Molecular taxonomic relationships in the genus Vigna based on RFLP analysis

Summary The taxonomy of the genus Vigna has been primarily based on morphological attributes. We have used 27 genomic clones from soybean, common bean, mungbean and cowpea to examine restriction fragment length polymorphism (RFLP) among 44 accessions of different species belonging to four subgenera of the genus Vigna. One accession each of common bean (Phaseolus vulgaris) and soybean (Glycine max) was included in the study. Total DNA from the various genotypes was digested with one restriction enzyme (Eco RV). Results of a numerical taxonomic analysis showed a high level of genetic variation within the genus with a remarkably higher amount of variation associated with Vigna sp. from Africa relative to those from Asia. The distinctness of the Asiatic grams in subgenus Ceratotropis, cowpea in section Catiang, bambara groundnut (V. subterranean) and members of the subgenus Plectotropis was elucidated by this study. Members of the subgenus Plectotropis were closer in genome homology to those of subgenus Vigna section Catiang than to those of subgenus Ceratotropis. The relative positions of some genotypes to one another on the dendrogram and minimum spanning tree were discussed in regard to hybridisations aimed generating well-saturated genomic maps and interspecies transfer of desirable genes.     

Novel Genetic Resources in the Genus Vigna Unveiled from Gene Bank Accessions

The genus Vigna (Fabaceae) consists of five subgenera, and includes more than 100 wild species. In Vigna, 10 crops have been domesticated from three subgenera, Vigna, Plectrotropis, and Ceratotropis. The habitats of wild Vigna species are so diverse that their genomes could harbor various genes responsible for environmental stress adaptation, which could lead to innovations in agriculture. Since some of the gene bank Vigna accessions were unidentified and they seemed to be novel genetic resources, these accessions were identified based on morphological traits. The phylogenetic positions were estimated based on the DNA sequences of nuclear rDNA-ITS and chloroplast atpB-rbcL spacer regions. Based on the results, the potential usefulness of the recently described species V. indica and V. sahyadriana, and some wild Vigna species, i.e., V. aconitifolia, V. dalzelliana, V. khandalensis, V. marina var. oblonga, and V. vexillata, was discussed.     

Isoenzyme Variation in Asian Beans

Electrophoretic variation of isoenzyme characters encoded by 20 gene loci has been studied in 9 species of Asian beans, comprising subgenus Ceratotropis of the genus Vigna. Four species of hypogeal germination type, V. angularis, V. umbellata, V. dalzelliana and V. minima, are shown to form a distinct monophyletic group in the subgenus, sharing common electromorphs of two major isoenzymes of aspartate aminotransferase. V. glabrescens is confirmed to be an allotetraploid derivate of two diploids closely related to V. radiata and V. umbellata, but divergent from their contemporary accessions analyzed. V. trilobata is the most variable species of the subgenus in isoenzyme characters. It reveals intraspecific differentiation at several isoenzyme loci correlated with the seed morphology and geographical localization.     

Molecular phylogeny of the subgenus Ceratotropis (genus Vigna, Leguminosae) reveals three eco-geographical groups and Late Pliocene-Pleistocene diversification: evidence from four plastid DNA region sequences

Background and Aims

The subgenus Ceratotropis in the genus Vigna is widely distributed from the Himalayan highlands to South, Southeast and East Asia. However, the interspecific and geographical relationships of its members are poorly understood. This study investigates the phylogeny and biogeography of the subgenus Ceratotropis using chloroplast DNA sequence data.

Methods

Sequence data from four intergenic spacer regions (petA-psbJ, psbD-trnT, trnT-trnE and trnT-trnL) of chloroplast DNA, alone and in combination, were analysed using Bayesian and parsimony methods. Divergence times for major clades were estimated with penalized likelihood. Character evolution was examined by means of parsimony optimization and MacClade.

Key Results

Parsimony and Bayesian phylogenetic analyses on the combined data demonstrated well-resolved species relationships in which 18 Vigna species were divided into two major geographical clades: the East Asia–Southeast Asian clade and the Indian subcontinent clade. Within these two clades, three well-supported eco-geographical groups, temperate and subtropical (the East Asia–Southeast Asian clade) and tropical (the Indian subcontinent clade), are recognized. The temperate group consists of V. minima, V. nepalensis and V. angularis. The subtropical group comprises the V. nakashimae–V. riukiuensis–V. minima subgroup and the V. hirtella–V. exilis–V. umbellata subgroup. The tropical group contains two subgroups: the V. trinervia–V. reflexo-pilosa–V. trilobata subgroup and the V. mungo–V. grandiflora subgroup. An evolutionary rate analysis estimated the divergence time between the East Asia–Southeast Asia clade and the Indian subcontinent clade as 3·62 ± 0·3 million years, and that between the temperate and subtropical groups as 2·0 ± 0·2 million years.

Conclusions

The findings provide an improved understanding of the interspecific relationships, and ecological and geographical phylogenetic structure of the subgenus Ceratotropis. The quaternary diversification of the subgenus Ceratotropis implicates its geographical dispersal in the south-eastern part of Asia involving adaptation to climatic condition after the collision of the Indian subcontinent with the Asian plate. The phylogenetic results indicate that the epigeal germination is plesiomorphic, and the germination type evolved independently multiple times in this subgenus, implying its limited taxonomic utility.     

Isoenzyme variation in the generaPhaseolus andVigna (Fabaceae) in relation to their systematics: Aspartate aminotransferase and superoxide dismutase

Evolutionary variation of aspartate aminotransferase and superoxide dismutase isoenzymes in 14 wild and cultivated species ofPhaseolus andVigna has been studied by electrophoresis and isoelectric focusing in polyacrylamide gel. The American cultivated beans of the genusPhaseolus s. str.,P. vulgaris, P. coccineus, P. lunatus andP. acutifolius, form a homogeneous group with only minor isoenzyme variation. The genusVigna, on the contrary, proves to be heterogeneous in isozyme characters. Several clusters of taxa can be distinguished in close correspondence with modern treatments of the genus. The isoenzyme data support the inclusion of the Asian Azuki beans of subg.Ceratotropis inVigna, but argue against the transfer of the S. American speciesP. adenantha. The cowpea complexV. unguiculata s. lato of sect.Catiang forms an uniform and isolated group, distinct from other sections of subg.Vigna, and shows affinity toPhaseolus s. str. by some isoenzymes. It is suggested to removeV. unguiculata s. lato from subg.Vigna and to recognize it as a separate subg.Catiang (DC.)Jaaska & Jaaska, stat. nov.     

Direct shoot regeneration from cotyledonary nodes as a marker for genomic groupings within the Asiatic Vigna (subgenus Ceratotropis {Piper} Verdc.) species

In vitro culture of cotyledonary node (cn)explants, decapitated and intact seedlings of four different AsiaticVigna species (germinated and subcultured in MS-B5 mediumwith 1.0 mgl^–1 BA) resulted in axillaryshoot formation only from the epigeal V. radiata and thehypogeal but allotetraploid V. glabrescens. The hypogealspecies V. angularis and V. umbellatafailed to exhibit this response. Shoot decapitation invivopromoted similar response only in V. radiata, indicatingthat in vitro culture in BA-supplemented medium isrequiredby V. glabrescens to achieve the same response.Histological observations of the cn explants from 4-d-oldin-vitro-germinated seedlings at d 0(inoculation day), d 4 and d 8 (after inoculation) revealed the formation ofprimary axillary shoots (pas) in both V. radiata andV. glabrescens. Secondary axillary branching at the baseofthe pas was observed at 8 d. Further examination by scanningelectron microscope (SEM) confirmed the presence of shoot buds enveloped by atleast two leaf primordia in the explants at d 0 in all epigeal species namelyV. radiata, V. mungo and V.aconitifolia together with the hypogeal but allotetraploidV. glabrescens. Consistently, these structures were absentin V. angularis and V. umbellata.Present histological and SEM observations support the previous findings ofAvenido and Hattori (Plant Cell Tissue Organ Cult, 1999) that the induction ornon-induction of shoots directly from the nodes of invitro-cultured cn explants is a new marker corresponding to thegenomic grouping within the Asiatic Vigna species. Basedonhybridization studies, Dana (Breeding Methods for Improvement of Crops, 1980)designates AA, A₁A₁ and A₁A₁/- toall epigeal, hypogeal and the hypogeal but allotetraploid AsiaticVigna species, respectively. Moreover, these findingsproved that the differential in vitro regenerationresponse(i.e., response to BA) arises from inherent anatomical and developmentaldifferences, and is supportive of the genomic grouping within subgenusCeratotropis of the genus vigna.     

Molecular phylogeny of Phalaenopsis Blume (Orchidaceae) based on the internal transcribed spacer of the nuclear ribosomal DNA

The internal transcribed spacer (ITS1, 5.8S rDNA, and ITS2) region of nuclear ribosomal DNA (nrDNA) was sequenced from 53 species, which represent most of the living species diversity in the genus Phalaenopsis (Orchidaceae). A phylogeny was developed for the genus based on the neighbor-joining and maximum parsimony analyses of molecular data. Results of these analyses provided support for the monophyly of the genus Phalaenopsis and concurred in that the genera Doritis and Kingidium should be treated as being parts of the genus Phalaenopsis as suggested by Christenson (2001). Within the genus Phalaenopsis, neither subgenera Aphyllae nor Parishianae were monophyletic, and they were highly clustered with subgenus Proboscidioides plus sections Esmeralda and Deliciosae of subgenus Phalaenopsis based on ITS data. Those species also have the same characters of morphology of four pollinia and similar biogeographies. Furthermore, neither subgenus Phalaenopsis nor Polychilos was monophyletic. Within the subgenus Phalaenopsis, only section Phalaenopsis was highly supported as being monophyletic. As for the subgenus Polychilos, only section Polychilos was moderately supported as being monophyletic. In conclusion, the present molecular data obtained from the ITS sequence of nrDNA of the genus Phalaenopsis provide valuable information for elucidating the phylogeny of this genus.     

TrnL–trnF Intergenic Spacer and trnL Intron Define Major Clades Within Luzula and Juncus (Juncaceae): Importance of Structural Mutations

Seven hundred fifty-two to one thousand ninety-seven base pairs of the trnL intron and trnL–trnF intergenic spacer of the chloroplast DNA of 55 Juncaceae taxa (Juncus, Luzula, Rostkovia, and Oxychloë) was sequenced. Seventeen structural mutations (13 indels marked A to M, 3 parts of the trnF pseudogene, and insertion o within a pseudogene) within the chloroplast trnL–trnF region were examined as possible indicators for phylogenetic relationships in Juncaceae. Juncus trifidus (section Steirochloa) was clearly separated from the other taxa by two large (>80 bp) indels. The Southern Hemisphere clade was strongly supported by a unique insertion (334 bp) in the trnL intron. The monophyly of Luzula was supported by three small (<10 bp) indels in the trnL-F spacer. They were found in all 22 examined members that represent the taxonomic and geographical diversity of the genus Luzula. A tandemly duplicated tRNA pseudogene was found in the Juncus subgenus Juncus species and is supported by four small unique indels too. The acceptor stem and D-domain-encoding regions are separated by a unique 8-bp insertion. The T-domain and acceptor stem-encoding regions were not found in the pseudogene repeats. Only the Juncus sections Ozophyllum and Iridifolii contain the 5 acceptor stem, D-domain, and anticodon domain of the tRNAF encoding DNA. The structural mutations in the trnL intron and the trnL–trnF intergenic spacer are useful for phylogenetic reconstruction in the Juncaceae.     

Differences in shoot regeneration response from cotyledonary node explants in Asiatic Vigna species support genomic grouping within subgenus Ceratotropis (Piper) Verdc.

The efficiency of any plant regeneration system lies in part in its wide applicability to diverse genotypes. In Asiatic Vigna, cotyledon and cotyledonary node explants from 4-day-old seedlings of 27 genotypes were cultured in a medium consisting of MS salts, B5 vitamins, 3.0% sucrose and 1.0 mg l^-1 BA. Direct and efficient multiple shoot regeneration (80–100%) from the cotyledonary nodes was obtained in all epigeal species namely radiata, mungo, aconitifolia, subspecies radiata var. sublobata, mungo var. silvestris and in the hypogeal but allotetraploid glabrescens. In contrast, two other hypogeal species V. angularis and V. umbellata failed to initiate shoots from the nodes. However, adventititious shoots developed at the basipetal cut (hypocotyl) in 35–67% of V. angularis explants. These results provide evidence in support of the existing genomic grouping within subgenus Ceratotropis, which designates AA, A₁A₁ and A₁A₁/- to epigeal, hypogeal and the allotetraploid species, respectively. Mean shoot production ranged from 3.3 to 10.4 shoots per explant during the first subculture and varied significantly among the responsive genotypes within 4 species. Additional shoots were obtained in all genotypes after subsequent subculture. However, cotyledons were not as regenerable as cotyledonary node explants. Although significant differences in rooting were observed among the shoots of the 15 genotypes, the response was generally higher in MS basal medium (MSO) than in MS with 1.0 mg l^-1 IAA. Regenerated plants were successfully transferred to soil (50–100% survival rate) and all surviving plants were reproductively fertile. This revised version was published online in June 2006 with corrections to the Cover Date.     

Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications

The evolution of 5S rRNA gene unit (5S gene unit) was studied among the ten species belonging to Vigna subgenus Ceratotropis by sequencing and analyzing the intra- and inter-specific sequence heterogeneity. The 5S unit from these species ranged from 214 to 342 bp in length as a result of several indels in the intergenic spacer (IGS) region. A large deletion (>100 bp) was found specifically in the IGS of V. radiata accessions. IGS showed high sequence variation with more than 50% polymorphic and 35.4% parsimony informative sites. However, the coding region (5S gene) was highly conserved, both in length and in sequence. Intra-genomic and intra-specific divergence was observed among some species, which indicated that the 5S unit is evolving at different rates among the Vigna species. Most Vigna species harbored one type of 5S unit indicating complete homogenization among them. Vigna glabrescens, a tetraploid species, also showed single type of 5S rDNA from only one of the diploid progenitor indicating loss or homogenization of the other type. However, V. nakashimae and V. riukiuensis harbored multiple, diverse, ‘intra-genomic 5S types’ indicating that 5S rDNA is not completely homogenized by concerted evolution and is still evolving. In general, the phylogeny based on IGS sequences was in agreement with many of the earlier reports except some surprising observations such as, V. glabrescens clustered with V. mungo in section Ceratotropis and unlike most of the species, wild and cultivated types of V. umbellata were present in different subclusters. Presence of divergent 5S sequences in V. nakashimae and V. riukiuensis caused errors in phylogeny reconstruction at species level and suggested a horizontal ‘gene transfer’ as a result of inter-species hybridization. The comparative analysis showed that 5S IGS sequences have better phylogenetic utility than chloroplast DNA sequences, such as atpB-rbcL and is comparable to ITS1 and ITS2 in this respect.     

Carex, subgenus Carex (Cyperaceae) – A phylogenetic approach using ITS sequences

To evaluate the sectional classification in Carex, subgenus Carex, the ITS region of 117 species belonging to 32 sections was analyzed with Neighbor Joining (NJ) and Markov chain Monte Carlo (MCMC) methods. In our analyses (1) species of subgenus Indocarex appear as a statistically well supported group within subgenus Carex. (2) The representatives of sections Vesicariae, Hirtae, Pseudocypereae, Ceratocystis, Spirostachyae, Bicolores, Paniceae, Trachychlaenae, Scirpinae, Atratae and Albae group in statistically supported clades with higher support in MCMC than in NJ. (3) C. rariflora clusters with representatives of section Limosae, however only weakly supported. (4) Taxa of section Phacocystis are divided in two statistically supported subclusters that are closely related to a core group of section Hymenochlaenae. (5) Species of sections Montanae, Pachystylae, Digitatae, Phacocystis, Rhomboidales, Careyanae and Frigidae are segregated into two or more clusters each. (6) Five species of section Frigidae cluster together, whereas the seven others are in scattered positions. Based on these results, delimitation of sections is discussed.     

Nuclear DNA contents, rDNAs, and karyotype evolution in subgenus Vicia: III. The heterogeneous section Hypechusa

Summary. Nuclear DNA contents, automated karyotype analyses, and sequences of internal transcribed spacers from ribosomal genes have been determined in the species belonging to section Hypechusa of the subgenus Vicia. Karyomorphological results and phylogenetic data generated from the comparison of rDNA (genes coding for rRNA) sequences showed that sect. Hypechusa is not monophyletic; however, some monophyletic units are apparent (one including Vicia galeata, V. hyrcanica, V. noeana, and V. tigridis, another including V. assyriaca, V. hybrida, V. melanops, V. mollis, and V. sericocarpa), which partly correspond to morphology-based infrasectional groups. The relationships among these species and the species in sections Faba, Narbonensis, Bithynicae, and Peregrinae have been also investigated. Correspondence and reprints: Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, via San Camillo de Lellis, 01100 Viterbo, Italy.     

Effect of a gap on gene flow between otherwise adjacent transgenic <Emphasis Type="Italic">Brassica napus</Emphasis> crops

The chloroplast DNA diversity of 33 accessions belonging to 16 species of five sections in Allium subgenus Rhizirideum was studied by analysing the sequence of three fragments: the trnL-F intergenic spacer, the rps 16 intron and rbcL (rubisco large subunit). The three sections Cepa, Schoenoprasum and Rhizirideum, representing the majority of the included species, each possess a separate clade after phylogenetic analysis. Exceptions to this general rule are the placement of Allium pskemense (section Cepa) connected to Allium senescens (section Rhizirideum) and Alium roylei, taking an intermediate position between sections Cepa and Schoenoprasum. Both species were located in their own section after nuclear DNA analysis. A range of crossing experiments has been carried out. The different position of A. roylei when comparing cpDNA and nDNA diversity was not confirmed with the production of hybrid seeds after crossing A. roylei with species other than those of section Cepa. The different position of A. pskemense in the cpDNA and the nDNA tree can not be compared to its crossability, since only a few crossing experiments are reported for this species. The hypothesis that a shorter distance between two species in a cpDNA tree compared to their distance in a nDNA tree will indicate interfertility at a certain level, is neither confirmed nor rejected by the currently available results.Communicated by R. Hagemann     

Phylogeny of Caragana (Fabaceae) based on DNA sequence data from rbcL, trnS–trnG, and ITS

Phylogenetic relationships of 48 species of Caragana (Fabaceae: tribe Hedysareae) and one representative each of Astragalus, Calophaca, Halimodendron, and Hedysarum are estimated from DNA sequences of the rbcL gene, trnS–trnG intron and spacer, and ITS region. At least one representative of all five sections and 12 series within Caragana are included. Analyses yielded strongly supported clades corresponding to sections Caragana, Bracteolatae, and Frutescentes. The species of section Jubatae are distributed among three strongly supported clades, i.e., one with the species of section Bracteolatae, another with two species of section Spinosae, and a third as sister to section Frutescentes. All but the last of these six clades are corroborated by at least one unambiguously traced morphological character. The placement of the other four species of section Spinosae are not well supported and lack unambiguous morphological synapomorphies, and the samples of Calophaca and Halimodendron nest within Caragana with weak support.     

Phylogenetic relationships in Carex, subgenus Vignea (Cyperaceae), based on ITS sequences

To evaluate the sectional classification in Carex, subgenus Vignea, the ITS region of 58 species of 20 sections was analyzed with Neighbor Joining (NJ) and Markov chain Monte Carlo (MCMC) methods. Sections Dioicae, Physodeae and Ovales are found to be monophyletic, with C. bohemica well integrated in the section Ovales. Section Heleonastes turns out to be monophyletic, if C. canescens is treated separately in section Canescentes. Section Elongatae is monophyletic, but C. remota is placed in section Remotae and C. bromoides in section Deweyanae. In both analyses, six representatives of section Arenariae cluster together in a terminal group, whereas C. disticha, C. repens and C. siccata form a basal cluster. C. maritima, as the only member of section Incurvae, shares this basal position. C. chordorrhiza is ascribed to section Chordorrhizeae and not ascribed to the paraphyletic section Divisae. C. vulpina and C. otrubae are assigned to section Vulpinae and separated from the heterogeneous section Stenorhynchae. The other members of sections Divisae, Muehlenbergianae, Multiflorae and Stenorhynchae are scattered throughout the trees. The representatives of section Foetidae are dispersed in both analyses, section Paniculatae appears to be non-monophyletic in the molecular results as well. The subgenus appears subdivided in at least four larger subgroups in all analyses. Whereas these subgroups are strongly supported, the relationships between these subgroups remain only poorly resolved.     

Molecular phylogeny of Alnus (Betulaceae), inferred from nuclear ribosomal DNA ITS sequences

The nuclear ITS region of 19 species of Alnus was amplified and sequenced. The inferred molecular phylogeny shows that all species of the genus Alnus form a monophyletic group close to Betula and that the fundamental dichotomy within the genus lies between the subgenera Alnaster and Gymnothyrsus, sensu Murai (1964). The subgenus Alnaster appears to be basal in the genus, based on archaism of morphological features, and branching close to the root of the trees due to low ITS divergence from genus Betula. The monophyly of the section Clethropsis is not supported by the present data: Alnus nepalensis is positioned in the subgenus Gymnothyrsus, away from A. nitida and A. maritima. Surprisingly, A. formosana sect. Japonicae is closely tied to A. maritima sect. Clethropsis, with which it shares few morphological traits, and is separate from A. japonica sect. Japonicae with which it shares many traits. An increase in substitution rate is noted in the group comprising A. formosana, A. maritima and A. nitida relative to the rest of the genus, which appears to have had, on the average, a very slow mutation rate. Alnus glutinosa, the designated type for the genus, appears to be representative of the genus both for morphological characters and evolutionary rate. North-East Asia is comforted in its position of origin of the genus since not only does it have the highest number of species and representatives in all deep branching lineages, there are also fewer transcontinental migrations when a North-East Asian ancestor is postulated than when a North American ancestor is postulated.     

Chemotaxonomy and evolution of Plantago L.

In continuation of our investigations of the genus Plantago L. (Plantaginaceae), sixteen species were investigated with respect to water-soluble glycosides. The iridoids auroside, strictoloside and globularicisin, as well as poliumoside, 3-[(4--D-glucopyranosyloxy)phenyl]propionic acid and 2-[4-(-D-glucopyranosyloxy)phenyl]acetic acid were isolated from Plantago for the first time. The latter compound has not previously been isolated as a natural product. Sorbitol was the main carbohydrate in all the species investigated. The distribution of iridoids correlates well with the morphological classification of Rahn and also with a recently published molecular phylogenetic study of nuclear ribosomal and plastid DNA sequences. A new chemotaxonomic finding is an abundance of iridoid glucosides present in one of the two groups within subgenus Coronopus section Coronopus, while the other group lacks iridoids, supporting a subdivision of this section. Moreover, in subgenus Albicans, 10-benzoylcatalpol is a characteristic constituent of section Gnaphaloides, while the corresponding cinnamoyl ester globularin occurs in section Lanceifolia. In biosynthetic experiments, labelled epideoxyloganic acid and deoxygeniposidic acid were incorporated into aucubin and geniposidic acid in Plantago ovata, consistent with earlier findings, but no incorporation into asperuloside was observed. The evolution of biosynthetic pathways in Plantago is discussed.     

Molecular phylogeny ofNothofagus (Nothofagaceae) based on theatpB-rbcL intergenic spacer of the chloroplast DNA

The genusNothofagus is distributed in the Southern Hemisphere from South America to Oceania, and its distribution has been assumed to be formed by continental drift by means of Gondwana break-up during the Mesozoic era. The phylogeny of the genus was elucidated by the sequences ofatpB-rbcL intergenic spacer of cpDNA for the better understanding of its evolution and biogeography. The phylogeny ofNothofagus corresponded completely to the pollen morphology which recognizes four pollen types in extant species, and agrees well with the taxonomic system of Hill and Read (1991) although there, the subgenusNothofagus showed in unresolved polytomy. The topology of the phylogenetic tree reveals that subgenusLophozonia was derived first, and thenFuscospora, Nothofagus andBrassospora. Species from South America and New Zealand were assigned to each cluster according to their pollen morphology. Therefore, diversification ofNothofagus should have already proceeded at the subgenus level before the completion of Gondwana break-up Tropical species distributed in New Guinea and New Caledonia whose evolutionary history has been controversial were revealed to be a derived group. All five New Caledonian species formed a monophyletic group with very few sequence divergences in the intergenic spacer of cpDNA, thus showing rapid adaptive radiation in the island. Evolutionary trends of several morphological traits ofNothofagus are discussed. The evolution of valve number of cupules, number of nuts per cupule, and habit of leaf-fall (evergreen or deciduous) which are diversified in the genus, were revealed as having occurred several times as the result of convergence.     

Phylogenetic analysis of Theobroma (Sterculiaceae) based on Kunitz-like trypsin inhibitor sequences

Trypsin inhibitor gene sequences were used to investigate the phylogenetic relationships among Theobroma and Herrania species, considered as sister-groups, with particular interest on the monophyly and infra-generic relationships of Theobroma. The presumed amino acid sequences of 23 analyzed samples, from 11 Theobroma and three Herrania species, comprising all sections from both genera, demonstrated a high similarity with a previously characterized T. cacao Kunitz trypsin inhibitor. The trypsin inhibitor gene accumulated mutations at faster rate than prior analyzed nuclear or chloroplastic genes. None of the sequences presented introns. The phylogeny of the trypsin inhibitor sequences was congruent with the phylogenetic hypotheses of the Theobroma and Herrania species based on morphology. The monophyly of Theobroma was not strongly supported, corroborating previously described absence of obvious synapomorphies for Theobroma. The species grouped consistently according to genus and section. The monophyly of all Theobroma sections was supported, except for section Glossopetalum, which was paraphyletic to section Andropetalum. Evidences sustain that T. mammosum may be included into section Glossopetalum. The potential use of trypsin inhibitor gene sequences in phylogenetic studies of Theobroma was demonstrated.We acknowledge the financial support by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); International Foundation of Science (IFS), and the permission from Empresa Brasileira de Pesquisas Agropecuária (EMBRAPA); Comissão Executiva do Plano da Lavoura Cacaueira (CEPLAC) to use the plant material. We thank the useful comments from the reviewers.     

Cladistic and phenetic analysis of relationships in Vicia subgenus Vicia (Fabaceae) by morphology and isozymes

 Variation of 80 multistate morphological characters and isozymes encoded by 13 loci among 23 vetch species of the type subgenus of the genus Vicia in comparison with V. dumetorum, V. pisiformis and V. sylvatica of the subgenus Cracca is described and analyzed with cladistic parsimony and phenetic neighbour-joining methods by using two different ways of coding. Morphological analyses showed the subgenus Vicia monophyletic and revealed subgroups in a general agreement with traditionally recognized sections, except showing V. faba nested within section Narbonensis and ambiguity in the position of V. lathyroides and V. bithynica. Parsimony analysis of orthozymes as presence/absence characters revealed in the subgenus two basic monophyletic clades: 1) V. faba and three species of the section Peregrinae, V. michauxii, V. aintabensis and V. peregrina, in one subclade linked with species of the Narbonensis and Hyperchusa sections together with V. pisiformis of subgenus Cracca in a second subclade; 2) species belonging to sections Vicia, Sepium, Pseudolathyrus and Lathyroides together with V. sylvatica of the subgenus Cracca. Neighbour-joining analysis of orthozymes revealed the same two basic groups, differing only in the relative position of some species in subclusters. Both isozyme analyses showed paraphyly of the subgenera Vicia and Cracca. Parsimony analysis of orthozymes as character states of isozymes yielded a largely unresolved strict consensus cladogram of 209 most parsimonious trees, and reweighting of characters failed to produce a stable tree. Phylogenetic congruence and discordance among morphological and isozyme analyses, coding ways, homoplasy and weighting of characters are discussed. Received November 20, 2001 Accepted January 31, 2002