimental Botany, Olomouc, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Andrea Koblížková
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Pavel Neumann
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Iva Fuková
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Olomouc, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Laura J. Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Ilia J. Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
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Zhang Y, Li Z, Peng Y, Wang X, Peng D, Li Y, He X, Zhang X, Ma X, Huang L, Yan Y. Clones of FeSOD, MDHAR, DHAR Genes from White Clover and Gene Expression Analysis of ROS-Scavenging Enzymes during Abiotic Stress and Hormone Treatments. Molecules 2015; 20:20939-54. [PMID: 26610459 PMCID: PMC6332117 DOI: 10.3390/molecules201119741] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 12/15/2022] Open
Abstract
Increased transcriptional levels of genes encoding antioxidant enzymes play important protective roles in coping with excessive accumulation of reactive oxygen species (ROS) in plants exposed to various abiotic stresses. To fully elucidate different evolutions and functions of ROS-scavenging enzymatic genes, we isolated iron superoxide dismutase (FeSOD), dehydroascorbate reductase (DHAR) and monodehydroascorbate reductase (MDHAR) from white clover for the first time and subsequently tested dynamic expression profiles of these genes together with previously identified other antioxidant enzyme genes including copper zinc superoxide dismutase (Cu/ZnSOD), manganese superoxide dismutase (MnSOD), glutathione reductase (GR), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) in response to cold, drought, salinity, cadmium stress and exogenous abscisic acid (ABA) or spermidine (Spd) treatment. The cloned fragments of FeSOD, DHAR and MDHAR genes were 630, 471 and 669 bp nucleotide sequences encoding 210, 157 and 223 amino acids, respectively. Phylogenetic analysis indicated that both amino acid and nucleotide sequences of these three genes are highly conservative. In addition, the analysis of genes expression showed the transcription of GR, POD, MDHAR, DHAR and Cu/ZnSOD were rapidly activated with relatively high abundance during cold stress. Differently, CAT, APX, FeSOD, Cu/ZnSOD and MnSOD exhibited more abundant transcripts compared to others under drought stress. Under salt stress, CAT was induced preferentially (3-12 h) compared to GR which was induced later (12-72 h). Cadmium stress mainly up-regulated Cu/ZnSOD, DHAR and MDHAR. Interestingly, most of genes expression induced by ABA or Spd happened prior to various abiotic stresses. The particular expression patterns and different response time of these genes indicated that white clover differentially activates genes encoding antioxidant enzymes to mitigate the damage of ROS during various environmental stresses.
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Affiliation(s)
- Yan Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Zhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yan Peng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiaojuan Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Dandan Peng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yaping Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiaoshuang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinquan Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiao Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Linkai Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yanhong Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Fan PH, Zang MT, Xing J. Oligosaccharides composition in eight food legumes species as detected by high-resolution mass spectrometry. J Sci Food Agric 2015; 95:2228-2236. [PMID: 25270891 DOI: 10.1002/jsfa.6940] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 07/22/2014] [Revised: 09/18/2014] [Accepted: 09/25/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND As probiotics, soy oligosaccharides have become popular as healthy foods to reduce disease risk. However, comprehensive information about oligosaccharides in different food legumes is limited. RESULTS In this study, eight oligosaccharides were well detected and quantified in different varieties of eight legume species using high-resolution mass spectrometry. It was determined that species could be distinguished by total content of oligosaccharides and their distribution modes. Among the studied species, Vigna unguiculata is a better resource of non-digestible oligosaccharides, while Vicia faba and black soybean (Glycine max) are at a disadvantage. Normally, stachyose predominates in non-digestible oligosaccharides, except in mung bean and broad bean, where verbascose predominates. For mung bean and green soybean, the seed coat should be taken into account for oligosaccharide consumption. The developed high-resolution mass spectrometry method greatly simplified the sample preparation process and permitted the identification of oligosaccharides without reference compounds. CONCLUSION This work involved extensive sample collecting and provided useful information for consumers. The developed method may be useful for rapid quantification of oligosaccharides in related foods.
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Affiliation(s)
- Pei-Hong Fan
- School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, People's Republic of China
| | - Mei-Tong Zang
- School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, People's Republic of China
| | - Jie Xing
- School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, People's Republic of China
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Lin LZ, Liu MC, Ma HY, Chen YF, Zhang DY, Liu F, Li SY. [Identification of Moghania philippinensis and Moghania macrophylla]. Zhong Yao Cai 2015; 38:1417-1421. [PMID: 26946838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To study the identification methods of Moghania philippinensis and Moghania macrophylla, and to establish a comprehensive precise discrimination method. METHODS TLC and HPLC were applied to analyze genistein in the root of Moghania philippinensis and Moghania macrophylla. DNA barcoding establishment was based on ITS2 sequcence. RESULTS A comprehensive differentiation method for Moghania philippinensis and Moghania macrophylla based on TLC was proposed, which was combined with HPLC for determination of genistein. The plants of Moghania philippinensis and Moghania macrophylla and their related species could be distinguished by DNA barcoding effectively. CONCLUSION TLC and HPLC profiles of Flemingia Radix provide alternative methods of identification using chemical approach. This integrated chemical and molecular approach allows accurate comprehensive fast identification of Moghania philippinensis and Moghania macrophylla, which avoids the methods limitations on the accuracy of identification. The differentiation methods based on TLC, HPLC and DNA barcoding are simple,which provide a new scientific evidence for the identification of authenticity of Flemingia Radix.
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Swanepoel W, le Roux MM, Wojciechowski MF, van Wyk AE. Oberholzeria (Fabaceae subfam. Faboideae), a new monotypic legume genus from Namibia. PLoS One 2015; 10:e0122080. [PMID: 25816251 PMCID: PMC4376691 DOI: 10.1371/journal.pone.0122080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/02/2015] [Indexed: 11/19/2022] Open
Abstract
Oberholzeria etendekaensis, a succulent biennial or short-lived perennial shrublet is described as a new species, and a new monotypic genus. Discovered in 2012, it is a rare species known only from a single locality in the Kaokoveld Centre of Plant Endemism, north-western Namibia. Phylogenetic analyses of molecular sequence data from the plastid matK gene resolves Oberholzeria as the sister group to the Genisteae clade while data from the nuclear rDNA ITS region showed that it is sister to a clade comprising both the Crotalarieae and Genisteae clades. Morphological characters diagnostic of the new genus include: 1) succulent stems with woody remains; 2) pinnately trifoliolate, fleshy leaves; 3) monadelphous stamens in a sheath that is fused above; 4) dimorphic anthers with five long, basifixed anthers alternating with five short, dorsifixed anthers, and 5) pendent, membranous, one-seeded, laterally flattened, slightly inflated but indehiscent fruits.
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Affiliation(s)
- Wessel Swanepoel
- Independent Researcher, Windhoek, Namibia
- H. G. W. J. Schweickerdt Herbarium, Department of Plant Science, University of Pretoria, Pretoria, South Africa
- * E-mail:
| | - M. Marianne le Roux
- Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
| | | | - Abraham E. van Wyk
- H. G. W. J. Schweickerdt Herbarium, Department of Plant Science, University of Pretoria, Pretoria, South Africa
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