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Figure 4 from: Ezekiel CN, Kraak B, Sandoval-Denis M, Sulyok M, Oyedele OA, Ayeni KI, Makinde OM, Akinyemi OM, Krska R, Crous PW, Houbraken J (2020) Diversity and toxigenicity of fungi and description of Fusarium madaense sp. nov. from cereals, legumes and soils in north-central Nigeria. MycoKeys 67: 95-124. https://doi.org/10.3897/mycokeys.67.52716
Figure 4 The first of 24 equally parsimonious trees obtained from Maximum-Parsimony (MP) analysis of BenA, CaM, RPB1, RPB2 and TEF-1a sequences of 42 isolates of Fusarium spp. Numbers on the nodes are MP bootstrap values (BS) and Maximum-Likelihood BS values above 70%. Branch lengths are proportional to distance. Ex-type strains are indicated with T. Strains corresponding to new species described here are shown in bold. The internal square shows MP statistics as follows: TL = tree length, CI = consistency index, RI = retention index and HI = homoplasy index.
Figure 5 from: Ezekiel CN, Kraak B, Sandoval-Denis M, Sulyok M, Oyedele OA, Ayeni KI, Makinde OM, Akinyemi OM, Krska R, Crous PW, Houbraken J (2020) Diversity and toxigenicity of fungi and description of Fusarium madaense sp. nov. from cereals, legumes and soils in north-central Nigeria. MycoKeys 67: 95-124. https://doi.org/10.3897/mycokeys.67.52716
Figure 5 Fusarium madaense sp. nov. (ex-type culture CBS 146669). A–C aspect of colonies on PDA, OA and SNA, respectively, after 14 d at 24°C in the dark D colony reverse on OA (up) and PDA (down) after 14 d at 24 °C in the dark E–G, J aerial conidiophores and phialides H, I sporodochia formed on the surface of carnation leaves K, L sporodochial conidiophores M, N chlamydospores O, P microconidia Q sporodochial conidia. Scale bars: 100 μm (H, I); 20 μm (J); 10 μm (all others).
Figure 1 from: Ezekiel CN, Kraak B, Sandoval-Denis M, Sulyok M, Oyedele OA, Ayeni KI, Makinde OM, Akinyemi OM, Krska R, Crous PW, Houbraken J (2020) Diversity and toxigenicity of fungi and description of Fusarium madaense sp. nov. from cereals, legumes and soils in north-central Nigeria. MycoKeys 67: 95-124. https://doi.org/10.3897/mycokeys.67.52716
Figure 1 Overall incidence of fungal genera recovered from food and soil in two states in north-central Nigeria.
Supplementary material 1 from: Klinger YP, Eckstein RL, Horlemann D, Otte A, Ludewig K (2020) Germination of the invasive legume Lupinus polyphyllus depends on cutting date and seed morphology. NeoBiota 60: 79-95. https://doi.org/10.3897/neobiota.60.56117
Model Tables
Light availability and rhizobium variation interactively mediate the outcomes of legume-rhizobium symbiosis
<p><span><span><span><span><span><span><span><span><span><span><span><b>Premise of the study:</b> Nutrients, light, water, and temperature are key factors limiting the growth of individual plants in nature. Mutualistic interactions between plants and microbes often mediate resource limitation for both partners. In the mutualism between legumes and rhizobia, plants provide rhizobia with carbon in exchange for fixed nitrogen.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Because partner quality in mutualisms is genotype-dependent, within-species genetic variation is expected to alter the responses of mutualists to changes in the resource environment. Here we ask whether partner quality variation in rhizobia mediates the response of host plants to changing light availability, and conversely, whether light alters the expression of partner quality variation. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods:</b> We inoculated clover hosts with 11 rhizobium strains that differed in partner quality, grew plants under either ambient or low light conditions in the greenhouse, and measured plant growth, nodule traits, and foliar nutrient composition. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Key results:</b> Light availability and rhizobium inocula interactively determined plant growth, and rhizobium partner quality variation was more apparent in ambient light. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Conclusions:</b> Our results suggest that variation in the costs and benefits of rhizobium symbionts mediate host responses to light availability, and that rhizobium variation might more important in higher-light environments. Our work adds to <span><span>a growing appreciation for the role of microbial intraspecific and interspecific diversity in mediating extended phenotypes in their hosts and suggests an important role for light availability in the ecology and evolution of legume-rhizobium symbiosis.</span></span></span></span></span></span></span></span></span></span></span></span></span></p>
Decreased coevolutionary potential and increased symbiont fecundity during the biological invasion of a legume-rhizobium mutualism
<p>Although most invasive species engage in mutualism, we know little about how mutualism evolves as partners colonize novel environments. Selection on cooperation and standing genetic variation for mutualism traits may differ between a mutualism's invaded and native ranges, which could alter cooperation and coevolutionary dynamics. To test for such differences, we compare mutualism traits between invaded- and native-range host-symbiont genotype combinations of the weedy legume, <i>Medicago polymorpha,</i> and its nitrogen-fixing rhizobium symbiont, <i>Ensifer medicae</i>, which have co-invaded North America. We find that mutualism benefits for plants are indistinguishable between invaded- and native-range symbioses. However, rhizobia gain greater fitness from invaded-range mutualisms than from native-range mutualisms, and this enhancement of symbiont fecundity could increase the mutualism's spread by increasing symbiont availability during plant colonization. Furthermore, mutualism traits in invaded-range symbioses show lower genetic variance and a simpler partitioning of genetic variance between host and symbiont sources, compared to native-range symbioses. This suggests that biological invasion has reduced mutualists' potential to respond to coevolutionary selection. Additionally, rhizobia bearing a locus (<i>hrrP</i>) that can enhance symbiotic fitness have more exploitative phenotypes in invaded-range than in native-range symbioses. These findings highlight the impacts of biological invasion on the evolution of mutualistic interactions.</p>
Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids
To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy region. Our study also indicates that rps16 has been independently lost at least five times in legumes, with additional gene and intron losses scattered among the papilionoids. Additionally, genera from two distinct lineages within the papilionoids, Lupinus and Robinia, have a parallel inversion of 36 kb and 39 kb, respectively. This parallel inversion is novel as it appears to be caused by a 29 bp repeat within two trnS genes. This repeat is present in all available legume plastid genomes indicating that there is the potential for this inversion to be present in more species. This case of a homoplasious inversion is also evidence that some inversion events may not be reliable phylogenetic markers.
Data from: N/P imbalance as a key driver for the invasion of oligothrophic dune systems by a woody legume
Oligotrophic ecosystems, previously considered to be more resilient to invasive plants, are now recognised to be highly vulnerable to invasions. In these systems, woody legumes show belowground ecosystem engineering characteristics that enable invasion, however, the underlying processes are not well understood. Using a Portuguese primary dune ecosystem as an oligotrophic model system, belowground biomass pools, turnover rates and stoichiometry of a native (Stauracanthus spectabilis) and an invasive legume (Acacia longifolia) were compared and related to changes in the foliage of the surrounding native (Corema album) vegetation. We hypothesized that the invasive legume requires less phosphorus per unit of biomass produced and exhibits an enhanced nutrient turnover compared to the native vegetation, which could drive invasion by inducing a systemic N/P imbalance. Compared with the native legumes, A. longifolia plants had larger canopies, higher SOM levels and lower tissue P concentrations. These attributes were strongly related to legume influence as measured by increased foliar N content and less depleted δ15N signatures in the surrounding C. album vegetation. Furthermore, higher root N concentration and increased nutrient turnover in the rhizosphere of the invader were associated with depleted foliar P in C. album. Our results emphasize that while A. longifolia itself maintains an efficient phosphorus use in biomass production, at the same time it exerts a strong impact on the N/P balance of the native system. Moreover, this study highlights the engineering of a belowground structure of roots and rhizosphere as a crucial driver for invasion, due to its central role in nutrient turnover. These findings provide new evidence that, under nutrient-limited conditions, considering co-limitation and nutrient cycling in oligotrophic systems is essential to understand the engineering character of invasive woody legumes.
Data from: Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula
Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50–75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and <15% of the variation in either synonymous rates (dS) or dN:dS. Among putative targets of selection were genes involved in defence against pathogens and herbivores, genes with roles in mediating the relationship with rhizobial symbionts and one-third of annotated histone-lysine methyltransferases. Adaptive evolution of the methyltransferases suggests that positive selection in gene expression may have occurred through evolution of enzymes involved in epigenetic modification.
Genotyping by sequencing data of five legume tree species widespread in the rainforests of West and Central Africa
<p>Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that arid conditions might have significantly reduced tree density during the Ice Ages. Our aim was to investigate whether the dry ice-age periods left a genetic signature on tree species that can be used to infer the date of the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five widespread Legume trees and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea), and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades -congruent across species- cannot be explained by geographic barriers, we tested other hypotheses with demographic model testing using ∂a∂I. The best estimates indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice-age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with non-assisted seed dispersal than for light-demanding species with long-distance wind dispersal. Different recolonisation abilities after recurrent cycles of forest fragmentation seem to explain why species with long-distance dispersal show more recent genetic admixture between the two clades than species with limited seed dispersal. Despite their old history, our results depict the African rainforests as a dynamic biome where tree species have expanded relatively recently after the last glaciation.</p>
Data from: Silicon-induced root nodulation and synthesis of essential amino acids in a legume is associated with higher herbivore abundance
Ecologists have become increasingly aware that silicon uptake by plants, especially the Poaceae, can have beneficial effects on both plant growth and herbivore defence. The effects of silicon on other plant functional groups, such as nitrogen-fixing legumes, have been less well studied. Silicon could, however, indirectly promote herbivore performance in this group if reported increases in N2-fixation caused improvements in host plant quality for herbivores. We tested how silicon supplementation in the legume Medico sativa affected plant growth rates, root nodulation and foliage quality (silicon content and amino acid profiles) for an insect herbivore (Acyrthosiphon pisum). Plants supplemented with silicon (Si+) grew three times as quickly as those without supplementation (Si-), almost entirely in shoot mass. While root growth was unaffected by silicon uptake, root nodules containing nitrogen-fixing bacteria were 44% more abundant on Si+ plants. Aphid abundance was twice as high on Si+ plants compared to Si- plants and was positively correlated with silicon-stimulated plant growth. Si+ plants accumulated more than twice as much silicon as Si- plants, but did not have higher silicon concentrations because of dilution effects linked to the rapid growth of Si+ plants. Si+ plants showed a 65% increase in synthesis of essential foliar amino acids, probably due to increased levels of root nodulation. These results suggest that increased silicon supply makes M. sativa more susceptible to A. pisum, mainly because of increased plant growth and resource availability (i.e. essential amino acids). While silicon augmentation of the Poaceae frequently improves herbivore defence, the current study illustrates that this cannot be assumed for other plant families where the beneficial effects of silicon on plant growth and nutrition may promote herbivore performance in some instances.
Data from: Genetic conflict with a parasitic nematode disrupts the legume-rhizobia mutualism
Genetic variation for partner quality in mutualisms is an evolutionary paradox. One possible resolution to this puzzle is that there is a tradeoff between partner quality and other fitness-related traits. Here, we tested whether a susceptibility to parasitism is one such tradeoff in the mutualism between legumes and nitrogen-fixing bacteria (rhizobia). We performed two greenhouse experiments with the legume Medicago truncatula. In the first, we inoculated each plant with the rhizobia Ensifer meliloti and with one of 40 genotypes of the parasitic root-knot nematode Meloidogyne hapla. In the second experiment, we inoculated all plants with rhizobia and half of the plants with a genetically variable population of nematodes. Using the number of nematode galls as a proxy for infection severity, we found that plant genotypes differed in susceptibility to nematode infection, and nematode genotypes differed in infectivity. Second, we showed that there was a genetic correlation between the number of mutualistic structures formed by rhizobia (nodules) and the number of parasitic structures formed by nematodes (galls). Finally, we found that nematodes disrupt the rhizobia mutualism: nematode-infected plants formed fewer nodules and had less nodule biomass than uninfected plants. Our results demonstrate that there is genetic conflict between attracting rhizobia and repelling nematodes in Medicago. If genetic conflict with parasitism is a general feature of mutualism, it could account for the maintenance of genetic variation in partner quality and influence the evolutionary dynamics of positive species interactions.
Data from: Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes
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.
Data from: Transcriptome sequencing and marker development for four underutilized legumes
Premise of the study: Combating threats to food and nutrition security in the context of climate change and global population increase is one of the highest priorities of major international organizations. Hundreds of species are grown on a small scale in some of the most drought/flood-prone regions of the world and as such may harbor some of the most environmentally tolerant crops (and alleles). Methods and Results: In this study, transcriptomes were sequenced, assembled, and annotated for four underutilized legume crops. Microsatellite markers were identified in each species, as well as a conserved orthologous set of markers for cross-family phylogenetics and comparative mapping, which were ground-truthed on a panel of diverse legume germplasm. Conclusions: An understanding of these underutilized legumes will inform crop selection and breeding by allowing the investigation of genetic variation and the genetic basis of adaptive traits to be established.
Data from: Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species-rich clades
The Leguminosae, the third-largest angiosperm family, has a global distribution and high ecological and economic importance. We examine how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the ca. 751 genera and ca. 19,500 species of legumes and then translate it into a phylogeny-based classification. We review the current state of knowledge of legume phylogeny and highlight where problems lie, for example in taxon sampling and phylogenetic resolution. We review approaches from bioinformatics and next-generation sequencing, which can facilitate the production of better phylogenetic estimates. Finally, we examine how morphology can be incorporated into legume phylogeny to address issues in comparative biology and classification. Our goal is to stimulate the research needed to improve our knowledge of legume phylogeny and evolution; the approaches that we discuss may also be relevant to other species-rich angiosperm clades.
Intercropping indices evaluation on grain legume-small grain cereals mixture: a critical meta-analysis review
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Supplementary material 2 from: Bruneau A, Queiroz LP, Ringelberg JJ, Borges LM, Bortoluzzi RLC, Brown GK, Cardoso DBOS, Clark RP, Conceição AS, Cota MMT, Demeulenaere E, Duno de Stefano R, Ebinger JE, Ferm J, Fonseca-Cortés A, Gagnon E, Grether R, Guerra E, Haston E, Herendeen PS, Hernández HM, Hopkins HCF, Huamantupa-Chuquimaco I, Hughes CE, Ickert-Bond SM, Iganci J, Koenen EJM, Lewis GP, Lima HC, Lima AG, Luckow M, Marazzi B, Maslin BR, Morales M, Morim MP, Murphy DJ, O'Donnell SA, Oliveira FG, Oliveira ACS, Rando JG, Ribeiro PG, Ribeiro CL, Santos FS, Seigler DS, Silva GS, Simon MF, Soares MVB, Terra V (2024) Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification. PhytoKeys 240: 1-552. https://doi.org/10.3897/phytokeys.240.101716
Phylogeny of Caesalpinioideae including all accessions
Figure 91 from: Bruneau A, Queiroz LP, Ringelberg JJ, Borges LM, Bortoluzzi RLC, Brown GK, Cardoso DBOS, Clark RP, Conceição AS, Cota MMT, Demeulenaere E, Duno de Stefano R, Ebinger JE, Ferm J, Fonseca-Cortés A, Gagnon E, Grether R, Guerra E, Haston E, Herendeen PS, Hernández HM, Hopkins HCF, Huamantupa-Chuquimaco I, Hughes CE, Ickert-Bond SM, Iganci J, Koenen EJM, Lewis GP, Lima HC, Lima AG, Luckow M, Marazzi B, Maslin BR, Morales M, Morim MP, Murphy DJ, O'Donnell SA, Oliveira FG, Oliveira ACS, Rando JG, Ribeiro PG, Ribeiro CL, Santos FS, Seigler DS, Silva GS, Simon MF, Soares MVB, Terra V (2024) Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification. PhytoKeys 240: 1-552. https://doi.org/10.3897/phytokeys.240.101716
Figure 91 Distribution of Mora based on quality-controlled digitised herbarium records. See Suppl. material 1 for the source of occurrence data.
Figure 87 from: Bruneau A, Queiroz LP, Ringelberg JJ, Borges LM, Bortoluzzi RLC, Brown GK, Cardoso DBOS, Clark RP, Conceição AS, Cota MMT, Demeulenaere E, Duno de Stefano R, Ebinger JE, Ferm J, Fonseca-Cortés A, Gagnon E, Grether R, Guerra E, Haston E, Herendeen PS, Hernández HM, Hopkins HCF, Huamantupa-Chuquimaco I, Hughes CE, Ickert-Bond SM, Iganci J, Koenen EJM, Lewis GP, Lima HC, Lima AG, Luckow M, Marazzi B, Maslin BR, Morales M, Morim MP, Murphy DJ, O'Donnell SA, Oliveira FG, Oliveira ACS, Rando JG, Ribeiro PG, Ribeiro CL, Santos FS, Seigler DS, Silva GS, Simon MF, Soares MVB, Terra V (2024) Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification. PhytoKeys 240: 1-552. https://doi.org/10.3897/phytokeys.240.101716
Figure 87 Generic relationships in tribe Dimorphandreae. For description of phylogeny and support values, see Fig. 6 caption (page 63).
Figure 88 from: Bruneau A, Queiroz LP, Ringelberg JJ, Borges LM, Bortoluzzi RLC, Brown GK, Cardoso DBOS, Clark RP, Conceição AS, Cota MMT, Demeulenaere E, Duno de Stefano R, Ebinger JE, Ferm J, Fonseca-Cortés A, Gagnon E, Grether R, Guerra E, Haston E, Herendeen PS, Hernández HM, Hopkins HCF, Huamantupa-Chuquimaco I, Hughes CE, Ickert-Bond SM, Iganci J, Koenen EJM, Lewis GP, Lima HC, Lima AG, Luckow M, Marazzi B, Maslin BR, Morales M, Morim MP, Murphy DJ, O'Donnell SA, Oliveira FG, Oliveira ACS, Rando JG, Ribeiro PG, Ribeiro CL, Santos FS, Seigler DS, Silva GS, Simon MF, Soares MVB, Terra V (2024) Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification. PhytoKeys 240: 1-552. https://doi.org/10.3897/phytokeys.240.101716
Figure 88 Leaves and inflorescences of tribe DimorphandreaeAMora paraensis (Ducke) Ducke (Simon 1663) BStachyothyrsus staudtii Harms CBurkea africana Hook. DDimorphandra mediocris Ducke (Simon 4209) EDimorphandra cuprea Sprague & Sandwith (Farroñay 1804) FDimorphandra parviflora Spruce ex Benth. (Simon 1176) GDimorphandra mollis Benth. HDimorphandra pennigera Tul. IDimorphandra ignea Ducke JDimorphandra vernicosa Spreng. ex Benth. (Cardoso 3279) KBurkea africanaLDimorphandra gardneriana Tul. (Silva 21). Photo credits A, D, F, G MF Simon B Nicolas Texier (CC-BY-NC-ND-3.0) C AR Lecuona (CC-BY-NC-4.0) E, H, I F Javier Farroñay Pacaya J D Cardoso K AE van Wyk and S Malan L G Sousa da Silva.
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