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The genome organization and gene content of plastome (plastid genome) are highly conserved among most flowering plant species. Plastome variation (in size and gene order) is rare in photosynthetic species but size variation, rearrangements and gene/intron losses is attributed to groups of seed plants. Fabaceae (legume family), in particular the subfamily Papilionoideae and the inverted repeat lacking clade (IRLC), a largest legume lineage, display the most dramatic and structural change which providing an excellent model for understanding of mechanisms of genomic evolution. The IRLC comprises 52 genera and ca 4000 species divided into seven tribes. In present study, we have sampled several representatives from each tribe across the IRLC from various herbaria and field. The ycf4 gene, which plays a role in regulating and assembly of photosystem I, is more variable in the tribe Fabeae than in other tribes. In certain species of Lathyrus, Pisum and Vavilovia, all belonging to Fabeae, the gene is either absent or a pseudogene. Our study suggests that ycf4 gene has undergone positive selection. Furthermore, the rapid evolution of the gene is locus and lineage specific and is not a shared character of the IRLC in legumes.

Comparative sequence analysis of symbiotic genes (nodA, nodC, nodD, nifH), which are elements of accessory component of the rhizobial genome, demonstrated that the strains of Rhizobium leguminosarum bv. viciae, isolated from the nodules of a relic legume, Vavilovia formosa, the closest relative of hypothetical common ancestor of the tribe Fabeae, represented a group separated from the strains of R. leguminosarum bv. viciae, isolated from other representatives of this tribe (Vicia, Lathyrus, Pisum, Lens). No isolation was observed relative to the genes representing the core component of the rhizobial genome (16S rDNA, ITS, glnII) or relative to host specificity of the rhizobia. The data obtained suggest that sequence divergence of symbiotic genes marks the initial stage of sympatric speciation, which can be classified as the isolation of the relic “vaviloviae” symbiotype, a possible evolutionary precursor of the “viciae” biotype.

Rhizobia are α- and s-proteobacteria that associate with legumes in symbiosis to fix atmospheric nitrogen. The chemical communication between roots and rhizobia begins in the rhizosphere. Using signature-tagged-Tn5 mutagenesis (STM) we performed a genome-wide screening for Ensifer meliloti genes that participate in colonizing the rhizospheres of alfalfa and other legumes. The analysis of ca. 6,000 mutants indicated that genes relevant for rhizosphere colonization account for nearly 2% of the rhizobial genome and that most (ca. 80%) are chromosomally located, pointing to the relevance and ancestral origin of the bacterial ability to colonize plant roots. The identified genes were related to metabolic functions, transcription, signal transduction, and motility/chemotaxis among other categories; with several ORFs of yet-unknown function. Most remarkably, we identified a subset of genes that impacted more severely the colonization of the roots of alfalfa than of pea. Further analyses using other plant species revealed that such early differential phenotype could be extended to other members of the Trifoliae tribe (Trigonella, Trifolium), but not the Fabeae and Phaseoleae tribes. The results suggest that consolidation of E. meliloti into its current symbiotic state should have occurred in a rhizobacterium that had already been adapted to rhizospheres of the Trifoliae tribe.

Twenty-two rhizobia strains isolated from three distinct populations (North Ossetia, Dagestan, and Armenia) of a relict legume Vavilovia formosa were analysed to determine their position within Rhizobium leguminosarum biovar viciae (Rlv). These bacteria are described as symbionts of four plant genera Pisum, Vicia, Lathyrus, and Lens from the Fabeae tribe, of which Vavilovia is considered to be closest to its last common ancestor (LCA). In contrast to biovar viciae, bacteria from Rhizobium leguminosarum biovar trifolii (Rlt) inoculate plants from the Trifolieae tribe. Comparison of house-keeping (hkg: 16S rRNA, glnII, gltA, and dnaK) and symbiotic (sym: nodA, nodC, nodD, and nifH) genes of the symbionts of V. formosa with those of other Rlv and Rlt strains reveals a significant group separation, which was most pronounced for sym genes. A remarkable feature of the strains isolated from V. formosa was the presence of the nodX gene, which was commonly found in Rlv strains isolated from Afghanistan pea genotypes. Tube testing of different strains on nine plant species, including all genera from the Fabeae tribe, demonstrated that the strains from V. formosa nodulated the same cross inoculation group as the other Rlv strains. Comparison of nucleotide similarity in sym genes suggested that their diversification within sym-biotypes of Rlv was elicited by host plants. Contrariwise, that of hkg genes could be caused by either local adaptation to soil niches or by genetic drift. Long-term ecological isolation, genetic separation, and the ancestral position of V. formosa suggested that symbionts of V. formosa could be responsible for preserving ancestral genotypes of the Rlv biovar.

The temperate and herbaceous genus Vicia L. is a member of the legume tribe Fabeae of the subfamily Papilionoideae. The genus Vicia comprises 166 annual or perennial species distributed mainly in Europe, Asia, and North America, but also extending to the temperate regions of South America and tropical Africa. The use of simple sequence repeat (SSR) markers for Vicia species has not been investigated as extensively as for other crop species. In this study, we assessed the potential for cross-species amplification of cDNA microsatellite markers developed from common vetch (Vicia sativa subsp. sativa). For cross-species amplification of the SSRs, amplification was carried out with genomic DNA isolated from two to eight accessions of 22 different Vicia species. For individual species or subspecies, the transferability rates ranged from 33% for V. ervilia to 82% for V. sativa subsp. nigra with an average rate of 52.0%. Because the rate of successful SSR marker amplification generally correlates with genetic distance, these SSR markers are potentially useful for analyzing genetic relationships between or within Vicia species.

Vavilovia formosa is a relict leguminous plant growing in hard-to-reach habitats in the rocky highlands of the Caucasus and Middle East, and it is considered as the putative closest living relative of the last common ancestor (LCA) of the Fabeae tribe. Symbionts of Vavilovia belonging to Rhizobium leguminosarum bv. viciae compose a discrete group that differs from the other strains, especially in the nucleotide sequences of the symbiotically specialised (sym) genes. Comparison of the genomes of Vavilovia strains with the reference group composed of R. leguminosarum bv. viciae strains isolated from Pisum and Vicia demonstrated that the vavilovia strains have a set of genomic features, probably indicating the important stages of microevolution of the symbiotic system. Specifically, symbionts of Vavilovia (considered as an ancestral group) demonstrated a scattered arrangement of sym genes (&gt, 90 kb cluster on pSym), with the location of nodT gene outside of the other nod operons, the presence of nodX and fixW, and the absence of chromosomal fixNOPQ copies. In contrast, the reference (derived) group harboured sym genes as a compact cluster (&lt, 60 kb) on a single pSym, lacking nodX and fixW, with nodT between nodN and nodO, and possessing chromosomal fixNOPQ copies. The TOM strain, obtained from nodules of the primitive &ldquo, Afghan&rdquo, peas, occupied an intermediate position because it has the chromosomal fixNOPQ copy, while the other features, the most important of which is presence of nodX and fixW, were similar to the Vavilovia strains. We suggest that genome evolution from the ancestral to the derived R. leguminosarum bv. viciae groups follows the &ldquo, gain-and-loss of sym genes&rdquo, and the &ldquo, compaction of sym cluster&rdquo, strategies, which are common for the macro-evolutionary and micro-evolutionary processes. The revealed genomic features are in concordance with a relict status of the vavilovia strains, indicating that V. formosa coexists with ancestral microsymbionts, which are presumably close to the LCA of R. leguminosarum bv. viciae.

Premise of the study In angiosperm seeds, the developing embryo acquires nutrients via a suspensor that typically undergoes programmed cell death (PCD) at the early cotyledon stage. However, in Leguminosae (the third largest angiosperm family), the suspensors can disappear at the heart-shaped stage (i.e., prior to the cotyledon stage) or still persist at the cotyledon stage. Here, in a comprehensive survey of legume suspensors and embryos, the variation and the evolutionary direction of timing of suspensor PCD in Leguminosae were characterized, and systematic implications were evaluated. Methods Suspensor development and morphology for 66 leguminous species from 49 genera, 21 tribes, and 3 subfamilies were comparatively studied using standard paraffin sectioning and light microscopy. Key results Three patterns of suspensor PCD were observed at the early cotyledon stage. (A) The suspensor persisted. (B) The suspensor separated from the wall of the embryo sac and persisted as a vestige at the radicle apex. (C) The suspensor disappeared completely, and the absorption of nutrients by embryo was carried out via a "contact zone" between the embryo and the endosperm. Pattern C of early suspensor PCD was found only in the tribe Fabeae. An ancestral character reconstruction revealed that the long-lived suspensors of pattern A represented a plesiomorphic condition in Leguminosae and that the suspensors of pattern C evolved only once in the common ancestor of Fabeae. Conclusions In Leguminosae, short-lived suspensors have thus evolved multiple times from long-lived suspensors. It remains largely unknown, however, how the embryo acquires nutrients after the early suspensor PCD.

The aims of the present study were (i) to compare the anatomical structures of roots from legume species belonging to the tribes Aeschynomeneae, Fabeae (syn. Vicieae), and Trifolieae (Papilionoideae); (ii) to characterize those developmental stages of roots that are most useful for comparative studies; (iii) to characterize root developmental patterns during their growth from primary to adult structures; and (iv) to identify developmental patterns that are typical for particular tribes within this plant group. To this end, serial transverse cuts of the main roots of 20 species belonging to the above-mentioned tribes were made from the root tip to the root collar. Vessel density, vessel diameter, secondary cortex area, and xylem area were quantified using appropriate software. Based on root ontogeny, four stages giving evidence for important developmental events were chosen based on which a comparison of the species-specific structures became possible. The first stage corresponds to the primary structure of a root. The second stage corresponds to the onset of cambium and phellogen division, when their first division products become differentiated. The third and fourth stages correspond to adult roots with a well-developed secondary structure. These developmental stages that allowed between-species comparison turned out to be useful characterising those patterns that best typify a particular tribe within the subfamily. Vessel density, vessel diameter, and the xylem transverse area were found to differ significantly between the tribes examined. Some of the analyzed morphological variables had a tribe-specific consistency, so that, together with other characteristics, they should be included in approaches to clarify systematic problems in the legume family.

The carbohydrate-binding sequences of the lectin genes from spring vetchling Lathyrus vernus (L.) Bernh., marsh vetchling L. palustris (L.), and Gmelin’s vetchling L. gmelinii (Fitsch) (Fabaceae) were determined. Computer-aided analysis revealed substantial differences between nucleotide and predicted amino acid sequences of the lectin gene regions examined in each of the three vetchling species tested. In the phylogenetic trees based on sequence similarity of carbohydrate-biding regions of legume lectins, the sequences examined formed a compact cluster with the lectin genes of the plants belonging to the tribe Fabeae. In each plant, L. vernus, L. palustris, and L. gmelinii, three different lectin-encoding genes were detected. Most of the substitutions were identified within the gene sequence responsible for coding the carbohydrate-binding protein regions. This finding may explain different affinity of these lectins to different carbohydrates, and as a consequence, can affect the plant host specificity upon development of symbiosis with rhizobium bacteria.

Summary: A considerable number of diverse ornamental forms of Lathyrus odoratus exist which require careful conservation if they are not to be lost. Other ornamental Lathyrus species may have potential for increasing their diversity. A seedbank has been established in the United Kingdom to conserve this diversity and make the material readily available to researchers and growers throughout the world. Conventional hybridisation provides an opportunity for the existing diversity in L. odoratus to be extended. Opportunities also exist to create improved decorative forms and new colours in some other species through intra-specifi c hybridisation. Inter-specifi c hybridisation within the genus is in its infancy but early results suggest exciting improvements might be introduced by this method. Such work might also provide benefi ts for comparative genomics in the tribe Fabeae.

Vavilovia (Vavilovia formosa (Stev.) Fed.) belongs to the tribe Fabeae along with peas, vetchlings, vetches and lentils. It prefers high mountain areas in Armenia, Azerbaijan, Georgia, Iran, Iraq, Lebanon, Russia, Syria and Turkey. A true success in the ex situ conservation has recently been achieved, within the display plot Flora and Vegetation of Armenia in the Yerevan Botanic Garden. The hybridization between vavilovia and other Fabeae was done in the N. I. Vavilov Institute of Plant Industry with F1 seeds and F1 plants that did not produce the next generation. The recent molecular research showed that vavilovia belongs to a Lathyrus-Pisum-Vavilovia clade with a clearly distinct status. Vavilovija (Vavilovia formosa (Stev.) Fed.) pripada tribusu Fabeae, zajedno sa graškovima, grahorima, grahoricama i sočivima. Vavilovija raste u visokoplaninskim oblastima Jermenije, Azerbejdžana, Gruzije, Iraka, Irana, Libana, Rusije, Sirije i Turske. Pravi uspeh u ex situ konzervaciji postignut je nedavno u okviru izložbenog polja 'Flora i vegetacija Jermenije' u botaničkoj bašti u Jerevanu. Hibridizacija između vavilovije i graška izvršena je u institutu Vavilov, sa F1 semenima i F1 biljkama koje nisu uspele da daju sledeće pokoljenje. Skorašnja molekularna istraživanja pokazala su da vavilovija pripada grupi Lathyrus - Pisum - Vavilovia sa jasno izraženim posebnim statusom.

Nodules in the family Leguminosae come in many different shapes and forms, depending partly on the host that bears them. This review focuses on the peripheral tissues that surround the infected tissues of four anatomically distinct classes of nodules: nodules with indeterminate meristems (from the Trifolieae and Fabeae tribes); desmodioid nodules with determinate meristems (from the Phaseoleae and Loteae tribes); aeschynomenoid nodules ( Arachis hypogaea L., peanut); and lupinoid nodules ( Lupinus sp. L., lupine). I have especially stressed the importance of the three-dimensionality of the organ, because not all nodules display a radial symmetry as it is often assumed. The goal of this review is to provide a strong base of nodule structure so that forthcoming molecular studies can integrate this information into their approach.

The approximately 27 New World species of Vicia (tribe Fabeae, family Leguminosae) were classified into four stylar type groups as follows: (1) a laterally compressed and evenly hairy stylar type (Le-type) group, (2) a dorsiventrally compressed and abaxially tufted hairy stylar type (Dabt-type) group, (3) a dorsiventrally compressed and evenly hairy stylar type (De-type) group, and (4) V. leuncophaea that is characterized by an arcuate style with a dense ring of stylar hairs at a considerable distance from the stigma. In the present study, the stylar distinctions among the groups were confirmed by morphological and anatomical studies on the stylar characters of representative species of the groups. The phylogenetic positions of these groups were then assessed using molecular phylogenetic analysis based on sequences from the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) region of the representative species. The New World Le-type stylar group was revealed to be a sister group to t...

Background Some clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus. Results The Trifolium plastomes fell into two groups: those of Trifolium boissieri, T. strictum and T. glanduliferum (representing subgenus Chronosemium and subg. Trifolium section Paramesus) were tractable, assembled readily and were not unusual in the general context of Fabeae plastomes. The other Trifolium species (“core Trifolium”) proved refractory to assembly mainly because of numerous short duplications. These species form a single clade, which we call the “refractory clade” (comprising subg, Trifolium sections Lupinaster, Trifolium, Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the refractory clade are the presence of numerous short duplications and 7-15% longer genomes than the tractable species. Molecular dating estimates that the origin of the most recent common ancestor (MRCA) of the refractory clade is approximately 13.1 million years ago (MYA). This is considerably younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA) and Trifolium subg. Trifolium (16.1 MYA). Conclusions We conclude that the unusual repetitive plastome type previously characterized in Trifolium subterraneum had a single origin within Trifolium and is characteristic of most (but not all) species of subgenus Trifolium. It appears that an ancestral plastome within Trifolium underwent an evolutionary change resulting in plastomes that either actively promoted, were permissive to, or were unable to control, duplications within the genome. The precise mechanism of this important change in the mode and tempo of plastome evolution deserves further investigation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0228-6) contains supplementary material, which is available to authorized users.

Background Tribe Fabeae comprises about 380 legume species, including some of the most ancient and important crops like lentil, pea, and broad bean. Breeding efforts in legume crops rely on a detailed knowledge of closest wild relatives and geographic origin. Relationships within the tribe, however, are incompletely known and previous molecular results conflicted with the traditional morphology-based classification. Here we analyse the systematics, biogeography, and character evolution in the tribe based on plastid and nuclear DNA sequences. Results Phylogenetic analyses including c. 70% of the species in the tribe show that the genera Vicia and Lathyrus in their current circumscription are not monophyletic: Pisum and Vavilovia are nested in Lathyrus, the genus Lens is nested in Vicia. A small, well-supported clade including Vicia hirsuta, V. sylvatica, and some Mediterranean endemics, is the sister group to all remaining species in the tribe. Fabeae originated in the East Mediterranean region in the Miocene (23–16 million years ago (Ma)) and spread at least 39 times into Eurasia, seven times to the Americas, twice to tropical Africa and four times to Macaronesia. Broad bean (V. faba) and its sister V. paucijuga originated in Asia and might be sister to V. oroboides. Lentil (Lens culinaris ssp. culinaris) is of Mediterranean origin and together with eight very close relatives forms a clade that is nested in the core Vicia, where it evolved c. 14 Ma. The Pisum clade is nested in Lathyrus in a grade with the Mediterranean L. gloeosperma, L. neurolobus, and L. nissolia. The extinct Azorean endemic V. dennesiana belongs in section Cracca and is nested among Mediterranean species. According to our ancestral character state reconstruction results, ancestors of Fabeae had a basic chromosome number of 2n=14, an annual life form, and evenly hairy, dorsiventrally compressed styles. Conclusions Fabeae evolved in the Eastern Mediterranean in the middle Miocene and spread from there across Eurasia, into Tropical Africa, and at least seven times to the Americas. The middle-Atlantic islands were colonized four times but apparently did not serve as stepping-stones for Atlantic crossings. Long-distance dispersal events are relatively common in Fabeae (seven per ten million years). Current generic and infrageneric circumscriptions in Fabeae do not reflect monophyletic groups and should be revised. Suggestions for generic level delimitation are offered.