The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis

The Caesalpinioideae subfamily contains many well-known trees that are important for the sustainability of the economy and human health, but the lack of genomic resources hindered the breeding and utilization of these plants. Here, we present chromosome-level reference genomes for two food and industrial trees Gleditsia sinensis (921 Mb) and Biancaea sappan (872 Mb), three shade and ornamental trees Albizia julibrissin (705 Mb), Delonix regia (580 Mb) and Acacia confusa (566 Mb), as well as two pioneer and hedgerow trees Leucaena leucocephala (1,338 Mb) and Mimosa bimucronata (641 Mb). Phylogeny inference showed that the mimosoid clade has a much higher evolution rate than the other clades of Caesalpinioideae. Macrosynteny comparison showed that the fusion and broken of an unstable chromosome was responsible for the difference in the basic chromosome number 13 and 14 for Caesalpinioideae. After the ancient whole genome duplication shared by all Caesalpinioideae species (CWGD, ∼72.0 MYA), we found two recent successive WGD events LWGD-1 (16.2-19.5 MYA) and LWGD-2 (7.1-9.5 MYA) in L. leucocephala. Then, ∼40% gene loss and genome size contraction occurred during the diploidization process in L. leucocephala. For the secondary metabolites, we identified all the gene copies involved in mimosine metabolism for these species and revealed that the abundance of mimosine biosynthesis genes in L. leucocephala largely explains its high mimosine production. Moreover, we identified all the potential genes involved in triterpenoid saponin biosynthesis in G. sinensis, which is more complete than the previous transcriptome-derived unigenes. Our analyzing results and the genomic resources will facilitate the biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.

Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree

We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.

The radiation of nodulated Chamaecrista species from the rainforest into more diverse habitats has been accompanied by a reduction in growth form and a shift from fixation threads to symbiosomes

All non-mimosoid nodulated genera in the legume subfamily Caesalpinioideae confine their rhizobial symbionts within cell wall-bound "fixation threads" (FTs). The exception is the large genus Chamaecrista in which shrubs and subshrubs house their rhizobial bacteroids more intimately within symbiosomes, whereas large trees have FTs. This study aimed to unravel the evolutionary relationships between Chamaecrista growth habit, habitat, nodule bacteroid type, and rhizobial genotype. The growth habit, bacteroid anatomy, and rhizobial symbionts of 30 nodulated Chamaecrista species native to different biomes in the Brazilian state of Bahia, a major centre of diversity for the genus, was plotted onto an ITS-TrnL-F-derived phylogeny of Chamaecrista. The bacteroids from most of the Chamaecrista species examined were enclosed in symbiosomes (SYM-type nodules), but those in arborescent species in the section Apoucouita, at the base of the genus, were enclosed in cell wall material containing homogalacturonan (HG) and cellulose (FT-type nodules). Most symbionts were Bradyrhizobium genotypes grouped according to the growth habits of their hosts, but the tree, C. eitenorum, was nodulated by Paraburkholderia. Chamaecrista has a range of growth habits that allow it to occupy several different biomes and to co-evolve with a wide range of (mainly) bradyrhizobial symbionts. FTs represent a less intimate symbiosis linked with nodulation losses, so the evolution of SYM-type nodules by most Chamaecrista species may have (a) aided the genus-wide retention of nodulation, and (b) assisted in its rapid speciation and radiation out of the rainforest into more diverse and challenging habitats.

Chromosome-level genome of the transformable northern wattle, Acacia crassicarpa

The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphologies. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. In this study, we identify an accession of Acacia crassicarpa with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone, and using comparative analyses, confirm a whole-genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in Acacia.

Chemical and Biological Evaluation of Amazonian Medicinal Plant Vouacapoua americana Aubl

Vouacapoua americana (Fabaceae) is an economically important tree in the Amazon region and used for its highly resistant heartwood as well as for medicinal purposes. Despite its frequent use, phytochemical investigations have been limited and rather focused on ecological properties than on its pharmacological potential. In this study, we investigated the phytochemistry and bioactivity of V. americana stem bark extract and its constituents to identify eventual lead structures for further drug development. Applying hydrodistillation and subsequent GC-MS analysis, we investigated the composition of the essential oil and identified the 15 most abundant components. Moreover, the diterpenoids deacetylchagresnone (1), cassa-13(14),15-dien-oic acid (2), isoneocaesalpin H (3), (+)-vouacapenic acid (4), and (+)-methyl vouacapenate (5) were isolated from the stem bark, with compounds 2 and 4 showing pronounced effects on Methicillin-resistant Staphylococcus aureus and Enterococcus faecium, respectively. During the structure elucidation of deacetylchagresnone (1), which was isolated from a natural source for the first time, we detected inconsistencies regarding the configuration of the cyclopropane ring. Thus, the structure was revised for both deacetylchagresnone (1) and the previously isolated chagresnone. Following our works on Copaifera reticulata and Vatairea guianensis, the results of this study further contribute to the knowledge of Amazonian medicinal plants.

Ethnomedical applications and conservation status of Leguminosae-Caesalpinioideae plants in Uttar Pradesh, India

BACKGROUND

This review highlights the folklore, ethnomedicinal uses and conservation status of Caesalpinioideae in Uttar Pradesh (India).

AIMS

It aims at compiling available data of traditional medicine, biological activity, phytochemical information and assessing the regional red list status of Caesalpinioideae in Uttar Pradesh. The information provided would help in formulating new drugs and medicines and addressing global conservation issues of such medicinally exploited species.

METHODS

The current study included an extensive and systematic review of available literature, the study of previous collections of herbarium specimens, random interviews with locals and tribals, field surveys, and GeoCAT tool-based assessment during 2016-2020. The study reports that the majority of species of Caesalpinioideae are used for curing digestive problems (about 20 species) and skin diseases (19 species).

RESULT

Almost all the species have antimicrobial and antioxidant properties. These pharmacological activities can be attributed to the presence of various types of anthraquinones in plants.

CONCLUSION

The regional conservation status reveals that eight species qualified for the status of regionally threatened category while two species fall under near threatened category.

Cross-species transcriptomes reveal species-specific and shared molecular adaptations for plants development on iron-rich rocky outcrops soils

Background

Canga is the Brazilian term for the savanna-like vegetation harboring several endemic species on iron-rich rocky outcrops, usually considered for mining activities. Parkia platycephala Benth. and Stryphnodendron pulcherrimum (Willd.) Hochr. naturally occur in the cangas of Serra dos Carajás (eastern Amazonia, Brazil) and the surrounding forest, indicating high phenotypic plasticity. The morphological and physiological mechanisms of the plants’ establishment in the canga environment are well studied, but the molecular adaptative responses are still unknown. To understand these adaptative responses, we aimed to identify molecular mechanisms that allow the establishment of these plants in the canga environment.

Results

Plants were grown in canga and forest substrates collected in the Carajás Mineral Province. RNA was extracted from pooled leaf tissue, and RNA-seq paired-end reads were assembled into representative transcriptomes for P. platycephala and S. pulcherrimum containing 31,728 and 31,311 primary transcripts, respectively. We identified both species-specific and core molecular responses in plants grown in the canga substrate using differential expression analyses. In the species-specific analysis, we identified 1,112 and 838 differentially expressed genes for P. platycephala and S. pulcherrimum, respectively. Enrichment analyses showed that unique biological processes and metabolic pathways were affected for each species. Comparative differential expression analysis was based on shared single-copy orthologs. The overall pattern of ortholog expression was species-specific. Even so, we identified almost 300 altered genes between plants in canga and forest substrates with conserved responses in the two species. The genes were functionally associated with the response to light stimulus and the circadian rhythm pathway.

Conclusions

Plants possess species-specific adaptative responses to cope with the substrates. Our results also suggest that plants adapted to both canga and forest environments can adjust the circadian rhythm in a substrate-dependent manner. The circadian clock gene modulation might be a central mechanism regulating the plants’ development in the canga substrate in the studied legume species. The mechanism may be shared as a common mechanism to abiotic stress compensation in other native species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08449-0.

A natural hybrid of Sindora (Fabaceae, Detarioideae) from Singapore

Sindora×changiensis L.M.Choo, Loo, W.F.Ang & K.Er is a new hybrid from the subfamily Detarioideae in Fabaceae. This is the first reported instance of natural hybridisation in Sindora. Based on population genetics analyses using ddRAD and morphological observations, this taxon represents a fertile hybrid between Sindoracoriacea and Sindoraechinocalyx. This new hybrid is so far only known to occur naturally from Changi at the north-eastern coast of Singapore. It has pods that are sparsely spiny. This is intermediate between the smooth, non-spiny pods of S.coriacea, and the densely spiny pods of S.echinocalyx. The calyx is smooth and unarmed, resembling S.coriacea. Last but not least, the ovary is entirely pubescent, different from S.coriacea and S.echinocalyx. The ovary of S.coriacea has a glabrous patch in the middle, while that of S.echinocalyx has minute spines protruding from the dense pubescence. A taxonomic description and an updated key to the Sindora of Singapore and Peninsular Malaysia are also provided.

Misleading fruits: The non-monophyly of Pseudopiptadenia and Pityrocarpa supports generic re-circumscriptions and a new genus within mimosoid legumes

Generic delimitation in Piptadenia and allies (mimosoid legumes) has been in a state of flux, particularly caused by over-reliance on fruit and seed morphology to segregate species out of Piptadenia into the genera Parapiptadenia, Pityrocarpa and Pseudopiptadenia. Although supporting their segregation from Piptadenia, previous phylogenetic analyses suggested that some of these segregated genera are not monophyletic. Here, we test the monophyly of Parapiptadenia, Pityrocarpa and Pseudopiptadenia with dense taxon sampling across these genera, including the type species of each genus. Our analysis recovers Parapitadenia as monophyletic, but places Pseudopiptadenia species in two distinct lineages, one of which includes all three species of Pityrocarpa. Given that the type species of both Pseudopiptadenia and Pityrocarpa are nested in the same clade, we subsume Pseudopiptadenia under the older name Pityrocarpa. The remaining Pseudopiptadenia species are assigned to the new genus Marlimorimia. Alongside high molecular phylogenetic support, recognition of Parapiptadenia, Pityrocarpa and Marlimorimia as distinct genera is also supported by combinations of morphological traits, several of which were previously overlooked.

Phytochemistry and poisoning in ruminants by Enterolobium contortisiliquum (Vell.) Morong (Fabaceae): A systematic review

Enterolobium contortisiliquum (Vell.) Morong (Fabaceae) is a plant widely distributed in several regions of Brazil, occurring in the phytogeographic domains of Atlantic Forest, Cerrado, and Caatinga. Cases of serious poisoning in cattle, goats, and sheep in the country caused by the ingestion of beans of this species have been reported by several studies. The present work aimed to carry out a systematic review of cases of poisoning by E. contortisiliquum in ruminants and list the main chemical compounds isolated from this plant. For this, searches were performed in the Google Academic, PubMed®, ScienceDirect®, and SciELO databases. A total of 26 articles published in the last 20 years (2001-2021) were included. Studies on cases of natural and experimental poisoning indicate that this species mainly causes photosensitization, abortions, digestive problems, and acute ruminal lactic acidosis in animals that ingest the pods of the plant. The main chemical compounds that occur in the species belong to the triterpene saponins, monoterpene, phenylpropene, and triterpene classes. It is likely that triterpene saponins isolated from E. contortisiliquum are associated with reported cases of photosensitization in cattle. New studies must be conducted to assess the mechanisms of action of chemical compounds isolated from this species in in vivo systems.

Plastome evolution in the Caesalpinia group (Leguminosae) and its application in phylogenomics and populations genetics

The chloroplast genomes of Caesalpinia group species are structurally conserved, but sequence level variation is useful for both phylogenomic and population genetic analyses. Variation in chloroplast genomes (plastomes) has been an important source of information in plant biology. The Caesalpinia group has been used as a model in studies correlating ecological and genomic variables, yet its intergeneric and infrageneric relationships are not fully solved, despite densely sampled phylogenies including nuclear and plastid loci by Sanger sequencing. Here, we present the de novo assembly and characterization of plastomes from 13 species from the Caesalpinia group belonging to eight genera. A comparative analysis was carried out with 13 other plastomes previously available, totalizing 26 plastomes and representing 15 of the 26 known Caesalpinia group genera. All plastomes showed a conserved quadripartite structure and gene repertoire, except for the loss of four ndh genes in Erythrostemon gilliesii. Thirty polymorphic regions were identified for inter- or intrageneric analyses. The 26 aligned plastomes were used for phylogenetic reconstruction, revealing a well-resolved topology, and dividing the Caesalpinia group into two fully supported clades. Sixteen microsatellite (cpSSR) loci were selected from Cenostigma microphyllum for primer development and at least two were cross-amplified in different Leguminosae subfamilies by in vitro or in silico approaches. Four loci were used to assess the genetic diversity of C. microphyllum in the Brazilian Caatinga. Our results demonstrate the structural conservation of plastomes in the Caesalpinia group, offering insights into its systematics and evolution, and provides new genomic tools for future phylogenetic, population genetics, and phylogeographic studies.

Implication of scanning electron microscopy in the seed morphology with special reference to three subfamilies of Fabaceae

The current research work was aimed to determine the morphological variation in the seeds of subfamilies Caesalpinioideae, Mimosoideae, and Papilionoideae using scanning electron microscope to investigate the different seed features including; Seed length, width, weight, hilum shape, position, fracture line pattern, pleurogram shape, texture crudeness, ornamentation wall, and surface ornamentation. A total of 12 species were collected. The study reveals that the seed types alters from psilate to rugose, pleurogram shape from lunar to U shape, hilum shape from elliptical to depressed, hilum position from terminal to subterminal, fracture line pattern from reticulate irregular ridges to psilate with regular ridges, texture crudeness from fine to coarse, surface ornamentation from reticulate to psilate, and ornamentation wall also varies from thin to thick. In all the studied species, it was found that seed surface was brown in color except in Senna alata, in which seed surface was black. Regarding the seed size, it was found that the smallest seed was observed for Sesbania sesban, while the largest seed was observed for Pongamia pinnata. The present research article indicates the taxonomic significance of seed morphology in the subfamilies Caesalpinioideae, Mimosaceae, and Papilionoideae.

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation

PREMISE

Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids.

METHODS

We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids.

RESULTS

Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well-supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids.

CONCLUSIONS

Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.

Cytotoxic components from the leaves of Erythrophleum fordii induce human acute leukemia cell apoptosis through caspase 3 activation and PARP cleavage

Cassaine diterpenoids as erythrofordins A-C (1-3), pseudo-erythrosuamin (4), and erythrofordin U (5) isolated from the leaves of Vietnamese Erythrophleum fordii Oliver were tested cytotoxic activity against human leukemia cancer cells. The results showed that these metabolites exhibited dose-dependent cytotoxicity against human leukemia HL-60 and KG cells with IC₅₀ values ranging from 15.2 ± 1.5 to 42.2 ± 3.6 µM. Treatment with erythrofordin B led to the apoptosis of HL-60 and KG cells due to the activation of caspase 3, caspase 9, and poly (ADP-ribose) polymerase (PARP). Erythrofordin B significantly increased Bak protein expression, but downregulated the anti-apoptotic protein Bcl-2, in HL-60 cells. In silico results demonstrated that erythrofordin B can bind to both the procaspase-3 allosteric site and the PARP-1 active site, with binding energies of -7.36 and -10.76 kcal/mol, respectively. These results indicated that the leaves of Vietnamese E. fordii, which contain cassaine diterpenoids, can induce the apoptosis of human leukemia cancer cells.

Seed germination and early seedling survival of the invasive species Prosopis juliflora (Fabaceae) depend on habitat and seed dispersal mode in the Caatinga dry forest

Background

Biological invasion is one of the main threats to tropical biodiversity and ecosystem functioning. Prosopis juliflora (Sw) DC. (Fabales: Fabaceae: Caesalpinioideae) was introduced in the Caatinga dry forest of Northeast Brazil at early 1940s and successfully spread across the region. As other invasive species, it may benefit from the soils and seed dispersal by livestock. Here we examine how seed dispersal ecology and soil conditions collectively affect seed germination, early seedling performance and consequently the P. juliflora invasive potential.

Methods

Seed germination, early seedling survival, life expectancy and soil attributes were examined in 10 plots located across three habitats (flooding plain, alluvial terrace and plateau) into a human-modified landscape of the Caatinga dry forest (a total of 12,000 seeds). Seeds were exposed to four seed dispersal methods: deposition on the soil surface, burial in the soil, passed through cattle (Boss taurus) digestive tracts and mixed with cattle manure and passed through mule (Equus africanus asinus × Equus ferus caballus) digestive tracts and mixed with mule manure. Seeds and seedlings were monitored through a year and their performance examined with expectancy tables.

Results

Soils differed among habitats, particularly its nutrient availability, texture and water with finely-textured and more fertile soils in the flooding plain. Total seed germination was relatively low (14.5%), with the highest score among seeds buried in the flooding plain (47.4 ± 25.3%). Seed dispersal by cattle and mule also positively impacted seed germination. Early seedling survival rate of P. juliflora was dramatically reduced with few seedlings still alive elapsed a year. Survival rate was highest in the first 30 days and declined between 30 and 60 days with stabilization at 70 days after germination in all seed treatments and habitats. However, survival and life expectancy were higher in the flooding plain at 75 days and lower in the plateau. Prosopis juliflora seedling survival and life expectancy were higher in the case seeds were mixed with cattle manure.

Synthesis

Prosopis juliflora seeds and seedlings are sensitive to water stress and habitat desiccation. Therefore, they benefit from the humid soils often present across human-disturbed flooding plains. This plant also benefits from seed deposition/dispersal by livestock in these landscapes, since cattle manure represents a nutrient-rich and humid substrate for both seeds and seedlings. The quality of the seed dispersal service varies among livestock species, but this key mutualism between exotic species is due to the arillate, hard-coated and palatable seeds. Prosopis juliflora traits allow this species to take multiple benefits from human presence and thus operating as a human commensal.

Dewerin and gilbertionol two new secondary metabolites from the stem bark of Gilbertiodendron dewevrei (De Wild) J. Leonard

The phytochemical investigation of the methanol extract of the stem bark of Gilbertiodendron dewevrei led to the isolation of two new secondary metabolites, 5,7-dihydroxy-4'-methoxyisoflavan-2,4-dione (1) and 23-hydroxy-2-tricosanone (2) along with 19 known compounds (3-21). The structure of these compounds were established by interpretation of their spectral data, mainly HR-TOFESIMS, 1 D NMR (¹H, ¹³C and DEPT) and 2 D NMR (¹H-¹H COSY, HSQC, HMBC, and NOESY), and by comparison with those reported in the literature. The methanol extract and some isolates were screened for their antiradical, antibacterial, and inhibitory properties against acetylcholinesterase.

Chemical constituents of the leaves of Anthonotha macrophylla (Leguminosae)

The present study deals with the isolation and the characterization of the chemical constituents from the leaves of Anthonotha macrophylla (Leguminosae). Using various chromatographic techniques (TLC, CC, HPLC), the methanolic extract of the leaves of Anthonotha macrophylla yielded one new alkaloid (1) as well as six known compounds amongst which an alkane (2), isolated for the first time from a natural product, an ester of fatty acid (3), two isocoumarines (4-5), a sterol (6) and a disaccharide (7). Their structures were elucidated using spectroscopic technics including extensive 1-D and 2-D NMR, HR-SM experiments.

Bradyrhizobium frederickii sp. nov., a nitrogen-fixing lineage isolated from nodules of the caesalpinioid species Chamaecrista fasciculata and characterized by tolerance to high temperature in vitro

The symbioses between legumes and nitrogen-fixing rhizobia make the greatest contribution to the global nitrogen input via the process of biological nitrogen fixation (BNF). Bradyrhizobium stands out as the main genus nodulating basal Caesalpinioideae. We performed a polyphasic study with 11 strains isolated from root nodules of Chamaecristafasciculata, an annual multi-functional native legume of the USA. In the 16S rRNA gene phylogeny the strains were clustered in the Bradyrhizobium japonicumsuperclade. The results of analysis of the intergenic transcribed spacer (ITS) indicated less than 89.9 % similarity to other Bradyrhizobium species. Multilocus sequence analysis (MLSA) with four housekeeping genes (glnII, gyrB, recA and rpoB) confirmed the new group, sharing less than 95.2 % nucleotide identity with other species. The MLSA with 10 housekeeping genes (atpD, dnaK, gap, glnII, gltA, gyrB, pnp, recA, rpoB and thrC) indicated Bradyrhizobium daqingense as the closest species. Noteworthy, high genetic diversity among the strains was confirmed in the analyses of ITS, MLSA and BOX-PCR. Average nucleotide identity and digital DNA-DNA hybridization values were below the threshold of described Bradyrhizobium species, of 89.7 and 40 %, respectively. In the nifH and nodC phylogenies, the strains were grouped together, but with an indication of horizontal gene transfer, showing higher similarity to Bradyrhizobium arachidis and Bradyrhizobium forestalis. Other phenotypic, genotypic and symbiotic properties were evaluated, and the results altogether support the description of the CNPSo strains as representatives of the new species Bradyrhizobiumfrederickii sp. nov., with CNPSo 3426^T (=USDA 10052^T=U686^T=CL 20^T) as the type strain.

New microsatellites for the Atacama Desert endemic Balsamocarpon brevifolium (Fabaceae)

PREMISE

Algarrobilla (Balsamocarpon brevifolium, Fabaceae) is an endemic xerophytic shrub restricted to the Atacama Desert in northern Chile. Extensive utilization of the region for coal production has endangered this species. Conservation efforts are underway, with genetic diversity analyses being key to the restoration of these populations.

METHODS AND RESULTS

Fifteen new microsatellite markers were developed for B. brevifolium and used to analyze three populations from the Atacama and Coquimbo regions in Chile. Microsatellites were highly polymorphic, with an average of 5.77 alleles per marker and an average level of expected heterozygosity of 0.72. These markers were evaluated and cross-amplified on two related species (Senna cumingii and Caesalpinia angulata) with partial success.

CONCLUSIONS

The development of this set of markers permits an extensive study of B. brevifolium populations for conservation purposes.

Global Succulent Biome phylogenetic conservatism across the pantropical Caesalpinia Group (Leguminosae)

The extent to which phylogenetic biome conservatism vs biome shifting determines global patterns of biodiversity remains poorly understood. To address this question, we investigated the biogeography and trajectories of biome and growth form evolution across the Caesalpinia Group (Leguminosae), a clade of 225 species of trees, shrubs and lianas distributed across the Rainforest, Succulent, Temperate and Savanna Biomes. We focused especially on the little-known Succulent Biome, an assemblage of succulent-rich, grass-poor, seasonally dry tropical vegetation distributed disjunctly across the Neotropics, Africa, Arabia and Madagascar. We reconstructed a time-calibrated phylogeny, assembled species occurrence data and assigned species to areas, biomes and growth forms. These data are used to estimate the frequency of transcontinental disjunctions, biome shifts and evolutionary transitions between growth forms and test for phylogenetic biome conservatism and correlated evolution of growth forms and biome shifts. We uncovered a pattern of strong phylogenetic Succulent Biome conservatism. We showed that transcontinental disjunctions confined within the Succulent Biome are frequent and that biome shifts to the Savanna, Rainforest and Temperate Biomes are infrequent and closely associated with shifts in plant growth forms. Our results suggest that the Succulent Biome comprises an ecologically constrained evolutionary arena spanning large geographical disjunctions across the tropics.

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

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.

Karyotype diversity and 2C DNA content in species of the Caesalpinia group

BACKGROUND

The Leguminosae family is the third-largest family of angiosperms, and Caesalpinioideae is its second-largest subfamily. A great number of species (approximately 205) are found in the Caesalpinia group within this subfamily; together with these species' phenotypic plasticity and the similarities in their morphological descriptors, make this a complex group for taxonomic and phylogenetic studies. The objective of the present work was to evaluate the karyotypic diversity and the 2C DNA content variation in 10 species of the Caesalpinia group, representing six genera: Paubrasilia, Caesalpinia, Cenostigma, Poincianella, Erythrostemon and Libidibia. The GC-rich heterochromatin and 45S rDNA sites (which are used as chromosome markers) were located to evaluate the karyotype diversity in the clade. The variation in the 2C DNA content was determined through flow cytometry.

RESULTS

The fluorochrome banding indicated that the chromomycin A₃⁺/4',6-diamidino-2-phenylindole^- blocks were exclusively in the terminal regions of the chromosomes, coinciding with 45S rDNA sites in all analyzed species. Physical mapping of the species (through fluorescence in situ hybridization) revealed variation in the size of the hybridization signals and in the number and distribution of the 45S rDNA sites. All hybridization sites were in the terminal regions of the chromosomes. In addition, all species had a hybridization site in the fourth chromosome pair. The 2C DNA content ranged from 1.54 pg in Erythrostemon calycina to 2.82 pg in the Paubrasilia echinata large-leaf variant. The Pa. echinata small-leaf variant was isolated from the other leaf variants through Scoot-Knott clustering.

CONCLUSIONS

The chromosome diversity and the variation in the 2C DNA content reinforce that the actual taxonomy and clustering of the analyzed taxa requires more genera that were previously proposed. This fact indicates that taxonomy, phylogeny and cytoevolutionary inference related to the complex Caesalpinia group have to be done through integrative evaluation.

Floral evolution and phylogeny of the Dialioideae, a diverse subfamily of tropical legumes

PREMISE OF THE STUDY

The Dialioideae is an early diverging clade of caesalpinioid legumes containing approximately 85 species in 17 genera. Dialioideae floral morphology is highly variable and may provide clues to caesalpinioid evolution, but a well-resolved phylogeny is needed. Here, we have carried out a comprehensive morphological study of 78 Dialioideae and four outgroup species.

METHODS

For all available Dialioideae DNA samples, the plastid rpS16 and trnL introns were sequenced. A combined phylogenetic analysis using the parsimony criterion was completed on a reduced taxon set for which both molecular and morphological data were available. Highly supported clades from the strict consensus tree of this analysis were then used to constrain the nodes of a second analysis on an expanded taxon set with missing molecular data for some taxa.

KEY RESULTS

Several new, highly supported relationships have been discovered at the species and genus levels. The loss of the antepetalous stamen whorl was found to be a synapomorphy for most of the clade.

CONCLUSIONS

A high degree of organ loss is common in the Dialioideae and often results in a bilaterally symmetrical flower. The absence of consistent morphological features in the Dialioideae, coupled with the small size of each florally diagnosed genus, suggests a lack of canalization in the floral evolution in early diverging legume lineages.

Flower development of Goniorrhachis marginata reveals new insights into the evolution of the florally diverse detarioid legumes

BACKGROUND AND AIMS

The study of floral morphology and ontogeny and the re-investigation of existing data help to uncover potential synapomorphic characters and foster our understanding of phylogenetic relationships that rely primarily on molecular analyses. Goniorrhachis marginata is a monotypic caesalpinioid legume (Leguminosae) that shows some interesting floral features, such as a long hypanthium and regular Rosaceae-like flowers. We studied the ontogeny and morphology of the flowers in detail and present our results in a broad phylogenetic context.

METHODS

Flower buds were collected in the field, fixed in 70 % ethanol and investigated using scanning electron microscopy. Older buds in spirit were carefully opened to investigate the direction of style bending. Characters of the style from 131 taxa from the main legume lineages were analysed and mapped on a Bayesian molecular phylogeny.

KEY RESULTS

The tetramerous calyx is the result of complete loss of one sepal. The formation of the radially symmetrical corolla starts in a typical caesalpinioid pattern with the adaxial petal innermost (ascending aestivation). The young style bends in the abaxial direction, which is a character found exclusively in all studied detarioid legumes and therefore a newly described synapomorphy for the clade.

CONCLUSIONS

We show that investigation of unstudied taxa and reinvestigation of published data can uncover new, previously overlooked and important characters. Curvature of the style can be detected in young buds with a hand lens and therefore is an important character for field botanists. Our study reveals the importance of including poorly studied and/or phylogenetically enigmatic taxa in molecular phylogenies and in detailed morphological and ontogenetic analyses.

A new generic system for the pantropical Caesalpinia group (Leguminosae)

The Caesalpinia group is a large pantropical clade of ca. 205 species in subfamily Caesalpinioideae (Leguminosae) in which generic delimitation has been in a state of considerable flux. Here we present new phylogenetic analyses based on five plastid and one nuclear ribosomal marker, with dense taxon sampling including 172 (84%) of the species and representatives of all previously described genera in the Caesalpinia group. These analyses show that the current classification of the Caesalpinia group into 21 genera needs to be revised. Several genera (Poincianella, Erythrostemon, Cenostigma and Caesalpinia sensu Lewis, 2005) are non-monophyletic and several previously unclassified Asian species segregate into clades that merit recognition at generic rank. In addition, the near-completeness of our taxon sampling identifies three species that do not belong in any of the main clades and these are recognised as new monospecific genera. A new generic classification of the Caesalpinia group is presented including a key for the identification of genera, full generic descriptions, illustrations (drawings and photo plates of all genera), and (for most genera) the nomenclatural transfer of species to their correct genus. We recognise 26 genera, with reinstatement of two previously described genera (Biancaea Tod., Denisophytum R. Vig.), re-delimitation and expansion of several others (Moullava, Cenostigma, Libidibia and Erythrostemon), contraction of Caesalpinia s.s. and description of four new ones (Gelrebia, Paubrasilia, Hererolandia and Hultholia), and make 75 new nomenclatural combinations in this new generic system.

New Boletaceae taxa from Guyana: Binderoboletus segoi gen. and sp. nov., Guyanaporus albipodus gen. and sp. nov., Singerocomus rubriflavus gen. and sp. nov., and a new combination for Xerocomus inundabilis

Binderoboletus segoi gen. and sp. nov., Guyanaporus albipodus gen. and sp. nov. and Singerocomus rubriflavus gen. and sp. nov. (Boletaceae, Boletales, Basidiomycota) are described from the Pakaraima Mountains and adjacent lowlands of Guyana. Xerocomus inundabilis, originally described from the central Brazilian Amazon and based solely on the type collection, is redescribed from numerous collections from Guyana and transferred into Singerocomus. These boletes occur in Neotropical forests dominated by ectomycorrhizal trees in the genera Dicymbe (Fabaceae subfam. Caesalpinioideae), Aldina (Fabaceae subfam. Papilionoideae) and Pakaraimaea (Dipterocarpaceae). Three of the species were repeatedly found in a multiyear sporocarp survey in Dicymbe corymbosa-monodominant forest. Macromorphological, micromorphological, habitat and multilocus DNA sequence data are provided for each species. A molecular phylogenetic analysis based on a large taxon set across the Boletaceae justifies erection of the new genera.

New sequestrate fungi from Guyana: Jimtrappea guyanensis gen. sp. nov., Castellanea pakaraimophila gen. sp. nov., and Costatisporus cyanescens gen. sp. nov. (Boletaceae, Boletales)

Jimtrappea guyanensis gen. sp. nov., Castellanea pakaraimophila gen. sp. nov., and Costatisporus cyanescens gen. sp. nov. are described as new to science. These sequestrate, hypogeous fungi were collected in Guyana under closed canopy tropical forests in association with ectomycorrhizal (ECM) host tree genera Dicymbe (Fabaceae subfam. Caesalpinioideae), Aldina (Fabaceae subfam. Papilionoideae), and Pakaraimaea (Dipterocarpaceae). Molecular data place these fungi in Boletaceae (Boletales, Agaricomycetes, Basidiomycota) and inform their relationships to other known epigeous and sequestrate taxa within that family. Macro- and micromorphological characters, habitat, and multi-locus DNA sequence data are provided for each new taxon. Unique morphological features and a molecular phylogenetic analysis of 185 taxa across the order Boletales justify the recognition of the three new genera.

Microsatellite development and flow cytometry in the African tree genus Afzelia (Fabaceae, Caesalpinioideae) reveal a polyploid complex

PREMISE OF THE STUDY

Microsatellites were developed in the vulnerable African rainforest tree Afzelia bipindensis to investigate gene flow patterns. •

METHODS AND RESULTS

Using 454 GS-FLX technique, 16 primer sets were identified and optimized, leading to 11 polymorphic and readable markers displaying each six to 25 alleles in a population. Up to four alleles per individual were found in each of the loci, without evidence of fixed heterozygosity, suggesting an autotetraploid genome. Cross-amplification succeeded for all loci in the African rainforest species A. pachyloba and A. bella, which appeared tetraploid, and for most loci in the African woodland species A. africana and A. quanzensis, which appeared diploid, but failed in the Asian species A. xylocarpa. Flow cytometry confirmed the suspected differences in ploidy. •

CONCLUSIONS

African Afzelia species are diploid or tetraploid, a situation rarely documented in tropical trees. These newly developed microsatellites will help in the study of their mating system and gene flow patterns.

Floral polymorphism in Chamaecrista flexuosa (Fabaceae-Caesalpinioideae): a possible case of atypical enantiostyly?

BACKGROUND AND AIMS

Reciprocal herkogamy, including enantiostyly and heterostyly, involves reciprocity in the relative positions of the sexual elements within the flower. Such systems result in morphologically and, since pollen is deposited on and captured from different parts of the pollinator, functionally distinct floral forms. Deviations from the basic pattern may modify the functionality of these mechanisms. For heterostylous species, such deviations are generally related to environmental disturbances, pollination services and/or reduced numbers of one floral morph. Deviations for enantiostylous species have not yet been reported. This study aims to investigate enantiostyly in Chamaecrista flexuosa, in particular the presence of deviations from the standard form, in an area of coastal vegetation in north-east Brazil.

METHODS

Observations and investigations of floral biology, the reproductive system, pollinator behaviour, floral morphology and morphometry were performed.

KEY RESULTS

In C. flexuosa flowers, anthers of different size but similar function are grouped. The flowers were self-compatible and set fruits after every treatment, except in the spontaneous self-pollination experiment, thereby indicating their dependence on pollen vectors. The flowers were pollinated by bees, especially Xylocopa cearensis and X. grisencens. Pollen is deposited and captured from the ventral portion of the pollinator's body. Variations in the spatial arrangement of floral elements allowed for the identification of floral morphs based on both morphological and functional criteria. Using morphological criteria, morphologically right (MR) and morphologically left (ML) floral morphs were identified. Three floral morphs were identified using functional criteria: functionally right (FR), functionally central (FC) and functionally left (FL). Combinations of morphologically and functionally defined morphs did not occur in equal proportions. There was a reduced frequency of the MR-FR combination.

CONCLUSIONS

The results indicate the occurrence of an atypical enantiostyly in C. flexuosa. This seems to improve reproductive success by increasing the efficiency of pollen deposition and capture.

A new species of Bauhinia L. (Caesalpinioideae, Leguminosae) from Nakhon Phanom Province, Thailand

A new liana species of the subfamily Caesalpinioideae (Leguminosae), namely Bauhinia nakhonphanomensis, collected from the Phulangkha National Park, Nakhon Pranom Province, Thailand, is described and illustrated. It is easily recognized by the following combination of characters: tendrilled liana, entire leaves, acuminate or caudate leaf apices, oblong or elliptic floral bud, floral bud 25-35 mm long, raceme or panicle inflorescence, 10-13 mm long hypanthium, anther opening by longitudinal slits. Important comparative morphological characters with some closely related species are discussed.