Nuclear genome size variation in fleshy-fruited Neotropical Myrtaceae

In Myrtaceae, reports regarding the nuclear DNA content are scarce. The aim of this study is to present genome size data for fleshy-fruited Myrteae, and to test their relation with chromosome number and ploidy, the available data for cytoevolutionary studies in Myrtaceae. Thirty species out of ten genera were investigated for chromosome number and genome size using flow cytometry. Twenty-eight species were diploid with 2n = 2x = 22 and two species were tetraploid with 2n = 4x = 44. All genome sizes measured are new. Among the diploid species, a gradual and small variation in 2C-values (0.486 pg in Gomidesia schaueriana to 0.636 pg in Eugenia multicostata) was observed, whereas the tetraploid genomes of Psidium acutangulum and P. cattleianum had about twice as much DNA (1.053 and 1.167 pg, respectively). The total interspecific variation of C-values was 2.45-fold. The fleshy-fruited Myrteae have smaller holoploid genomes than the capsular-fruited Eucalypteae and Melaleuceae.     

Relative DNA content in diploid,polyploid, and multiploid species of <Emphasis Type="Italic">Paspalum</Emphasis> (Poaceae) with relation to reproductive mode and taxonomy

It is generally accepted that polyploids have downsized basic genomes rather than additive values with respect to their related diploids. Changes in genome size have been reported in correlation with several biological characteristics. About 75 % of around 350 species recognized for Paspalum (Poaceae) are polyploid and most polyploids are apomictic. Multiploid species are common with most of them bearing sexual diploid and apomictic tetraploid or other ploidy levels. DNA content in the embryo and the endosperm was measured by flow cytometry in a seed-by-seed analysis of 47 species including 77 different entities. The relative DNA content of the embryo informed the genome size of the accession while the embryo:endosperm ratio of DNA content revealed its reproductive mode. The genome sizes (2C-value) varied from 0.5 to 6.5 pg and for 29 species were measured for the first time. Flow cytometry provided new information on the reproductive mode for 12 species and one botanical variety and supplied new data for 10 species concerning cytotypes reported for the first time. There was no significant difference between the mean basic genome sizes (1Cx-values) of 32 sexual and 45 apomictic entities. Seventeen entities were diploid and 60 were polyploids with different degrees. There were no clear patterns of changes in 1Cx-values due to polyploidy or reproductive systems, and the existing variations are in concordance with subgeneric taxonomical grouping.     

NUCLEAR DNA CONTENT VARIATION WITHIN THE ROSACEAE

Nuclear DNA content has been estimated using flow cytometry for 17 species and eight cultivars of Malus and for 44 species of 29 other genera within the Rosaceae. Compared to other angiosperms, diploid genome sizes vary little within the family Rosaceae and within the genus Malus. C-values of genera within the subfamilies Spiraeoideae and Rosoideae are among the smallest of flowering plants thus far reported. In general, the Maloideae have the largest diploid genomes of the family, consistent with their higher chromosome numbers and presumed polyploid origin.     

Untangling Nucleotide Diversity and Evolution of the H Genome in Polyploid Hordeum and Elymus Species Based on the Single Copy of Nuclear Gene DMC1

Numerous hybrid and polypoid species are found within the Triticeae. It has been suggested that the H subgenome of allopolyploid Elymus (wheatgrass) species originated from diploid Hordeum (barley) species, but the role of hybridization between polyploid Elymus and Hordeum has not been studied. It is not clear whether gene flow across polyploid Hordeum and Elymus species has occurred following polyploid speciation. Answering these questions will provide new insights into the formation of these polyploid species, and the potential role of gene flow among polyploid species during polyploid evolution. In order to address these questions, disrupted meiotic cDNA1 (DMC1) data from the allopolyploid StH Elymus are analyzed together with diploid and polyploid Hordeum species. Phylogenetic analysis revealed that the H copies of DMC1 sequence in some Elymus are very close to the H copies of DMC1 sequence in some polyploid Hordeum species, indicating either that the H genome in theses Elymus and polyploid Hordeum species originated from same diploid donor or that gene flow has occurred among them. Our analysis also suggested that the H genomes in Elymus species originated from limited gene pool, while H genomes in Hordeum polyploids have originated from broad gene pools. Nucleotide diversity (π) of the DMC1 sequences on H genome from polyploid species (π = 0.02083 in Elymus, π = 0.01680 in polyploid Hordeum) is higher than that in diploid Hordeum (π = 0.01488). The estimates of Tajima''s D were significantly departure from the equilibrium neutral model at this locus in diploid Hordeum species (P<0.05), suggesting an excess of rare variants in diploid species which may not contribute to the origination of polyploids. Nucleotide diversity (π) of the DMC1 sequences in Elymus polyploid species (π = 0.02083) is higher than that in polyploid Hordeum (π = 0.01680), suggesting that the degree of relationships between two parents of a polyploid might be a factor affecting nucleotide diversity in allopolyploids.     

Genetic relationships in hibiscus sect. Furcaria

The eighteen species studied form an allopolyploid series (x=18). The morphology, crossing behavior, and geographical distribution of 6 diploid, 9 tetraploid, 2 octoploid, and 1 decaploid species were studied. From over 26,500 crosses, 19 hybrid combinations and several derived allopolyploids and three-species hybrids were obtained. Chromosome pairing in the hybrids showed that a minimum of 6 and a maximum of 14 well-differentiated genome groups exist in sect. Furcaia, at least two of which appear to be confined to the Old World. No evidence was found that New World genomes are represented in the Old World. The primary radiation of the diploid genomes probably occurred at about the same time as that of the diploid genomes of Gossypium, whereas the tetraploids and one of the octoploid species (H. furcatus Roxb., non Willd.) seem to be of later origin (late Pleistocene or Recent). Octoploid H. diversifolius Jacq., a circumtropical species, may be a relict of a much earlier round of polyploid evolution.     

Genomic analysis in the genus Aegilops.

Summary Hybrids between different Aegilops species and Secale cereale were studied at metaphase I by means of a C-banding technique. On the basis of differences in the C-banding patterns of some of the chromosomes of these hybrids it was possible to carry out an accurate analysis of several types of Aegilops-Aegilops and Aegilops-Secale chromosome associations and, consequently, to establish intraspecific and intergeneric genome relationships. Genomes present in the majority of polyploid Aegilops species are shown to maintain similar patterns of evolutionary affinity to those reported for their proposed diploid parents although in some species there are differences indicating either that differentiations occurred during the evolution of the polyploid species or, on the contrary, that the diploid donors proposed are not the correct ones. On the other hand, differences in the relationships not only between the R genome and different Aegilops genomes but also among different homoeologous groups have been found.     

Linked by Ancestral Bonds: Multiple Whole-Genome Duplications and Reticulate Evolution in a Brassicaceae Tribe

Pervasive hybridization and whole-genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. Although frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (∼60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring postpolyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.     

Analysis of metaphase I chromosome association in species of the genus Aegilops

Summary Metaphase-I chromosome associations in every diploid and polyploid species of the genus Aegilops were studied using C-banding in order to analyse the cytogenetic behaviour of the whole complement as well as of specific genomes in different polyploid species. Differences were observed in the frequency of associations per cell among different species of the same ploidic level and even between species sharing the same genomic constitution. Differences were also found between different genomes within the same polyploid species and between the same genome when present in several diploid and polyploid species. Several factors proposed as having an influence on the frequency of metaphase-I associations, such as chromosome morphology, C-heterochromatin content, genetic control and genome interactions, are discussed. Most of the polyploid Aegilops species showed a diploid-like behaviour at metaphase I although multivalents involving homoeologous associations were occasionally observed in Ae. biuncialis, Ae. juvenalis and Ae. crassa(6x); therefore, the Aegilops diploidising genetic system is not equally effective in all polyploid species.     

A first assessment of genome size diversity in Monogonont rotifers

This study provides the first analysis of genome size diversity in Monogonont rotifers. Measurements were made using flow cytometry, with Drosophila melanogaster and chicken erythrocytes as internal standards. Nuclear DNA content (??2C????assuming diploid genomes) in eight different species of four different genera ranged almost fourfold, from 0.12 to 0.46 pg. A comparison with previously published values for Bdelloid rotifers suggested that the genomes of Monogononts are significantly smaller than those of Bdelloids. When compared to other Metazoans, Monogonont rotifers seem to have relatively small genomes. For instance, the C-values of the two species with the smallest genomes, Brachionus dimidiatus and Synchaeta pectinata, were only 0.06 and 0.085 pg, respectively. Various explanations for genome size diversity within Monogononta are discussed.     

Differential Dynamics of Transposable Elements during Long-Term Diploidization of Nicotiana Section Repandae (Solanaceae) Allopolyploid Genomes

Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo drastic reorganization. However, timing and mechanisms of structural diploidization over evolutionary timescales are still poorly known. As transposable elements (TEs) represent major and labile components of plant genomes, they likely play a pivotal role in fuelling genome changes leading to long-term diploidization. Here, we exploit the 4.5 MY old allopolyploid Nicotiana section Repandae to investigate the impact of TEs on the evolutionary dynamics of genomes. Sequence-specific amplified polymorphisms (SSAP) on seven TEs with expected contrasted dynamics were used to survey genome-wide TE insertion polymorphisms. Comparisons of TE insertions in the four allopolyploid species and descendents of the diploid species most closely related to their actual progenitors revealed that the polyploids showed considerable departure from predicted additivity of the diploids. Large numbers of new SSAP bands were observed in polyploids for two TEs, but restructuring for most TE families involved substantial loss of fragments relative to the genome of the diploid representing the paternal progenitor, which could be due to changes in allopolyploids, diploid progenitor lineages or both. The majority of non-additive bands were shared by all polyploid species, suggesting that significant restructuring occurred early after the allopolyploid event that gave rise to their common ancestor. Furthermore, several gains and losses of SSAP fragments were restricted to N. repanda, suggesting a unique evolutionary trajectory. This pattern of diploidization in TE genome fractions supports the hypothesis that TEs are central to long-term genome turnover and depends on both TE and the polyploid lineage considered.     

Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region

The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurately assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (A^uA^u) was analyzed by comparing its 277-kb large genomic region carrying the important Glu-1 locus with the homologous regions from the A genomes of the diploid T. monococcum (A^mA^m), tetraploid T. turgidum (AABB), and hexaploid T. aestivum (AABBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the A^u genome and the A genomes in polyploid wheats, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats originated from the diploid A^u genome. The difference in the compared region between A^u and A is mainly caused by four differential TE insertion and two deletion events between these genomes. The estimated divergence time of A genomes calculated on nucleotide substitution rate in both shared TEs and collinear genes further supports the closer evolutionary relationship of A to A^u than to A^m. The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the A^u sequence for mapping the A genome in hexaploid wheat. Eighty percent of these repeat junction markers were successfully mapped to the corresponding region in hexaploid wheat, suggesting that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat.     

Intergenomic rearrangements after polyploidization of Kengyilia thoroldiana (Poaceae: Triticeae) affected by environmental factors

Polyploidization is a major evolutionary process. Approximately 70–75% species of Triticeae (Poaceae) are polyploids, involving 23 genomes. To investigate intergenomic rearrangements after polyploidization of Triticeae species and to determine the effects of environmental factors on them, nine populations of a typical polyploid Triticeae species, Kengyilia thoroldiana (Keng) J.L.Yang et al. (2n = 6x = 42, StStPPYY), collected from different environments, were studied using genome in situ hybridization (GISH). We found that intergenomic rearrangements occurred between the relatively large P genome and the small genomes, St (8.15%) and Y (22.22%), in polyploid species via various types of translocations compared to their diploid progenitors. However, no translocation was found between the relatively small St and Y chromosomes. Environmental factors may affect rearrangements among the three genomes. Chromosome translocations were significantly more frequent in populations from cold alpine and grassland environments than in populations from valley and lake-basin habitats (P<0.05). The relationship between types of chromosome translocations and altitude was significant (r = 0.809, P<0.01). Intergenomic rearrangements associated with environmental factors and genetic differentiation of a single basic genome should be considered as equally important genetic processes during species'' ecotype evolution.     

Phylogeny of the a genomes of wild and cultivated wheat species

Diploid species of the genus Triticum L. are its most ancient representatives and have the A genome, which was more recently inherited by all polyploid species. Studies of the phylogenetic relationships among diploid and polyploid wheat species help to identify the donors of elementary genomes and to examine the species specificity of genomes. In this study, molecular analysis of the variable sequences of three nuclear genes (Acc-1, Pgk-1, and Vrn-1) was performed for wild and cultivated wheat species, including both diploids and polyploids. Based on the sequence variations found in the genes, clear differences were observed among elementary genomes, but almost no polymorphism was detected within each genome in polyploids. At the same time, the regions of the three genes proved to be rather heterogeneous in the diploid species Triticum boeoticum Boiss., T. urartu Thum. ex Gandil., and T. monococcum L., thus representing mixed populations. A genome variant identical to the A genome of polyploid species was observed only in T. urartu. Species-specific molecular markers discriminating the diploid species were not found. Analysis of the inheritance of morphological characters also failed to identify a species-specific character for the three diploid wheat species apart from the hairy leaf blade type, described previously.     

Molecular evolution and nucleotide diversity of nuclear plastid phosphoglycerate kinase (PGK) gene in Triticeae (Poaceae)

Levels of nucleotide divergence provide key evidence in the evolution of polyploids. The nucleotide diversity of 226 sequences of pgk1 gene in Triticeae species was characterized. Phylogenetic analyses based on the pgk1 gene were carried out to determine the diploid origin of polyploids within the tribe in relation to their A^u, B, D, St, Ns, P, and H haplomes. Sequences from the Ns genome represented the highest nucleotide diversity values for both polyploid and diploid species with π = 0.03343 and θ = 0.03536 for polyploid Ns genome sequences and π = 0.03886 and θ = 0.03886 for diploid Psathyrostachys sequences, while Triticum urartu represented the lowest diversity among diploid species at π = 0.0011 and θ = 0.0011. Nucleotide variation of diploid Aegilops speltoides (π = 0.2441, presumed the B genome donor of Triticum species) is five times higher than that (π = 0.00483) of B genome in polyploid species. Significant negative Tajima's D values for the St, A^u, and D genomes along with high rates of polymorphisms and low sequence diversity were observed. Origins of the A^u, B, and D genomes were linked to T. urartu, A. speltoides, and A. tauschii, respectively. Putative St genome donor was Pseudoroegneria, while Ns and P donors were Psathyrostachys and Agropyron. H genome diploid donor is Hordeum.     

Phylogenetic inferences in Avena based on analysis of FL intron2 sequences

The development and application of molecular methods in oats has been relatively slow compared with other crops. Results from the previous analyses have left many questions concerning species evolutionary relationships unanswered, especially regarding the origins of the B and D genomes, which are only known to be present in polyploid oat species. To investigate the species and genome relationships in genus Avena, among 13 diploid (A and C genomes), we used the second intron of the nuclear gene FLORICAULA/LEAFY (FL int2) in seven tetraploid (AB and AC genomes), and five hexaploid (ACD genome) species. The Avena FL int2 is rather long, and high levels of variation in length and sequence composition were found. Evidence for more than one copy of the FL int2 sequence was obtained for both the A and C genome groups, and the degree of divergence of the A genome copies was greater than that observed within the C genome sequences. Phylogenetic analysis of the FL int2 sequences resulted in topologies that contained four major groups; these groups reemphasize the major genomic divergence between the A and C genomes, and the close relationship among the A, B, and D genomes. However, the D genome in hexaploids more likely originated from a C genome diploid rather than the generally believed A genome, and the C genome diploid A. clauda may have played an important role in the origination of both the C and D genome in polyploids.     

Genome sizes of Eucomis L’Hér. (Hyacinthaceae) and a description of the new species Eucomis grimshawii G.D.Duncan & Zonneveld

Nuclear genome size, as measured by flow cytometry with propidium iodide, was used to investigate the relationships within the genus Eucomis L’Hér. (Hyacinthaceae). Most species of Eucomis have the same basic chromosome number, x = 15. However, the somatic DNA 2C-value (2C) is shown to range from 21 to 31 pg for the diploids. The largest genome contains roughly 10¹⁰ more base pairs than the smallest. Genome sizes are evaluated here in combination with available morphological and geographical data. Therefore, the taxonomy proposed here is not based on genome size alone. The genus Eucomis, as here determined, has 12 species. These can be divided into two groups: mainly dwarf diploid species and large-sized, tetraploid species. A small diploid plant, Eucomis (autumnalis subsp.) amaryllidifolia, is restored to species status, as a diploid subspecies seems incongruent with an allotetraploid Eucomis autumnalis. Moreover, as a diploid it is separated reproductively from the allotetraploid E. autumnalis. A new diploid species that has the lowest C value, E. grimshawii, is described here. On the basis of DNA content and other morphological characters, possible parents are suggested for all tetraploid species. Nuclear DNA content as measured by using flow cytometry may conveniently be used to produce systematic data. It is applicable even in dormant bulbs or sterile plants for the monitoring of the trade in bulbous species.     

Phylogeny and molecular evolution of the DMC1 gene within the StH genome species in Triticeae (Poaceae)

To estimate the phylogeny and molecular evolution of a single-copy nuclear disrupted meiotic cDNA (DMC1) gene within the StH genome species, two DMC1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from seven diploid taxa representing the St and H genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) there is a close relationship among North American StH genome species; (2) the DMC1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct; (3) the StH genome polyploids have higher levels of sequence diversity in the St genome homoeolog than the H genome homoeolog; (4) the DMC1 sequence may evolve faster in the polyploid species than in the diploids; (5) high dN and dN/dS values in the St genome within polyploid species could be caused by low selective constraints or AT-biased mutation pressure. Our result provides some insight on evolutionary dynamics of duplicate DMC1 gene, the polyploidization events and phylogeny of the StH genome species.     

Comparison of the primary structure ofwaxy proteins (granule-bound starch synthase) between polyploid wheats and related diploid species

Thewaxy proteins encoded by the genomes A, B, and D in polyploid wheats and related diploid species were isolated by SDS-PAGE. The N-terminal amino acid sequences of mature proteins and V8 protease-induced fragments were determined. A total of five amino acid substitutions was detected in these sequences, which represent about 10% of the whole sequences of thewaxy proteins. A comparison of these sequences in polyploid wheats with those in related diploid species revealed the following: (i)waxy proteins encoded by the A genome of polyploid wheats were identical to that ofTriticum monococcum, (ii) thewaxy protein encoded by the B genome ofT. turgidum was identical to that ofT. searsii, but differed from those ofT. speltoides andT. longissimum by one amino acid substitution, (iii) thewaxy protein encoded by the B genome ofT. aestivum differed from that encoded by the B genome ofT. turgidum by one amino acid substitution, and (iv) thewaxy protein encoded by the D genome ofT. aestivum was identical to that ofT. tauschii.     

CYTOTAXONOMY OF CESPITOSE ZINNIAS

Torres , Andrew M. (U. Wisconsin, Milwaukee.) Cytotaxonomy of cespitose zinnias. Amer. Jour. Bot. 49(10): 1033–1037. Illus. 1962.—The results of hybridization studies among 5 of the 6 cespitose species of Zinnia are reported. Analyses of meiosis in the F₁ hybrids suggest there are 2 genomes, A and B, in the polyploid taxa. The A genome apparently exists in the diploid state in 2 species, but the B genome is known only from polyploid taxa. The chromosome number of Z. oligantha (2n = 20) is reported for the first time.     

Spatio‐temporal patterns of genome evolution in allotetraploid species of the genus Oryza

Despite knowledge that polyploidy is widespread and a major evolutionary force in flowering plant diversification, detailed comparative molecular studies on polyploidy have been confined to only a few species and families. The genus Oryza is composed of 23 species that are classified into ten distinct ‘genome types’ (six diploid and four polyploid), and is emerging as a powerful new model system to study polyploidy. Here we report the identification, sequence and comprehensive comparative annotation of eight homoeologous genomes from a single orthologous region (Adh1–Adh2) from four allopolyploid species representing each of the known Oryza genome types (BC, CD, HJ and KL). Detailed comparative phylogenomic analyses of these regions within and across species and ploidy levels provided several insights into the spatio‐temporal dynamics of genome organization and evolution of this region in ‘natural’ polyploids of Oryza. The major findings of this study are that: (i) homoeologous genomic regions within the same nucleus experience both independent and parallel evolution, (ii) differential lineage‐specific selection pressures do not occur between polyploids and their diploid progenitors, (iii) there have been no dramatic structural changes relative to the diploid ancestors, (iv) a variation in the molecular evolutionary rate exists between the two genomes in the BC complex species even though the BC and CD polyploid species appear to have arisen <2 million years ago, and (v) there are no clear distinctions in the patterns of genome evolution in the diploid versus polyploid species.