Genetic relations among basil taxa (Ocimum L.) based on molecular markers, nuclear DNA content, and chromosome number

Twenty-eight basil accessions including six Ocimum species and six botanical varieties or cultivars of O. basilicum were studied using molecular markers, nuclear DNA content, and chromosome counting. This is the first study reporting the nuclear DNA content in the genus Ocimum. The results supported the existence of more infrageneric groups within the genus. The section Ocimum was further divided into two separate clades. The first clade contained the accessions belonging to different botanical varieties and cultivars of O. basilicum as well as O. minimum, indicating that the separate species rank of O. minimum was not justified. The second clade, comprising O. americanum, O. africanum, and two O. basilicum var. purpurascens accessions, could represent a set of allopolyploid species sharing some common parental genomes. O. tenuiflorum was the most divergent species according to genetic distance; it had the smallest genome size, organized in small chromosomes, and the lowest chromosome number. Chromosome data obtained in our research could indicate that the basic chromosome number for species belonging to section Ocimum is x = 12. This suggestion implies that species belonging to O. basilicum clade are tetraploids, while species belonging to O. americanum clade are hexaploids. It seems that the basic chromosome number for O. gratissimum could be x = 10 and for O. tenuiflorum x = 9. The differences in genome size and chromosome number among Ocimum species indicate that evolution of their genomes was accompanied by both sequence deletion/amplification and chromosome rearrangements and polyploidization.     

Phylogenetic relationships and infrageneric classification of Epidendrum subgenus Amphiglottium (Laeliinae, Orchidaceae)

Epidendrum L. is the largest genus of Orchidaceae in the Neotropical region; it has an impressive morphological diversification, which imposes difficulties in delimitation of both infrageneric and interspecific boundaries. In this study, we review infrageneric boundaries within the subgenus Amphiglottium and try to contribute to the understanding of morphological diversification and taxa delimitation within this group. We tested the monophyly of the subgenus Amphiglottium sect. Amphiglottium, expanding previous phylogenetic investigations and reevaluated previous infrageneric classifications proposed. Sequence data from the trnL-trnF region were analyzed with both parsimony and maximum likelihood criteria. AFLP markers were also obtained and analyzed with phylogenetic and principal coordinate analyses. Additionally, we obtained chromosome numbers for representative species within the group. The results strengthen the monophyly of the subgenus Amphiglottium but do not support the current classification system proposed by previous authors. Only section Tuberculata comprises a well-supported monophyletic group, with sections Carinata and Integra not supported. Instead of morphology, biogeographical and ecological patterns are reflected in the phylogenetic signal in this group. This study also confirms the large variability of chromosome numbers for the subgenus Amphiglottium (numbers ranging from 2n = 24 to 2n = 240), suggesting that polyploidy and hybridization are probably important mechanisms of speciation within the group.     

Evolution of Iris subgenus Xiphium based on chromosome numbers, FISH of nrDNA (5S, 45S) and trnL–trnF sequence analysis

The subgenus Xiphium is one of the six infrageneric divisions of the genus Iris. Chromosome numbers of six of the seven Xiphium species are known. Here the aim was to infer genetic and phylogenetic relationships based on chromosome numbers, chromosome markers and plastid sequences. Chromosomal locations of 5S and 45S rDNA loci were determined in 19 populations of the 7 species by fluorescence in situ hybridization (FISH). Additionally, the trnL–trnF plastid spacer was sequenced and a phylogenetic analysis performed. Based on chromosome markers, subgenus Xiphium species were classified into four groups that differed in the number and locations of both types of nrDNA: (1) I. tingitana (2n = 28), I. filifolia (2n = 30, 34) and I. xiphium (2n = 34), (2) I. juncea (2n = 32) and I. boissieri (2n = 36), (3) I. serotina (2n = 34) and (4) I. latifolia (2n = 42). Although the trnL–trnF phylogeny was not fully resolved, the sequence analysis showed a well-supported subgroup of I. filifolia, I. tingitana and I. xiphium, as well as I. juncea. FISH physical maps of the Iris subgenus Xiphium taxa are species dependent. I. filifolia, I. tingitana and I. xiphium are very closely related species and share cytogenetic characteristics. Disploidy appears to have been central in the evolution of this subgenus, given a series of chromosome numbers (2n = 28, 30, 32, 34, 36, 42) and our phylogenetic results. Clear differences were found among European and African populations of I. filifolia. A different taxonomic treatment of I. filifolia is supported for populations on both sides of the Strait of Gibraltar.     

Taxonomic studies in Chiloscyphus Corda (Jungermanniales: Lophocoleaceae) based on nrITS sequences and morphology

Maximum parsimony and likelihood analyses of 40 Lophocoleaceae nrITS sequences and 6 Plagiochilaceae sequences (outgroup) lead to a robust phylogeny of Chiloscyphus. Four main lineages are assigned to as Chiloscyphus subgenera Chiloscyphus, Lophocolea, Connati and Notholophocolea. Chiloscyphus subgen. Connati is resolved sister to the remainder of this genus. Chiloscyphus subgenus Lophocolea is subdivided into sections Heterophylli (incl. sect. Semiteretes, syn. nov.), Lophocolea, Microlophocolea, and Novae-Zeelandiae. Five accessions of Chiloscyphus pallescens with a chromosome number of n = 18 form a robust monophyletic lineage that is placed sister to a well supported clade with 4 accessions of C. polyanthos [n = 9]. Chiloscyphus mandonii is placed in the synonymy of C. latifolius.     

Karyological data of 47 accessions of 28 Artemisia (Asteraceae, Anthemideae) species from Iran, with first new reports for Iranian populations and first absolute counts in three species

Somatic chromosome numbers of 47 accessions representing 28 Artemisia species are provided from Iran. Two basic chromosome numbers, x = 8, 9, each with diploid, tetraploid and hexaploid levels, were found. Different chromosome numbers, 2n = 16, 16 + 1B, 16 + 5B, 32, 48, and 2n = 18, 18 + 1B, 19, 36, 36 + 1B, 36 + 2B, 37, 49 + 2B, 49 + 3B, 51 + 6B, 54, 54 + 1B, 54 + 3B, 54 + 5B, in studied accessions were identified. Chromosome numbers are reported for the first time in three species, counts in four species are new for Iran, and other counts have been thoroughly compared to previous data. Forty percent of the studied accessions are polyploid and B-chromosome(s) are reported in 17 % of accessions. Aneuploidy and aneusomy are other relevant cytological phenomena. Some karyological parameters, total karyotype length, karyotype formula, mean value of centromeric indices, mean arm ratio, A ₁ and A ₂ indices, were estimated to characterize the karyotypes numerically. A ₁ and A ₂ indices showed that karyotypes tend to be asymmetric in polyploid and dysploid taxa. PCA analysis of all karyological parameters has shown some systematic and evolutionary implications. The consideration of all these chromosome numbers and cytogenetic mechanisms has led us to infer the different patterns of chromosomal evolution in the genus.     

Chromosome numbers in Pinguicula (Lentibulariaceae): survey, atlas, and taxonomic conclusions

Our study (survey, atlas of 136 microphotographs and 67 drawings) points out the actual chromosome numbers of 82 taxa of the genus Pinguicula L. They were gathered from literature and critically examined. In addition, numerous counts are published for the first time. They represent about 80% of all the taxa known. The basic chromosome numbers are x = 6, 8, 9, 11, and 14; the ploidy levels are 2n (diploid), 4n (tetraploid), 8n (octoploid) and 16n (hexadecaploid). The basic number x = 6 is a one-off, x = 8 and 11 are the most frequent in the genus; x = 14 indicates a hybridogenous differentiation process in the past. The caryological differentiation—chromosome numbers and ploidy level—is discussed with regard to distribution pattern, growth type, and infrageneric classification (at the level of sections).     

The systematic value of nuclear genome size for “all” species of Tulipa L. (Liliaceae)

Nuclear genome size, as measured by flow cytometry with propidium iodide, was used to investigate the relationships within the genus Tulipa L. (Liliaceae). More than 400 accessions representing 123 taxa from mainly wild-collected plants were investigated. Most species of Tulipa have the same basic chromosome number, 2n = 2x = 24. However, the somatic DNA 2C value (2C) is shown to range from 32 to 69 pg for the diploids. The largest genome contains roughly 3.4 × 10¹⁰ more base pairs than the smallest and has chromosomes that are more than twice as large. These large differences in the amount of nuclear DNA predict that the hybrids, if any arise, are usually sterile. Depending on the size of the total genome, 1 pg amounts to several thousand genes. Moreover, genome sizes are evaluated here in combination with available morphological, geographical, and molecular data. Therefore, the taxonomy proposed here is not a single-character taxonomy based on genome size alone. The genus Tulipa, as here determined, has 87 species, 29 more than accepted by van Raamsdonk et al. [Acta Hort (ISHS) 430:821–828, 1997], but including 25 species that were not available to them. Of these 87 species, 28 were not seen by Hall (The genus Tulipa, The Royal Horticultural Society, London, 1940) in a living state and placed by him in an addendum. Species of the subgenus Clusianae (Baker) Zonn. differ strongly in nuclear DNA content (DNA 2C value), 32 versus 40–68 pg for all other tulips, and are placed here in a separate subgenus. Also Orithyia, the only group with a style and with only 38–39 pg is placed in a separate subgenus. Therefore, all tulips are attributed to four subgenera, Clusianae (Baker) Zonn., Tulipa, Eriostemones Raamsd., and Orithyia (D. Don) Baker and divided further into 12 sections. Seven of the eight series of section Eichleres (A.D. Hall) Raamsd. are now placed in four sections: (1) section Lanatae (Raamsd.) Zonn., mainly confined to species from the Pamir-Alay and including series Lanatae Raamsd., (2) section Multiflorae (Raamsd.) Zonn. (including series Glabrae Raamsd.), (3) section Vinistriatae (Raamsd.) Zonn. (including series Undulatae Raamsd.), and (4) section Spiranthera Vved. ex Zonn. and Veldk. Triploids, tetraploids, and pentaploids were found in several species. DNA content confirmed the close relationships of the species within the different sections. The rather similar looking and therefore often confused T. armena Boiss. (51.8 pg), T. systola Stapf (56.3 pg), and T. julia K., Koch (61.6 pg) could be clearly distinguished. The same is true for T. biebersteiniana Schult. f. (56.9 pg), T. sylvestris ssp. australis (Link) Pamp. (62.0 pg), and T. primulina Baker (64.6 pg). T. doerfleri Gand. and T. whittalli (Dykes) Hall could be placed as polyploid forms of T. orphanidea Boiss. ex Heldr. On the basis of DNA content, a systematic association between T. julia K. Koch and the triploid T. aleppensis Boiss. and between T. systola Stapf and the triploid T. praecox Tenore was suggested. The new species T. lemmersii Zonn., Peterse, and de Groot is described, and four possible new species are indicated. Genome size as measured by using flow cytometry may conveniently be used to produce systematic data. It is applicable even in the case of dormant bulbs or sterile plants for monitoring the trade in bulbous species.     

Genetic relationship among Paspalum species of the subgenus Anachyris: Taxonomic and evolutionary implications

Paspalum is one of the most important genera of the Poaceae family due to its large number of species and diversity. The subgenus Anachyris comprises six species mainly from South America grouped together by sharing rare spikelet characteristics. A genetic analysis using ISSR markers, compared with the morphological and phenotypic variation observed in each one species, was used to establish genetic relationships among 40 accessions with several ploidy levels, belonging to 5 species of the subgenus Anachyris. Fourteen accessions of Paspalum malacophyllum (2x and 4x), 12 of P. simplex (2x, 3x, 4x and 6x), 4 of P. procurrens (2x and 4x), 4 of P. usterii (4x) and 6 of P. volcanensis (4x) were analysed. A total of 227 ISSR loci (98.7% polymorphic) were detected among all accessions, with variable loci number and percentages of polymorphism according to species delimitations. Six main groups were identified by cluster analysis based on Jaccard's genetic distance and UPGMA, four of which matched all the respective accessions of P. simplex, P. procurrens, P. usterii and P. volcanensis, while the other two were consistent with two different groups of accessions of P. malacophyllum, one involving most tetraploid accessions, and the other one grouping together a tetraploid and two diploid accessions. The distinctive morphological characteristics and the separate clustering of these tetraploid and diploid cytotypes suggest to consider a new multiploid species complex inside the subgenus Anachyris. Both cytotypes of P. procurrens, and the four co-specific cytotypes of P. simplex consistently clustered together forming two specific groups for the two multiploid taxons. This is in agreement with the existence of high phenotypic similarities between diploid and tetraploid cytotypes of P. procurrens, and among diploid, triploid, tetraploid and hexaploid cytotypes of P. simplex. Since the polyploid cytotypes of these species are reproduced by apomixis, the specific genetic clustering by ISSR markers and morphological and cytological results support the hypothesis that the two multiploid species were originated by autopolyploidy. Our results confirm previous studies suggesting a monophyletic origin for the subgenus Anachyris and are concordant with previous data regarding genomic homologies and phylogenetic analyses in the genus.     

Chromosome studies in southern species of Mimosa (Fabaceae,Mimosoideae) and their taxonomic and evolutionary inferences

In this work, chromosome numbers and karyotype parameters of 36 taxa of the genus Mimosa were studied, especially from the southern South America center of diversification. Results support that x = 13 is the basic chromosome number in the genus. Polyploidy is very frequent, ca. 56 % of the total of the studied species here are polyploid, confirming that polyploids are more frequent at higher latitudes. The most common ploidy levels found are 2x and 4x, but some species studied exhibit 6x and 8x. In different groups, several ploidy levels were found. Parameters of chromosome size show statistically significant differences between close species, and asymmetry index A ₂ exhibited low variation between them. It is possible to infer variations of chromosome size between diploids and tetraploids and between basal and derived taxa. The present studies confirm or reveal polyploidy in several groups of South America which are highly diversified in the southernmost area of distribution of the genus, such as sect. Batocaulon ser. Stipellares and sect. Calothamnos. Our data are discussed in a taxonomic context, making inferences about the origin of some polyploid taxa. Polyploidy could be an important phenomenon that increases the morphologic diversity and specific richness in southern South America. On basis of our data, it is possible to hypothesize hybridization between same-ploidy level or different ploidy level taxa. As already shown in the literature, our results confirm the importance of the polyploidy in the speciation of the genus.     

Karyological studies of Iranian <Emphasis Type="Italic">Allium</Emphasis> L. (Amaryllidaceae) species with focus on sect. <Emphasis Type="Italic">Acanthoprason</Emphasis>. 1. Mitotic chromosomes

Eighteen species and subspecies (34 accessions) of Allium sect. Acanthoprason and 11 species (17 accessions) belonging to other subgenera and sections of Allium were karyologically investigated and include first reports for 12 species. The examined plants of 47 accessions were diploid, three accessions of two species were tetraploid, and in the A. bisotunense accession, we found a mix of di- and triploid individuals. B chromosomes were found in 10 accessions. A basic chromosome number of x = 8 was confirmed for all investigated members of subg. Melanocrommyum and subg. Allium, and x = 9 for Allium tripedale of subg. Nectaroscordum. Idiograms were drawn for each accession, and metaphase images are presented illustrating observed chromosomal variations. Also, karyotype features and asymmetry parameters were calculated for all accessions. Chromosomal aberrations, e.g. aneuploid cells or loss of whole or parts of chromosome arms, were rarely observed. In general, the karyotypes showed low variation in inter- and intrachromosomal asymmetry especially inside of the taxonomic groups, though satellited chromosomes were good markers for subgenera and even specific for two studied sections of subg. Allium. Six different types of satellites were recognized, two of them were newly described: Type P was prevalent in subg. Melanocrommyum, and type O in sect. Codonoprasum. Statistical analyses were performed on five karyological parameters to test correct relationships and also to test previous grouping hypotheses. Although our data confirm distinct karyological characters for the subgenera investigated, the remarkable morphological diversity inside of subg. Melanocrommyum is not mirrored by striking karyological differences.     

Bertilia — A new monotypic genus in the Senecioneae (Asteraceae) from South Africa

The unusual disjunct distribution of the yellow-flowered, radiate, Northern Cape endemic Emilia hantamensis J.C.Manning & Goldblatt, relative to the other Emilia species in southern Africa, prompted investigation into its phylogenetic position and relationships. Phylogenies based on the ITS and trnL–trnF regions reveal that it is not a member of the genus Emilia but belongs in a well-supported clade with Bolandia, a genus comprising five species mainly from the Western and Northern Cape, and the monotypic genera Stilpnogyne and Mesogramma. It is placed sister to Bolandia and its cypselas match those of Bolandia in shape, colour and indumentum, except for a distinct ridge of hairs on the inner rib of the ray cypselas. It is further distinguished from Bolandia by its annual habit and conical disc floret style apices and obtuse to rounded ray floret style apices. It is recognised and described here as a new monotypic genus, Bertilia Cron with the single species B. hantamensis (J.C.Manning & Goldblatt) Cron.     

A cyto-evolutional study of Campanumoea Blume (Campanulaceae) and a possible pathway for secondary karyotype formation

Campanumoea is a small genus in the family Campanulaceae, with species divided into sections Campanumoea and Cyclocodon. Sixteen accessions from Campanumoea and related genera native to China were used to study their karyotype. The results showed that chromosome characteristics were different between the two sections. For Campanumoea, the karyotypic formula was 2n = 2X = 2m + 12sm + 2st = 16,3A and for Cyclocodon it was 2n = 2X = 6m + 12sm = 18,3B. These data, combined with chromosomal length characteristics, support the restoration of section Cyclocodon as a genus. However, the incorporation of section Campanumoea into Codonopsis requires more evidence. Comparison of chromosomal length and haploid set length revealed that chromosomal segment rearrangements occurred within sections of Campanumoea and between genera, with the difference within sections being greater than that between genera. Therefore, chromosomal segment rearrangements are present in Campanulaceae, implying that chromosomal segment rearrangement plays an important role in the evolution of diversity in Campanulaceae. By comparing the chromosomal characteristic in section Campanumoea and the genus Adenophora, we concluded that the secondary chromosome type such as n = 17, 18 would be derived by autopolyploidization of n = 9, and by chromosome fusion.     

Phylogenetic position of African and Malagasy Pimpinella species and related genera (Apiaceae, Pimpinelleae)

The phylogenetic position of the African and Malagasy species of Pimpinella is assessed using nrDNA ITS sequence data and a representative sampling of the genus, including 16 species from Africa and Madagascar and 26 species from Eurasia. The results of maximum parsimony and Bayesian analyses of these data show that the African and Malagasy species ally with their Eurasian counterparts in Pimpinelleae. The genus Pimpinella is rendered paraphyletic by the inclusion of African Cryptotaenia and the small African and Malagasy endemic genera Frommia and Phellolophium. Within a paraphyletic Pimpinella, three major clades are recovered, with the African species occupying two of these clades. The current sectional classification of the genus, based predominantly on fruit vestiture, is largely artificial. Chromosome base number, however, was found to be consistent with the groupings recovered in the molecular analyses. Those African and Malagasy Pimpinella species with a chromosome base number of x = 11 and largely glabrous petals and fruits, form the earliest diverging clade together with Frommia, which also has a base count of n = 11 and glabrous petals and fruits. The remaining African species ally with several Eurasian species of Pimpinella and share a chromosome base number of x = 9 and usually hairy petals and fruits.     

Caryological analysis of South American species of Vernonia (Vernonieae,Asteraceae)

Abstract

In the present study 16 populations belonging to 13 species of the genus Vernonia Schreb. were examined cytologically. In total, six different chromosome numbers, which represent three basic numbers: x = 10, x = 16 and x = 17, were found. These results include the first chromosome number reports for the following four species: V. lanifera Cristóbal & Dematt. (2n = 2x = 32), V. membranacea Gardner (2n = 2x = 34), V. salzmannii DC. (2n = 2x = 20) and V. scabrifoliata Hieron. (2n = 2x = 128). Besides, a new chromosome number was found in V. saltensis Hieron. (2n = 2x = 32), for which only tetraploid populations have been previously recorded. The data obtained in this work, along with the information available from the literature, show that the genus Vernonia in South America is heterogeneous with basic chromosome numbers that range between x = 9 and x = 19. These numbers suggest that a combination of polyploidy and aneuploidy has played an important role in the evolution of the genus.     

Karyology of some Convolvulaceae species occurring in NE Brazil inselbergs

Eighteen species belonging to family Convolvulaceae occurring in northeastern Brazil were analyzed to identify the karyotypic variability among rupicolous and non-rupicolous species. The count of 2n = 56 for Evolvulus sp., is the first report of polyploidy for the genus. The similarities among the karyotypes of species of Ipomoea, Merremia, and Operculina suggest that x = 15 is the basic secondary number for these genera, while x = 13 has been observed in Evolvulus. The genus Jacquemontia, with 2n = 18 is karyologically distinct from the other genera of the family. Intraspecific numerical chromosomal variations were not detected, nor were any karyological variations related to the rocky habitat characteristic of inselbergs. The occurrence of other plant groups with polyploid forms linked to this type of habitat suggests that the family Convolvulaceae is karyologically stable. We discuss variations in chromosome numbers, base numbers, and their implications in the evolution of the principal groups within the Convolvulaceae.     

Chromosome numbers in the genus Mimosa L.: cytotaxonomic and evolutionary implications

Chromosome numbers were determined for 125 accessions of 92 taxa of Mimosa from all five of Barneby??s (Mem New York Bot Gard 65:1?C835, 1991) taxonomic sections. For 69 species, 1 subspecies and 8 varieties, chromosome numbers are presented for the first time, for 6 species and 1 variety previously published data have been confirmed and for 3 species and 2 varieties different numbers were found. Results show that 74% of the accessions were diploid (2n?=?2x?=?26) and 26% polyploid, these mostly tetraploid (2n?=?4x?=?52) but with two triploid (2n?=?3x?=?39). These results double the number of Mimosa species for which the chromosome count is known from less than 10% previously reported to more than 20%, representing an important advance in the cytotaxonomy of this legume genus. These results together with literature data show that ca. 78% of Mimosa species are diploid. Polyploids are present in most of the taxonomic sections and in different lineages across the genus. No particular chromosome number is restricted to a given section or lineage. A possible relation between geography, species distribution, polyploidy and invasiveness was detected, however, further studies based on more accessions, especially from higher latitudes, are required before firm conclusions can be drawn.     

Goodbye or welcome Gondwana? – insights into the phylogenetic biogeography of the leafy liverwort Plagiochila with a description of Proskauera, gen. nov. (Plagiochilaceae, Jungermanniales)

Molecular phylogenies based on chloroplast gene rps4 sequences and nuclear ribosomal ITS sequences have been generated to investigate relationships among species and putative segregates in Plagiochila (Plagiochilaceae), the largest genus of leafy liverworts. About a fourth of the ca. 450 accepted binomials of Plagiochilaceae are included in these phylogenetic analyses, several represented by multiple accessions. A clade with Chiastocaulon, Pedinophyllum, and Plagiochilion is placed sister to a clade with numerous accessions of Plagiochila. Plagiochila pleurata and P. fruticella are resolved sister to the remainder of Plagiochilaceae and transferred to the new Australasian genus Proskauera which differs from all other Plagiochilaceae by the occurrence of spherical leaf papillae. The historical biogeography of Plagiochilaceae is explored based on the reconstructions of the phylogeny, biogeographic patterns and diversification time estimates. The results indicate that the current distribution of Plagiochilaceae cannot be explained exclusively by Gondwanan vicariance. A more feasible explanation of the range is a combination of short distance dispersal, rare long distance dispersal events, extinction, recolonization and diversification.     

Molecular phylogeny and biogeography of Malagasy frogs of the genus Gephyromantis

The genus Gephyromantis is a clade within the Malagasy-Comoroan family Mantellidae composed of rainforest frogs that live and breed to varying degrees independently from water. Based on DNA sequences of five mitochondrial and five nuclear genes we inferred the phylogeny of these frogs with full taxon coverage at the species level. Our preferred consensus tree from a partitioned Bayesian analysis of 5843 base pairs of 51 nominal and candidate species supports various major clades within the genus although the basal relationships among these remain unresolved. The data provide strong evidence for the monophyly of the subgenera Gephyromantis (after exclusion of Gephyromantis klemmeri), Laurentomantis, Vatomantis, and Phylacomantis. Species assigned to the subgenus Duboimantis belong to two strongly supported clades of uncertain relationships. G. klemmeri, previously in the subgenus Gephyromantis, was placed with high support sister to the Laurentomantis clade, and the Laurentomantis + G. klemmeri clade was sister to Vatomantis. A reconstruction of ancestral distribution areas indicates a diversification of several subgenera in the northern biogeographic regions of Madagascar and the dispersal out of northern Madagascar for several clades.