Species, genomes, and section relationships in the genus Arachis (Fabaceae): a molecular phylogeny

The economically important genus Arachis (Fabaceae) comprises 80 species restricted to South America. One monograph on the genus divided it into nine sections and included an intuitive assessment of evolutionary relationships. There is no comprehensive phylogenetic study of the genus. To test the current systematic treatment of the genus, we reconstructed a phylogeny for Arachis using nuclear ITS and plastid trnT–trnF sequences from 46 species representing all nine sections. ITS cloning of the allotetraploid species of section Arachis indicated the presence of A and B genome alleles and chimeric sequences. Our study revealed that species from section Extranervosae were the first emerging lineage in the genus, followed by sections Triseminatae and Caulorrhizae, and two terminal major lineages, which we refer to as erectoides and arachis. The lineage erectoides comprises members of sections Erectoides, Heteranthae, Procumbentes, Rhizomatosae, and Trierectoides. Species in the arachis lineage form two major clades, arachis I (B and D genomes species and the aneuploids) and arachis II (A genome species). Our results substantiated the sectional treatment of Caulorrhizae, Extranervosae, and Triseminatae, but demonstrated that sections Erectoides, Procumbentes, and Trierectoides are not monophyletic. A detailed study of the genus Arachis with denser taxon sampling, additional genomic regions, plus information from morphology and cytogenetics is needed for comprehensive assessment of its systematics.     

Novel polymorphic microsatellite markers in section Caulorrhizae (Arachis,Fabaceae)

This work reports the characterization of 11 polymorphic microsatellite loci in section Caulorrhizae. The primer pairs were designed from Arachis pintoi and showed full transferability to Arachis repens species. These new markers were used to evaluate the genetic diversity in germplasm (accessions and cultivars) of section Caulorrhizae. This new set of markers detected greater gene diversity than morphological and molecular markers such as AFLP (amplified fragment length polymorphism) and RAPD (rapid analysis of polymorphic DNA) previously used in this germplasm.     

Characterization of Brazilian accessions of wild Arachis species of section Arachis (Fabaceae) using heterochromatin detection and fluorescence in situ hybridization (FISH)

The cytogenetic characterization of Arachis species is useful for assessing the genomes present in this genus, for establishing the relationship among their representatives and for understanding the variability in the available germplasm. In this study, we used fluorescence in situ hybridization (FISH) to examine the distribution patterns of heterochromatin and rDNA genes in 12 Brazilian accessions of five species of the taxonomic section Arachis. The heterochromatic pattern varied considerably among the species: complements with centromeric bands in all of the chromosomes (A. hoehnei) and complements completely devoid of heterochromatin (A. gregoryi, A. magna) were observed. The number of 45S rDNA loci ranged from two (A. gregoryi) to eight (A. glandulifera), while the number of 5S rDNA loci was more conserved and varied from two (in most species) to four (A. hoehnei). In some species one pair of 5S rDNA loci was observed adjacent to 45S rDNA loci. The chromosomal markers revealed polymorphism in the three species with more than one accession (A. gregoryi, A. magna and A. valida) that were tested. The previous genome assignment for each of the species studied was confirmed, except for A. hoehnei. The intraspecific variability observed here suggests that an exhaustive cytogenetic and taxonomic analysis is still needed for some Arachis species.     

Isoenzyme diversity and phylogenetic affinities among thePhaseolus beans (Fabaceae)

Polyacrylamide gel electrophoretic study of 8 isoenzyme systems encoded by 16 putative gene loci in 23 species of American beans of the genusPhaseolus s. str. and in the Asian moth beanVigna aconitifolia revealed in total 98 allozymes, including 34 taxon-specific and unique, 14 rare-unique and 50 shared allozymes. —P. xanthotrichus var.xanthotrichus and var.zimapanensis differed in allozymes of AAT-A, AAT-D and ADH-C.P. xanthotrichus var.zimapanensis andP. hintonii shared same allozymes of AAT-A and AAT-D, but differed in allozymes of ADH-A and ADH-C. It is proposed to recognizeP. xanthotrichus var.zimapanensis in species rank asP. zimapanensis. — P. acutifolius var.acutifolius and var.tenuifolius, except one accession of the latter, differed in allozymes of AAT-D, ADH-C and FDH-A. — Cladistic analysis of the allozymic data as unordered absence-presence characters disclosed in the genus two major monophyletic species clusters: (1)P. polystachyus, P. ritensis, P. maculatus, P. marechalii, P. jaliscanus, P. salicifolius, P. lunatus, P. filiformis, P. angustissimus, P. acutifolius, P. coccineus, P. vulgaris, P. parvulus, P. pauciflorus, andP. pluriflorus; (2)P. grayanus, P. neglectus, P. pedicellatus, P. microcarpus, P. hintonii, andP. zimapanensis. P. xanthotrichus s. str. andP. zimapanensis are discriminated as paraphyletic, supporting their specific delimitation. — Phenetic analysis of the allozyme data with the UPGMA clustering revealed essentially the same pattern of genetic affinities between the species and additionally clarified the extent of allozymic divergence by taking into account species-specific and unique allozymes.     

Astragalus (Fabaceae): A molecular phylogenetic perspective

Nucleotide sequences of the plastidmatK gene and nuclear rDNA internal transcribed spacer region were sampled fromAstragalus L. (Fabaceae), and its closest relatives within tribe Galegeae, to infer phylogenetic relationships and estimate ages of diversification. Consistent with previous studies that emphasized sampling for nrDNA ITS primarily within either New World or Old World species groups,Astragalus, with the exception of a few morphologically distinct species, is strongly supported as monophyletic based on maximum parsimony and Bayesian analyses ofmatK sequences as well as a combined sequence dataset. ThematK data provides better resolution and stronger clade support for relationships amongAstragalus and traditionally related genera than nrDNA ITS.Astragalus sensu stricto plus the genusOxytropis are strongly supported as sister to a clade composed of strictly Old World (African, Australasian) genera such asColutea. Sutherlandia, Lessertia, Swainsona, andCarmichaelia, plus several morphologically distinct segregates of EurasianAstragalus. Ages of these clades and rates of nucleotide substitution estimated from a fossil-constrained, rate-smoothed, Bayesian analysis ofmatK sequences sampled from Hologalegina indicateAstragalus diverged from its sister group,Oxtropis, 12–16 Ma, with divergence of Neo-Astragalus beginning ca 4.4. Ma. Estimates of absolute rates of nucleotide substitution forAstragalus and sister groups, which range from 8.9 to 10.2×10⁻¹⁰ substitutions per site per year, are not unusual when compared to those estimated for other, mainly temperate groups of papilionoid legumes. The results of previously published work and other recent developments on the phylogenetic relationships and diversification ofAstragalus are reviewed.     

Relationships of the woody Medicago species (section Dendrotelis) assessed by molecular cytogenetic analyses

Background and Aims

The organization of rDNA genes in the woody medic species from the agronomically important Medicago section Dendrotelis was analysed to gain insight into their taxonomic relationships, to assess the levels of infraspecific variation concerning ribosomal loci in a restricted and fragmented insular species (M. citrina) and to assess the nature of its polyploidy.

Methods

Fluorescence in situ hybridization (FISH) was used for physical mapping of 5S and 45S ribosomal DNA genes in the three species of section Dendrotelis (M. arborea, M. citrina, M. strasseri) and the related M. marina from section Medicago. Genomic in situ hybridization (GISH) was used to assess the genomic relationships of the polyploid M. citrina with the putatively related species from section Dendrotelis.

Key Results

The diploid (2n = 16) M. marina has a single 45S and two 5S rDNA loci, a pattern usually detected in previous studies of Medicago diploid species. However, polyploid species from section Dendrotelis depart from expectations. The tetraploid species (2n = 32) M. arborea and M. strasseri have one 45S rDNA locus and two 5S rDNA loci, whereas in the hexaploid (2n = 48) M. citrina four 45S rDNA and five 5S rDNA loci have been detected. No single chromosome of M. citrina was uniformly labelled after using genomic probes from M. arborea and M. strasseri. Instead, cross-hybridization signals in M. citrina were restricted to terminal chromosome arms and NOR regions.

Conclusions

FISH results support the close taxonomic interrelationship between M. arborea and M. strasseri. In these tetraploid species, NOR loci have experienced a diploidization event through physical loss of sequences, a cytogenetic feature so far not reported in other species of the genus. The high number of rDNA loci and GISH results support the specific status for the hexaploid M. citrina, and it is suggested that this species is not an autopolyploid derivative of M. arborea or M. strasseri. Further, molecular cytogenetic data do not suggest the hypothesis that M. arborea and M. strasseri were involved in the origin of M. citrina. FISH mapping can be used as an efficient tool to determine the genomic contribution of M. citrina in somatic hybrids with other medic species.Key words: Medicago arborea, M. citrina, M. strasseri, rRNA genes, 18S-5·8S-25-S, 5S, FISH mapping, GISH, polyploidy     

Diversity of seed storage protein patterns in wild peanut (Arachis,Fabaceae) species

55 accessions of wild peanuts (Arachis spp.) introduced from South America were analyzed for seed storage protein composition using SDS-PAGE electrophoresis. The objectives of the study were to evaluate variability within sect.Arachis and to classify taxa based on protein composition. 25 different band positions were resolved. Individual accessions had 11 to 18 bands which included the conarachin region (MW > 50 kD), two to five bands in the acidic arachin region (MW 38–49.9 kD), three to seven in the intermediate MW region (23 to 37.9 kD), two to five bands in the basic arachin region (18–22.9 kD), and one to three bands in the low MW protein region (14–17.9 kD). These data were utilized in a principal coordinate analysis based on the matrix of genetic distances between all pairs of the 55 accessions. Several groups of accessions conformed to expected species classification includingA. batizocoi, A. stenosperma, andA. monticola; whileA. duranensis, A. cardenasii, A. helodes, andA. correntina did not form good groups. The study showed that great diversity exists for protein profiles and seed storage proteins have potential for aiding species classification and for serving as markers for interspecific hybridization studies.     

Karyological and molecular characterisation of subgenus Vicia (Fabaceae)

In the present report, we have analysed the subgenus Vicia by karyological and molecular approaches with the aim to clarify the relationships among Vicia species included in this subgenus by previously evidenced morphological investigations. Multivariate analysis using several karyomorphological parameters in addition to symmetry indices has allowed the construction of a dendrogram of linkage distances very useful to compare and to include in a phylogenetic tree obtained by internal transcribed spacer (ITS) rDNA sequences. Moreover, a separate analysis was performed combining our molecular data on ITS sequences with those reported in the literature for the section Vicilla. Our analyses partly confirm the monophyletic status of the various sections in which the subgenus Vicia has been divided, however questioning, in some cases, the real need to maintain all the nine sections so far accepted and the placement of some individual species in the two subgenera Vicia and Vicilla.     

Genetic relationships between peanut and wild species ofArachis sect.Arachis (Fabaceae): Evidence from RAPDs

Twenty-six accessions of wildArachis species and domesticated peanuts,A. hypogaea, introduced from South America were analyzed for random amplified polymorphic DNA (RAPD). The objective of the study was to investigate inter- and intraspecific variation and affinities among species of sect.Arachis which have been proposed as possible progenitors for the domesticated peanut. Ten primers resolved 132 DNA bands which were useful for separating species and accessions. The most variation was observed among accessions ofA. cardenasii andA. glandulifera whereas the least amount of variation was observed inA. hypogaea andA. monticola. The two tetraploid species could not be separated by using RAPDs.Arachis duranensis was most closely related to the domesticated peanut and is believed to be the donor of the A genome. The data indicated thatA. batizocoi, a species previously hypothesized to contribute the B genome toA. hypogaea, was not involved in its evolution. The investigation showed that RAPDs can be used to analyze both inter- and intraspecific variation in peanut species. Southern hybridization of RAPD probes to blots containing RAPD of theArachis species provided information on genomic relationships and revealed the repetitive nature of the amplified DNA.     

Origins of resistances to rust and late leaf spot in peanut (Arachis hypogaea,Fabaceae)

The cultivated peanut (Arachis hypogaea, Fabaceae) is believed to have originated along the eastern slopes of the Andes in Bolivia and northern Argentina. The crop is now grown throughout tropical and warm temperate regions. Among diseases attacking peanuts, rust caused byPuccinia arachidis and late leaf spot caused byPhaeoisariopsis personata are the most important and destructive on a worldwide scale. Both pathogens, restricted in host range to Arachis, probably originated and coevolved in South America along with their hosts. In recent years there has been much emphasis on screening of peanut germplasm for resistance to these diseases. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISA T), India, some 10,000 peanut germplasm accessions were screened for resistance to rust and late leaf spot during 1977–1985 and sources of resistance indentified for either or both pathogens. Of the resistant genotypes, about 87% belonged to A. hypogaea var.fastigiata and 13% to var.hypogaea; 84% originated in South America or had South American connections. A high percentage (75%) had their origin in Peru (believed to be a secondary gene center for var.hirsuta and var.fastigiata,), suggesting that resistance to rust and late leaf spot diseases might have evolved in that country.     

Growth rates and auxin effects in graviresponding gynophores of the peanut, Arachis hypogaea (Fabaceae)

The gynophore of the peanut plant (Arachis hypogaea) is a specialized organ that carries and buries the fertilized ovules into the soil in order for seed and fruit development to occur underground. The rates of growth of vertically and horizontally oriented gynophores were measured using a time-lapse video imaging system. We found that the region of maximum extension growth due to elongation (termed the Central Elongation Zone) is located on average at 2-5 mm from the tip. In the first 0-4 h after horizontal reorientation (gravistimulation), new zones of growth emerge on the upper surface, while the elongation zone of the lower side decreases in size and magnitude. Four to six hours after reorientation the zones of maximum growth are almost equal in size and location on the upper and lower sides. The growth rate and the gravitropic response decreased dramatically, upon the excision of the ovule region (terminal 1.5 mm), but a gravitropic growth response could be restored by applying the auxin indole-3-acetic acid exogenously to the excised tip. The addition of napthylphthalamic acid (an auxin transport inhibitor) at the ovule region allowed some growth to occur, but the gynophores do not respond normally to gravity, upon horizontal reorientation. We discuss the role of auxin in the gravitropic response of the gynophore.     

Taxonomic notes on astragalus section leptocarpi subsection californici (Fabaceae)

A recently completed study of Astragalus sect. Leptocarpi subsect. Californici shows that the following taxonomic adjustments are required: 1) Astragalus tener var. ferrisiae, a new variety, is described. It is compared to A. tener var. tener, as well as to A. rattanii var. jepsonianus in which it was previously included, and to the superficially similar A. clarianus with which it was confused. An illustration of the new variety, and of the fruits of these related taxa, is included. 2) Astragalus nyensis was placed in subsect. Californici by Barneby in his 1964 monograph. Morphological, anatomical, and allozyme data suggest that A. nyensis should be placed in the subsect. Leptocarpi closely allied to A. nuttallianus.     

Molecular cytogenetic characterisation and phylogenetic analysis of the seven cultivated Vigna species (Fabaceae)

The genomic organisation of the seven cultivated Vigna species, V. unguiculata, V. subterranea, V. angularis, V. umbellata, V. radiata, V. mungo and V. aconitifolia, was determined using sequential combined PI and DAPI (CPD) staining and dual‐colour fluorescence in situ hybridisation (FISH) with 5S and 45S rDNA probes. For phylogenetic analyses, comparative genomic in situ hybridisation (cGISH) onto somatic chromosomes and sequence analysis of the internal transcribed spacer (ITS) of 45S rDNA were used. Quantitative karyotypes were established using chromosome measurements, fluorochrome bands and rDNA FISH signals. All species had symmetrical karyotypes composed of only metacentric or metacentric and submetacentric chromosomes. Distinct heterochromatin differentiation was revealed by CPD staining and DAPI counterstaining after FISH. The rDNA sites among all species differed in their number, location and size. cGISH of V. umbellata genomic DNA to the chromosomes of all species produced strong signals in all centromeric regions of V. umbellata and V. angularis, weak signals in all pericentromeric regions of V. aconitifolia, and CPD‐banded proximal regions of V. mungo var. mungo. Molecular phylogenetic trees showed that V. angularis and V. umbellata were the closest relatives, and V. mungo and V. aconitifolia were relatively closely related; these species formed a group that was separated from another group comprising V. radiata, V. unguiculata ssp. sesquipedalis and V. subterranea. This result was consistent with the phylogenetic relationships inferred from the heterochromatin and cGISH patterns; thus, fluorochrome banding and cGISH are efficient tools for the phylogenetic analysis of Vigna species.     

Astragalus sect. Semnanenses (Fabaceae): a new monotypic section from Iran

The systematic position of Astragalus semnanensis is studied. Morphological and micromorphological features of this species are not in accordance with the old position of this species as a member of A. sect. Leucocercis. Within A. subgen. Astragalus this species is intermediate between A. sect. Acanthophace and A. sect. Megalocystis , but it shows critical differences from them. Therefore, a new section, A. sect. Semnanenses is described.     

A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae)

Cultivated peanut (Arachis hypogaea) is an important crop, widely grown in tropical and subtropical regions of the world. It is highly susceptible to several biotic and abiotic stresses to which wild species are resistant. As a first step towards the introgression of these resistance genes into cultivated peanut, a linkage map based on microsatellite markers was constructed, using an F₂ population obtained from a cross between two diploid wild species with AA genome (A. duranensis and A. stenosperma). A total of 271 new microsatellite markers were developed in the present study from SSR-enriched genomic libraries, expressed sequence tags (ESTs), and by “data-mining” sequences available in GenBank. Of these, 66 were polymorphic for cultivated peanut. The 271 new markers plus another 162 published for peanut were screened against both progenitors and 204 of these (47.1%) were polymorphic, with 170 codominant and 34 dominant markers. The 80 codominant markers segregating 1:2:1 (P<0.05) were initially used to establish the linkage groups. Distorted and dominant markers were subsequently included in the map. The resulting linkage map consists of 11 linkage groups covering 1,230.89 cM of total map distance, with an average distance of 7.24 cM between markers. This is the first microsatellite-based map published for Arachis, and the first map based on sequences that are all currently publicly available. Because most markers used were derived from ESTs and genomic libraries made using methylation-sensitive restriction enzymes, about one-third of the mapped markers are genic. Linkage group ordering is being validated in other mapping populations, with the aim of constructing a transferable reference map for Arachis.Electronic supplementary material is available for this at     

Characterization of two distinct species of Arvicanthis (Rodentia: Muridae) in West Africa: cytogenetic, molecular and reproductive evidence

The unstriped grass rat, Arvicanthis Lesson 1842, is one of the most common genera of murid rodents in African savannas. However, from a systematic viewpoint, very little is known about this group. Following recent investigations which showed karyotypic variability within the species A. niloticus , the present study attempts to clarify the nature and distribution of these chromosomal variants, as well as to determine their taxonomic rank.
The chromosomes of 15 individuals from different West African localities were prepared from fibroblast cultures, and R- and C-banded karyotypes were constructed. In addition, the levels of genetic divergence (DNA/DNA hybridization) and reproductive isolation (attempted crossbreeding in captivity) were examined. The results confirm the existence of two differentiated karyomorphs, differing by numerous chromosomal rearrangements such as pericentric inversions and translocations, as well as differences in the quantity of constitutive heterochromatin. These karyomorphs appear to be genetically and reproductively isolated and are parapatrically distributed; their areas of distribution correspond to the sahelian and sudano-guinean domains, respectively. The distinctness of these karyomorphs, the absence of hybrids in laboratory crosses, and the pronounced genetic divergence provide good evidence for the recognition of two distinct sibling species. We propose to keep the designation A. niloticus for the northern sahelian form and discuss the naming alternatives for the other.     

Genomic imbalances in esophageal squamous cell carcinoma identified by molecular cytogenetic techniques

This review summarizes the chromosomal changes detected by molecular cytogenetic approaches in esophageal squamous cell carcinoma (ESCC), the ninth most common malignancy in the world. Whole genome analyses of ESCC cell lines and tumors indicated that the most frequent genomic gains occurred at 1, 2q, 3q, 5p, 6p, 7, 8q, 9q, 11q, 12p, 14q, 15q, 16, 17, 18p, 19q, 20q, 22q and X, with focal amplifications at 1q32, 2p16-22, 3q25-28, 5p13-15.3, 7p12-22, 7q21-22, 8q23-24.2, 9q34, 10q21, 11p11.2, 11q13, 13q32, 14q13-14, 14q21, 14q31-32, 15q22-26, 17p11.2, 18p11.2-11.3 and 20p11.2. Recurrent losses involved 3p, 4, 5q, 6q, 7q, 8p, 9, 10p, 12p, 13, 14p, 15p, 18, 19p, 20, 22, Xp and Y. Gains at 5p and 7q, and deletions at 4p, 9p, and 11q were significant prognostic factors for patients with ESCC. Gains at 6p and 20p, and losses at 10p and 10q were the most significant imbalances, both in primary carcinoma and in metastases, which suggested that these regions may harbor oncogenes and tumor suppressor genes. Gains at 12p and losses at 3p may be associated with poor relapse-free survival. The clinical applicability of these changes as markers for the diagnosis and prognosis of ESCC, or as molecular targets for personalized therapy should be evaluated.     

Experimental evidence on the affinities ofPapaver somniferum (Papaveraceae)

Results obtained from crossing experiments betweenP. somniferum subsp.somniferum (2n = 22) and subsp.setigerum (2n = 44),P. glaucum (2n = 14) andP. gracile (2n = 14) and from the observation of meiotic chromosome pairing in the various hybrids obtained do not provide straightforward evidence for the hypothesis thatP. somniferum originated as a triploid hybrid between taxa similar toP. glaucum andP. gracile (Kadereit 1986a, b).—On the one hand, the pattern of crossability found reflects the closer similarity of subsp.somniferum toP. glaucum and of subsp.setigerum toP. gracile, which was interpreted as segregation of parental characters, and the high frequency of 2n = 28 chromosomes among F₂-progeny from the hybrid subsp.somniferum × subsp.setigerum (2n = 33) might reveal n = 7 as the base number also ofP. somniferum. On the other hand, however, the general difficulty of obtaining hybrids, and the low incidence of bivalent formation in their meiosis, probably indicating a lack of chromosome homology between the different species, do not fit the above hypothesis.—These results are in marked contrast to the morphological similarity between the three species involved.     

Bi-parental cytoplasmic DNA inheritance in Wisteria (Fabaceae): evidence from a natural experiment

Cytoplasmic inheritance was investigated in interspecific hybrids of Wisteria sinensis and W. floribunda. Species-specific nuclear, mitochondrial and plastid DNA markers were identified from wild-collected plants of each species in its native range. These markers provide evidence for the bi-parental transmission of plastids in hybrid swarms of these two species in the southeastern USA. These population level molecular data corroborate previous cytological evidence of this phenomenon in Wisteria.