A phylogeny of the chloroplast gene rbcL in the Leguminosae: taxonomic correlations and insights into the evolution of nodulation

Phylogenetic analysis of the chloroplast-encoded rbcL gene in Leguminosae are consistent with previous hypotheses in suggesting that the family as a whole is monophyletic, but that only two of its three subfamilies are natural. The earliest dichotomies in the family appear to have involved tribes Cercideae or Cassieae (subtribe Dialiinae), followed by Detarieae/ Macrolobieae, all of which are members of subfamily Caesalpinioideae. The remainder of the family is divided into two clades: (1) Mimosoideae and the caesalpinioid tribes Caeasalpinieae and Cassieae (subtribes Ceratoniinae and Cassiinae); (2) Papilionoideae. Basal groups within Papilionoideae are, as expected, elements of the grade tribes Sophoreae and Swartzieae. Major clades within Papilionoideae include: (1) a Genistoid Alliance comprising Genisteae, Crotalarieae, Podalyrieae, Thermopsideae, Euchresteae, and also some Sophoreae; (2) a clade marked by the absence of one copy of the chloroplast inverted repeat, with which are associated Robinieae. Loteae, and some Sophoreae; (3) Phaseoleae, Desmodieae. Psoraleeae, and most Millettieae, a group also marked by presence of pseudoracemose inflorescences; and (4) a well-supported clade comprising Aeschynomeneae, Adesmieae, and some Dalbergieae. Nodulation is most parsimoniously optimized on the rbcL strict consensus tree as three parallel gains, occurring in Papilionoideae, the caesalpioioid ancestors of Mimosoideae, and in the genus Chamaecrista (Caesalpinieae: Cassieae).     

Phylogenetic systematics of the tribe Millettieae (Leguminosae) based on chloroplast trnK/matK sequences and its implications for evolutionary patterns in Papilionoideae

Phylogenetic relationships in the tribe Millettieae and allies in the subfamily Papilionoideae (Leguminosae) were reconstructed from chloroplast trnK/matK sequences. Sixty-two accessions representing 57 traditionally recognized genera of Papilionoideae were sampled, including 27 samples from Millettieae. Phylogenies were constructed using maximum parsimony and are well resolved and supported by high bootstrap values. A well-supported "core Millettieae" clade is recognized, comprising the four large genera Millettia, Lonchocarpus, Derris, and Tephrosia. Several other small genera of Millettieae are not in the core Millettieae clade. Platycyamus is grouped with Phaseoleae (in part). Ostryocarpus, Austrosteenisia, and Dalbergiella are neither in the core Millettieae or Phaseoleae clade. These taxa, along with core Millettieae and Phaseoleae, form a monophyletic sister group to Indigofereae. Cyclolobium and Poecilanthe are close to Brongniartieae. Callerya and Wisteria belong to a large clade that includes all the legumes that lack the inverted repeat in their chloroplast genome, which confirms previous rbcL and phytochrome gene family phylogenies. The evolutionary history of four characters was examined in Millettieae and allies: the presence of canavanine, inflorescence types, the dehiscence of pods, and the presence of winged pods. trnK/matK sequence analysis suggests that the presence of a pseudoraceme or pseudopanicle and the accumulation of nonprotein amino acids are phylogenetically informative for Millettieae and allies with only a few exceptions.     

THE GRANULAR INTERSTITIUM IN THE POLLEN OF SUBFAMILY PAPILIONOIDEAE (LEGUMINOSAE)

A wide range of transitional forms of granular interstitia from simple to complex and from random to ordered occur in the pollen of the subfamily Papilionoideae. Three main types are described: 1) large, widely spaced irregular granules (Type A); 2) densely packed groups of columellae and granules (Type B); and 3) a mass of more or less disorganized granules (Type C). In the genus Calopogonium (tribe Phaseoleae) all three types have been found in different species. Two of the types have been found in different species of the genus Psoralea (tribe Psoraleeae). Granular structures so far occur in six tribes: Desmodieae, Indigofereae, Loteae, Phaseoleae, Psoraleeae, and Vicieae. All of the tribes are regarded as being evolutionarily advanced in both macro and micro characters and many, but not all, show specialized pollen characters. It is concluded that the granular interstitium is a derived structure in papilionoid legumes.     

CHROMOSOME NUMBERS IN THE LEGUMINOSAE II: AFRICAN SPECIES,INCLUDING PHYLETIC INTERPRETATIONS

Turner , B. L., and O. S. Fearing . (U. Texas, Austin.) Chromosome numbers in the Leguminosae. II. African species, including phyletic interpretations. Amer. Jour. Bot. 46(1) : 49-57. Illus. 1959.—Chromosome numbers for 30 African legume species have been reported. These include first reports for 28 taxa, including 12 genera (Bolusanthus, Calpurnia, Melolobium, Lessertia, Sulherlandia, Colophospermum, Guibourtia, Burkea, Julbernardia, Schotia, Piliostigma and Swartzia). The counts are discussed with respect to those previously reported for related groups, and this chromosomal information was used to construct hypothetical phyletic lines at the tribal level within the subfamilies Papilionoideae and Caesalpinioideae. A phyletic scheme for the Leguminosae (excluding the Mimosoideae) based on this evidence from chromosome studies is presented. Notable departures from previously suggested phyletic treatments include: (1) Suggestion for inclusion of genera of the Galegeae and Hedysareae with base numbers of x = 10 and 11 with the Phaseoleae and Dalbergieae. (2) Derivation of the Papilionoideae through caesalpinoid prototypes, possibly from Swartzia-like ancestors. (3) Recognition of several very old chromosomal lines stemming from the subfamily Caesalpinioideae, and the suggestion that parts of the tribes Sclerolobieae, Cynometreae, Swartzieae and Sophoreae are, perhaps, more closely related to each other and to the Papilionoideae than they are to the remaining caesalpinoid tribal lines.     

Broad screening of the legume family for variability in seed insecticidal activities and for the occurrence of the A1b-like knottin peptide entomotoxins

Pea albumin 1b (PA1b) is a small sulphur-rich peptide from pea seeds, also named leginsulin because of the binding characteristics of its soybean orthologue. Its insecticidal properties were discovered more recently. By using a combination of molecular, biochemical and specific insect bioassays on seed extracts, we characterised genes from numerous Papilionoideae, but not from Caesalpinioideae or Mimosoideae, although the last group harboured species with partially positive cues (homologous biological activities). The A1b defence peptide family, therefore, appears to have evolved relatively late in the legume lineage, maybe from the sophoroid group (e.g. Styphnolobium japonicum). However, unambiguous sequence information is restricted to a group of tribes within the subfamily Papilionoideae (Psoraleae, Millettieae, Desmodieae, Hedysareae, Phaseoleae, Vicieae, and the now clearly polyphyletic "Trifolieae" and "Galegeae"). Recent diversification by gene duplications has occurred in many species, or longer ago in some lineages (Medicago truncatula), as well as probable gene or expression losses at different taxonomic levels (Loteae, Vigna subterranea).     

Serological relationships among Sophoreae, Thermopsideae and Genisteae (Fabaceae)

A comparison among 20 genera, representatives of Sophoreae, Thermopsideae and Genisteae based on the serological cross reactivity of the seed proteins, indicates: (a) Sophoreae are highly heterogeneous – there is little similarity among genera of the New World, genera of tropical austral Africa, and genera of temperate Eurasia; (b) Sophora and Maackia are strictly related both to Thermopsidae and to Genisteae; (c) Thermopsideae are not intermediate between Sophoreae and Genisteae; (d) Primitive Thermopsideae and Genisteae (Anagyris, Hesperolaburnum) are serologically related among themselves and to the Sophoreae; (e) derived herbaceous genera (Baptisia, Lupinus) are serologically divergent.     

Rhizobium sp. strain NGR234 and R. fredii USDA257 share exceptionally broad, nested host ranges

Genetically, Rhizobium sp. strain NGR234 and R. fredii USDA257 are closely related. Small differences in their nodulation genes result in NGR234 secreting larger amounts of more diverse lipo-oligosaccharidic Nod factors than USDA257. What effects these differences have on nodulation were analyzed by inoculating 452 species of legumes, representing all three subfamilies of the Leguminosae, as well as the nonlegume Parasponia andersonii, with both strains. The two bacteria nodulated P. andersonii, induced ineffective outgrowths on Delonix regia, and nodulated Chamaecrista fasciculata, a member of the only nodulating genus of the Caesalpinieae tested. Both strains nodulated a range of mimosoid legumes, especially the Australian species of Acacia, and the tribe Ingeae. Highest compatibilities were found with the papilionoid tribes Phaseoleae and Desmodieae. On Vigna spp. (Phaseoleae), both bacteria formed more effective symbioses than rhizobia of the "cowpea" (V. unguiculata) miscellany. USDA257 nodulated an exact subset (79 genera) of the NGR234 hosts (112 genera). If only one of the bacteria formed effective, nitrogen-fixing nodules it was usually NGR234. The only exceptions were with Apios americana, Glycine max, and G. soja. Few correlations can be drawn between Nod-factor substituents and the ability to nodulate specific legumes. Relationships between the ability to nodulate and the origin of the host were not apparent. As both P. andersonii and NGR234 originate from Indonesia/Malaysia/Papua New Guinea, and NGR234's preferred hosts (Desmodiinae/Phaseoleae) are largely Asian, we suggest that broad host range originated in Southeast Asia and spread outward.     

EVOLUTIONARY SIGNIFICANCE OF THE LOSS OF THE CHLOROPLAST-DNA INVERTED REPEAT IN THE LEGUMINOSAE SUBFAMILY PAPILIONOIDEAE

The distribution of a rare chloroplast-DNA structural mutation, the loss of a large inverted repeat, has been determined for 95 species representing 77 genera and 25 of the 31 tribes in the legume subfamily Papilionoideae. This mutation, which is regarded as a derived feature of singular origin within the subfamily, marks a group comprising six temperate tribes, the Galegeae, Hedysareae, Carmichaelieae, Vicieae, Cicereae, and Trifolieae, an assemblage traditionally considered to be monophyletic. This mutation also occurs in the chloroplast genome of Wisteria, a member of the tropical tribe Millettieae whose other members so far surveyed lack the mutation. These new DNA data, together with traditional evidence, support the hypothesis that Wisteria is an unspecialized member of a lineage that gave rise to the temperate tribes marked by the chloroplast-DNA mutation; the probable paraphylesis of Millettieae is revealed. Two other tribes, Loteae and Coronilleae (traditionally regarded as a derived element of the aforesaid temperate tribes) do not possess this chloroplast-DNA structural mutation and, therefore, presumably represent a distinct temperate lineage. This hypothesis is supported by additional evidence from pollen, inflorescence, and root-nodule morphology that suggests that the Loteae and Coronilleae share a more recent ancestry with tropical tribes such as Phaseoleae and Millettieae than with other temperate tribes.     

Inflorescence and floral development of Dahlstedtia species (Leguminosae: Papilionoideae: Millettieae)

Inflorescence and floral development of two tropical legume trees, Dahlstedtia pinnata and Dahlstedtia pentaphylla, occurring in the Atlantic Forest of south-eastern and southern Brazil, were investigated and compared with other papilionoids. Few studies have been made of floral development in tribe Millettieae, and this paper is intended to fill that gap in our knowledge. Dahlstedtia species have an unusual inflorescence type among legumes, the pseudoraceme, which comprises axillary units of three or more flowers, each with a subtending bract. Each flower exhibits a pair of opposite bracteoles. The order of flower initiation is acropetal; inception of the floral organs is as follows: sepals (5), petals (5), carpel (1) plus outer stamens (5) and finally inner stamens (5). Organ initiation in sepal, petal and inner stamen whorls is unidirectional; the carpel cleft is adaxial. The vexillum originates from a tubular-shaped primordium in mid-development and is larger than other petals at maturity, covering the keels. The filament tube develops later after initiation of inner-stamen primordia. Floral development in Dahlstedtia is almost always similar to other papilionoids, especially species of Phaseoleae and Sophoreae. But one important difference is the precocious ovule initiation (open carpel with ovules) in Dahlstedtia, the third citation of this phenomenon for papilionoids. No suppression, organ loss or anomalies occur in the order of primordia initiation or structure. Infra-generic differences in the first stages of ontogeny are rare; however, different species of Dahlstedtia are distinguished by the differing distribution pattern of secretory cavities in the flower.     

Phylogeny and genomic organization of the TIR and non-tIR NBS-LRR resistance gene family in Medicago truncatula

Sequences homologous to the nucleotide binding site (NBS) domain of NBS-leucine-rich repeat (LRR) resistance genes were retrieved from the model legume M. truncatula through several methods. Phylogenetic analysis classified these sequences into TIR (toll and interleukin-1 receptor) and non-TIR NBS subfamilies and further subclassified them into several well-defined clades within each subfamily. Comparison of M. truncatula NBS sequences with those from several closely related legumes, including members of the tribes Trifoleae, Viceae, and Phaseoleae, reveals that most clades contain sequences from multiple legume species. Moreover, sequences from species within the closely related Trifoleae and Viceae tribes (e.g., Medicago and Pisum spp.) tended to be cophyletic and distinct from sequences of Phaseoleae species (e.g., soybean and bean). These results suggest that the origin of major clades within the NBS-LRR family predate radiation of these Papilionoid legumes, while continued diversification of these sequences mirrors speciation within this legume subfamily. Detailed genetic and physical mapping of both TIR and non-TIR NBS sequences in M. truncatula reveals that most NBS sequences are organized into clusters, and few, if any, clusters contain both TIR and non-TIR sequences. Examples were found, however, of physical clusters that contain sequences from distinct phylogenetic clades within the TIR or non-TIR subfamilies. Comparative mapping reveals several blocks of resistance gene loci that are syntenic between M. truncatula and soybean and between M. truncatula and pea.     

POLLEN BRUSH OF PAPILIONOIDEAE (LEGUMINOSAE): MORPHOLOGICAL VARIATION AND SYSTEMATIC UTILITY

The pollen brush commonly is referred to as a “bearded” or “pubescent” style in taxonomic literature and traditionally is taken to be an aggregation of trichomes on the distal end of the style, and occasionally including the stigma. We present data that support the taxonomic utility of the pollen brush but define it more specifically as a dense aggregation of erect trichomes emanating from the style (not stigma or ovary) and functioning in secondary pollen presentation. We recommend avoiding such vague terminology as bearded or pubescent styles as these refer not only to the pollen brush but also to ciliate and penicillate stigmas and ciliate styles. The latter three conditions have some taxonomic use, and since their occurrence is not necessarily correlated with the presence of a pollen brush, they should be distinguished from it. We estimate that the pollen brush has arisen independently in the following eight taxa: 1) Crotalaria and Bolusia (Crotalaraieae), 2) subtribe Coluteinae (Galegeae), 3) Tephrosia subgenus Barbistyla (Millettieae), 4) Adenodolichos (Phaseoleae subtribe Cajaninae), 5) Clitoria (Phaseoleae subtribe Clitoriinae), 6) the subtribe Phaseolinae (Phaseoleae), 7) the Robinia group (Robinieae), and 8) the tribe Vicieae. Its hypothesized homology within each of these groups is supported by a cooccurrence with other taxonomic characters, both morphological and molecular.     

A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family

Phylogenetic analysis of 330 plastid matK gene sequences, representing 235 genera from 37 of 39 tribes, and four outgroup taxa from eurosids I supports many well-resolved subclades within the Leguminosae. These results are generally consistent with those derived from other plastid sequence data (rbcL and trnL), but show greater resolution and clade support overall. In particular, the monophyly of subfamily Papilionoideae and at least seven major subclades are well-supported by bootstrap and Bayesian credibility values. These subclades are informally recognized as the Cladrastis clade, genistoid sensu lato, dalbergioid sensu lato, mirbelioid, millettioid, and robinioid clades, and the inverted-repeat-lacking clade (IRLC). The genistoid clade is expanded to include genera such as Poecilanthe, Cyclolobium, Bowdichia, and Diplotropis and thus contains the vast majority of papilionoids known to produce quinolizidine alkaloids. The dalbergioid clade is expanded to include the tribe Amorpheae. The mirbelioids include the tribes Bossiaeeae and Mirbelieae, with Hypocalypteae as its sister group. The millettioids comprise two major subclades that roughly correspond to the tribes Millettieae and Phaseoleae and represent the only major papilionoid clade marked by a macromorphological apomorphy, pseudoracemose inflorescences. The robinioids are expanded to include Sesbania and members of the tribe Loteae. The IRLC, the most species-rich subclade, is sister to the robinioids. Analysis of the matK data consistently resolves but modestly supports a clade comprising papilionoid taxa that accumulate canavanine in the seeds. This suggests a single origin for the biosynthesis of this most commonly produced of the nonprotein amino acids in legumes.     

Antigenic relationship of legume seed proteins to the 7S seed storage protein of soybean

Extracts enriched for globulin proteins were prepared from the seeds of a large number of legume species and were tested for homology to antisera prepared against the glycosylated 7S seed storage protein of the soybean (Glycine max). Electrophoretic identification and subsequent analysis of proteins precipitated with 7S antisera was useful at relatively short taxonomic distances, particularly within the tribe Phaseoleae, to which G. max belongs. Glycine and most other members of the subtribe Glycininae are unusual within the Phaseoleae in having high molecular weight ($\text{> 70 000}$ dalton) subunit polypeptides. Seeds from other plants representing other subtribes of the Phaseoleae also contained proteins that cross-reacted with the G. max antisera; the molecular weights of these proteins varied from 30 000 to nearly 90 000 daltons. Homology was detected across a wider range of legume tribes within the subfamily Papilionoideae by enzyme-linked immunosorbent assay (ELISA). The results of these experiments suggest both that the 7S proteins of these tribes are evolutionarily related and that at least some features of these apparently rapidly-evolving proteins are under relatively strong selectional constraint.     

DISTRIBUTION AND EVOLUTION OF A GLUCOSEPHOSPHATE ISOMERASE DUPLICATION IN THE LEGUMINOSAE

In the common bean, Phaseolus vulgaris, two loci encode cytosolic glucosephosphate isomerase (GPI) subunits, whereas in the garden pea, Pisum sativum, only one locus is expressed. As a working model, we proposed that this change in isozyme number was produced by a gene-duplication event in the lineage leading to Phaseolus after divergence from that leading to Pisum. This model was tested by analyzing the GPI phenotypes in 119 legume genera, representing all three subfamilies and 23 of the 30 tribes of the Papilionoideae. The duplication was detected in 13 of the 20 papilionoid tribes surveyed, including several members of the putatively primitive tribe Sophoreae. Thus, the duplication appears to be an ancient event, a finding incompatible with the initial hypothesis. Instead, gene silencing is postulated to account for the absence of the duplicated phenotype in many tribes, including such advanced groups as Vicieae, Trifolieae, and Cicereae. Furthermore, silencing has occurred numerous times at lower taxonomic levels, including the subtribe Phaseolinae (Phaseoleae), a monophyletic group in which ten genera were found to have duplicated phenotypes and only one (Strophostyles) appeared to have an unduplicated phenotype. Analysis of GPI phenotypes also revealed numerous cases of partial silencing of duplicate loci as well as nearly equal expression of both loci in many, taxonomically widely scattered species. If our revised hypothesis is correct, this latter result implies that most of the subtribes had formed before significant divergence between the GPI isozymes occurred and, thus, that the radiation of the Papilionoideae was rapid relative to the rate of gene silencing.     

Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)

Chickpea (Cicerarietinum, Leguminosae), an important grain legume, is widely used for food and fodder throughout the world. We sequenced the complete plastid genome of chickpea, which is 125,319bp in size, and contains only one copy of the inverted repeat (IR). The genome encodes 108 genes, including 4 rRNAs, 29 tRNAs, and 75 proteins. The genes rps16, infA, and ycf4 are absent in the chickpea plastid genome, and ndhB has an internal stop codon in the 5'exon, similar to other legumes. Two genes have lost their introns, one in the 3'exon of the transpliced gene rps12, and the one between exons 1 and 2 of clpP; this represents the first documented case of the loss of introns from both of these genes in the same plastid genome. An extensive phylogenetic survey of these intron losses was performed on 302 taxa across legumes and the related family Polygalaceae. The clpP intron has been lost exclusively in taxa from the temperate "IR-lacking clade" (IRLC), whereas the rps12 intron has been lost in most members of the IRLC (with the exception of Wisteria, Callerya, Afgekia, and certain species of Millettia, which represent the earliest diverging lineages of this clade), and in the tribe Desmodieae, which is closely related to the tribes Phaseoleae and Psoraleeae. Data provided here suggest that the loss of the rps12 intron occurred after the loss of the IR. The two new genomic changes identified in the present study provide additional support of the monophyly of the IR-loss clade, and resolution of the pattern of the earliest-branching lineages in this clade. The availability of the complete chickpea plastid genome sequence also provides valuable information on intergenic spacer regions among legumes and endogenous regulatory sequences for plastid genetic engineering.     

Alkaloid distribution in some species of the papilionaceous tribes sophoreae,dalbergieae, loteae,brongniartieae and bossiaeeae

Quinolizidine and dipiperidine alkaloid profiles have been determined for various plant parts of ten papilionaceous species in the tribes Sophoreae, Da     

Support for the removal of Cyclolobium from tribe Millettieae (Leguminosae) from its quinolizidine alkaloid status

Fruits of Cyclolobium brasiliense Benth. (Leguminosae; Papilionoideae) were found to contain quinolizidine alkaloids. Several tetracyclic sparteine-type alkaloids, the bipiperidyl alkaloid ammodendrine and the α-pyridone alkaloid N-methylcytisine were identified. The presence of quinolizidine alkaloids in this monotypic genus supports a relationship with tribe Brongniartieae and genistoid tribes rather than its current placement in tribe Millettieae.     

The shape of leguminous nodules and the colour of leguminous roots

Summary The nodule shape of more than four hundred species of wild legumes indigenous to Rhodesia is found to be related to the tribal classification of the host. Characteristic nodule-shapes of the papilionaceous tribes Galegeae, Genisteae, Hedysareae, and Phaseoleae, and of the subfamilies Mimosoideae and Caesalpinioideae are described and figured. Non-nodulating species were found to have coloured roots much more frequently than nodulating species.     

Phylogeny of the tribe Indigofereae (Leguminosae-Papilionoideae): Geographically structured more in succulent-rich and temperate settings than in grass-rich environments

This analysis goes beyond many phylogenies in exploring how phylogenetic structure imposed by morphology, ecology, and geography reveals useful evolutionary data. A comprehensive range of such diversity is evaluated within tribe Indigofereae and outgroups from sister tribes. A combined data set of 321 taxa (over one-third of the tribe) by 80 morphological characters, 833 aligned nuclear ribosomal ITS/5.8S sites, and an indel data set of 33 characters was subjected to parsimony analysis. Notable results include the Madagascan dry forest Disynstemon resolved as sister to tribe Indigofereae, and all species of the large genus Indigofera comprise just four main clades, each diagnosable by morphological synapomorphies and ecological and geographical predilections. These results suggest niche conservation (ecology) and dispersal limitation (geography) are important processes rendering signature shapes to the Indigofereae phylogeny in different biomes. Clades confined to temperate and succulent-rich biomes are more dispersal limited and have more geographical phylogenetic structure than those inhabiting tropical grass-rich vegetation. The African arid corridor, particularly the Namib center of endemism, harbors many of the oldest Indigofera lineages. A rates analysis of nucleotide substitutions confirms that the ages of the oldest crown clades are mostly younger than 16 Ma, implicating dispersal in explaining the worldwide distribution of the tribe.     

Nodule formation and haemoglobin content in some species of Papilionaceae

Summary Characteristics of nodule formation in eleven genera of the Leguminosae, belonging to the tribes Galegeae, Genisteae, Hedysareae and Phaseoleae of the sub-family Papilionaceae are described. Variation existed in the type, size and weight of nodules formed on the legumes when inoculated with effective cowpea rhizobia, in field conditions of plant growth. Among the legumes, the haemoglobin content of nodules indicated their possible effectiveness. Dolichos lablab L., had a higher haemoglobin content per unit nodule volume than other legumes. This host may have a greater potential than the other species in symbiotic activity with legume bacteria.