Interstitial Arabidopsis-Type Telomeric Repeats in Asteraceae

Tandem repeats of telomeric-like motifs at intra-chromosomal regions, known as interstitial telomeric repeats (ITR), have drawn attention as potential markers of structural changes, which might convey information about evolutionary relationships if preserved through time. Building on our previous work that reported outstanding ITR polymorphisms in the genus Anacyclus, we undertook a survey across 132 Asteraceae species, focusing on the six most speciose subfamilies and considering all the ITR data published to date. The goal was to assess whether the presence, site number, and chromosomal location of ITRs convey any phylogenetic signal. We conducted fluorescent in situ hybridization (FISH) using an Arabidopsis-type telomeric sequence as a probe on karyotypes obtained from mitotic chromosomes. FISH signals of ITR sites were detected in species of subfamilies Asteroideae, Carduoideae, Cichorioideae, Gymnarhenoideae, and Mutisioideae, but not in Barnadesioideae. Although six small subfamilies have not yet been sampled, altogether, our results suggest that the dynamics of ITR formation in Asteraceae cannot accurately trace the complex karyological evolution that occurred since the early diversification of this family. Thus, ITRs do not convey a reliable signal at deep or shallow phylogenetic levels and cannot help to delimitate taxonomic categories, a conclusion that might also hold for other important families such as Fabaceae.

Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review

The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies.

Chromosome diversity in species of the genus Arachis, revealed by FISH and CMA/DAPI banding, and inferences about their karyotype differentiation

The species of the genus Arachis (Leguminosae) are ordered into nine sections. The assignment of genome types in this genus has been based on cross-compatibility analysis and molecular cytogenetic studies. The latter has also allowed karyotypically establishing well-defined genomes and reassigning the genome of several species. However, most of these studies have been focused mainly on the sections Arachis and Rhizomatosae. To increase the knowledge about the chromosome diversity of the whole genus, here we performed a detailed karyotype characterization of representative species of most of the sections and genomes of Arachis. This characterization included chromosome morphology, CMA/DAPI chromosome banding, and chromosome marker localization (rDNAloci and one satDNA sequence) by fluorescent in situ hybridization (FISH). Based on the data obtained and other previously published data, we established the karyotype similarities by cluster analysis and defined eleven karyotype groups. The grouping was partly coincident with the traditional genome assignment, except for some groups and some individual species. Karyotype similarities among some genomes were also found. The main characteristics of each karyotype group of Arachis were summarized. Together, our results provide information that may be beneficial for future cytogenetic and evolutionary studies, and also contribute to the identification of interspecific hybrids.

Genome size variation at constant chromosome number is not correlated with repetitive DNA dynamism in Anacyclus (Asteraceae)

BACKGROUND AND AIMS

Changes in the amount of repetitive DNA (dispersed and tandem repeats) are considered the main contributors to genome size variation across plant species in the absence of polyploidy. However, the study of repeatome dynamism in groups showing contrasting genomic features and complex evolutionary histories is needed to determine whether other processes underlying genome size variation may have been overlooked. The main aim here was to elucidate which mechanism best explains genome size evolution in Anacyclus (Asteraceae).

METHODS

Using data from Illumina sequencing, we analysed the repetitive DNA in all species of Anacyclus, a genus with a reticulate evolutionary history, which displays significant genome size and karyotype diversity albeit presenting a stable chromosome number.

KEY RESULTS

By reconstructing ancestral genome size values, we inferred independent episodes of genome size expansions and contractions during the evolution of the genus. However, analysis of the repeatome revealed a similar DNA repeat composition across species, both qualitative and quantitative. Using comparative methods to study repeatome dynamics in the genus, we found no evidence for repeat activity causing genome size variation among species.

CONCLUSIONS

Our results, combined with previous cytogenetic data, suggest that genome size differences in Anacyclus are probably related to chromosome rearrangements involving losses or gains of chromosome fragments, possibly associated with homoploid hybridization. These could represent balanced rearrangements that do not disrupt gene dosage in merged genomes, for example via chromosome segment exchanges.

Pre-labelled oligo probe-FISH karyotype analyses of four Araliaceae species using rDNA and telomeric repeat

BACKGROUND

The family Araliaceae contains many medicinal species including ginseng of which the whole genome sequencing analyses have been going on these days.

OBJECTIVE

To characterize the chromosomal distribution of 5S and 45S rDNAs and telomeric repeat in four ginseng related species of Aralia elata (Miq.) Seem., Dendropanax morbiferus H. Lév., Eleutherococcus sessiliflorus (Rupr. Et Maxim.) Seem., Kalopanax septemlobus (Thunb. ex A.Murr.) Koidz.

METHOD

Pre-labelled oligoprobe (PLOP)-fluorescence in situ hybridization (FISH) was carried out.

RESULTS

The chromosome number of A. elata was 2n = 24, whereas that of the other three species of D. morbiferus, E. sessiliflorus, and K. septemlobus was 2n = 48, corresponding to diploid and tetraploid, respectively, based on the basic chromosome number x = 12 in Araliaceae. In all four species, one pair of 5S signals were detected in the proximal regions of the short arms of chromosome 3, whereas in K. septemlobus, the 5S rDNA signals localized in the subtelomeric region of short arm of chromosome 3, while all the 45S rDNA signals localized at the paracentromeric region of the short arm of chromosome 1. And the telomeric repeat signals were detected at the telomeric region of both short and long arms of most chromosomes.

CONCLUSION

The PLOP-FISH was very effective compared with conventional FISH method. These results provide useful comparative cytogenetic information to better understand the genome structure of each species and will be useful to trace the history of ginseng genomic constitution.

The fate of ribosomal RNA genes in spontaneous polyploid dogrose hybrids [Rosa L. sect. Caninae (DC.) Ser.] exhibiting non-symmetrical meiosis

Dogroses represent an exceptional system for studying the effects of genome doubling and hybridization: their asymmetrical meiosis enables recombination in bi-parentally inherited chromosomes but prevents it in maternally inherited ones. We employed fluorescent in situ hybridization, genome skimming, amplicon sequencing of genomic and cDNA as well as conventional cloning of nuclear ribosomal DNA in two phylogenetically distinct pentaploid (2n = 5x = 35) species, Rosa canina and Rosa inodora, and their naturally occurring reciprocal hybrids, Rosa dumalis (5x) and Rosa agrestis (5x, 6x). Both progenitor species differed in composition, meiotic behaviour and expression of rDNA loci: R. canina (five 18S and 5-8 5S loci) was dominated by the Canina ribotypes, but R. inodora (four 18S loci and 7-8 5S loci) by the Rubiginosa ribotype. The co-localized 5S/18S loci occurred on either bivalent-forming (R. canina) or univalent-forming (R. inodora) chromosomes. Ribosomal DNA loci were additively inherited; however, the Canina ribotypes were dominantly expressed, even in genotypes with relatively low copy number of these genes. Moreover, we observed rDNA homogenization towards the paternally transmitted Canina ribotype in 6x R. agrestis. The here-observed variation in arrangement and composition of rDNA types between R. canina and R. inodora suggests the involvement of different genomes in bivalent formation. This results supports the hypothesis that the asymmetrical meiosis arose at least twice by independent ancient hybridization events.

Cytogenetic evidences on the evolutionary relationships between the tetraploids of the section Rhizomatosae and related diploid species (Arachis, Leguminosae)

Rhizomatosae is a taxonomic section of the South American genus Arachis, whose diagnostic character is the presence of rhizomes in all its species. This section is of particular evolutionary interest because it has three polyploid (A. pseudovillosa, A. nitida and A. glabrata, 2n = 4x = 40) and only one diploid (A. burkartii, 2n = 2x = 20) species. The phylogenetic relationships of these species as well as the polyploidy nature and the origin of the tetraploids are still controversial. The present study provides an exhaustive analysis of the karyotypes of all rhizomatous species and six closely related diploid species of the sections Erectoides and Procumbentes by cytogenetic mapping of DAPI/CMA heterochromatin bands and 5S and 18-26S rDNA loci. Chromosome banding showed variation in the DAPI heterochromatin distribution pattern, which, together with the number and distribution of rDNA loci, allowed the characterization of all species studied here. The bulk of chromosomal markers suggest that the three rhizomatous tetraploid species constitute a natural group and may have at least one common diploid ancestor. The cytogenetic data of the diploid species analyzed evidenced that the only rhizomatous diploid species-A. burkartii-has a karyotype pattern different from those of the rhizomatous tetraploids, showing that it is not likely the genome donor of the tetraploids and the non-monophyletic nature of the section Rhizomatosae. Thus, the tetraploid species should be excluded from the R genome, which should remain exclusively for A. burkartii. Instead, the karyotype features of these tetraploids are compatible with those of different species of the sections Erectoides and Procumbentes (E genome species), suggesting the hypothesis of multiple origins of these tetraploids. In addition, the polyploid nature and the group of diploid species closer to the tetraploids are discussed.

Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database

The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n = 16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n = 24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S-type organisation (ancestral condition), the L-type arrangement has arisen independently several times during plant evolution. A non-terminal position of 35S rDNA was found in about 25% of single-locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single-locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid-like state over time.

FISH and AgNor mapping of the 45S and 5S rRNA genes in wild and cultivated species of Capsicum (Solananceae)

Chromosome number and position of rDNA were studied in 12 wild and cultivated species of the genus Capsicum with chromosome numbers x = 12 and x = 13 (22 samples). For the first time in these species, the 5S and 45S rRNA loci were localized and physically mapped using two-color fluorescence in situ hybridization and AgNOR banding. We focused on the comparison of the results obtained with both methods with the aim of accurately revealing the real functional rRNA genes. The analyzes were based on a previous work that reported that the 18S-5.8S-25S loci mostly coincide with GC-rich heterochromatic regions and likely have given rise to satellite DNAs, which are not active genes. These data show the variability of rDNA within karyotypes of the genus Capsicum, providing anchor points for (comparative) genetic maps. In addition, the obtained information might be useful for studies on evolution of repetitive DNA.

Cytogenetic relationships among Citrullus species in comparison with some genera of the tribe Benincaseae (Cucurbitaceae) as inferred from rDNA distribution patterns

Background

Comparative mapping of 5S and 45S rDNA by fluorescent in situ hybridization (FISH) technique is an excellent tool to determine cytogenetic relationships among closely related species.

Results

In this study, the number and position of 5S and 45S rDNA loci in all Citrullus species and subspecies were determined. The cultivated watermelon (C. lanatus subsp. vulgaris), C. lanatus subsp. mucosospermus, C. colocynthis and C. naudinianus (or Acanthosicyos naudinianus) had two 45S rDNA loci and one 5S rDNA locus which was located syntenic to one of the 45S rDNA loci. C. ecirrhosus and C. lanatus subsp. lanatus had one 45S rDNA locus and two 5S rDNA loci, each located on a different chromosome. C. rehmii had one 5S and one 45S rDNA locus positioned on different chromosomes. The distribution of 5S and 45S rDNA in several species belonging to other genera in Benincaseae tribe was also investigated. The distribution pattern of rDNAs showed a great difference among these species.

Conclusions

The present study confirmed evolutionary closeness among cultivated watermelon (C. lanatus subsp. vulgaris), C. lanatus subsp. mucosospermus and C. colocynthis. Our result also supported that C. lanatus subsp. lanatus was not a wild form of the cultivated watermelon instead was a separate crop species. In addition, present cytogenetic analysis suggested that A. naudinianus was more closely related to Cucumis than to Citrullus or Acanthosicyos, but with a unique position and may be a link bridge between the Citrullus and the Cucumis.

The striking and unexpected cytogenetic diversity of genus Tanacetum L. (Asteraceae): a cytometric and fluorescent in situ hybridisation study of Iranian taxa

BACKGROUND

Although karyologically well studied, the genus Tanacetum (Asteraceae) is poorly known from the perspective of molecular cytogenetics. The prevalence of polyploidy, including odd ploidy warranted an extensive cytogenetic study. We studied several species native to Iran, one of the most important centres of diversity of the genus. We aimed to characterise Tanacetum genomes through fluorochrome banding, fluorescent in situ hybridisation (FISH) of rRNA genes and the assessment of genome size by flow cytometry. We appraise the effect of polyploidy and evaluate the existence of intraspecific variation based on the number and distribution of GC-rich bands and rDNA loci. Finally, we infer ancestral genome size and other cytogenetic traits considering phylogenetic relationships within the genus.

RESULTS

We report first genome size (2C) estimates ranging from 3.84 to 24.87 pg representing about 11 % of those recognised for the genus. We found striking cytogenetic diversity both in the number of GC-rich bands and rDNA loci. There is variation even at the population level and some species have undergone massive heterochromatic or rDNA amplification. Certain morphometric data, such as pollen size or inflorescence architecture, bear some relationship with genome size. Reconstruction of ancestral genome size, number of CMA+ bands and number of rDNA loci show that ups and downs have occurred during the evolution of these traits, although genome size has mostly increased and the number of CMA+ bands and rDNA loci have decreased in present-day taxa compared with ancestral values.

CONCLUSIONS

Tanacetum genomes are highly unstable in the number of GC-rich bands and rDNA loci, although some patterns can be established at the diploid and tetraploid levels. In particular, aneuploid taxa and some odd ploidy species show greater cytogenetic instability than the rest of the genus. We have also confirmed a linked rDNA arrangement for all the studied Tanacetum species. The labile scenario found in Tanacetum proves that some cytogenetic features previously regarded as relatively constant, or even diagnostic, can display high variability, which is better interpreted within a phylogenetic context.

Swarm of terminal 35S in Cheirolophus (Asteraceae, Centaureinae)

Island radiation constitutes a playground for species diversification, which has long fascinated researchers and still does today. Because only a small subset of taxa within the pool of island colonizers is concerned by this process, the question is raised on whether some factors could make a taxon prone to radiate. Cheirolophus is the only genus of Centaureinae subtribe to have experienced a radiation in the Canary Islands. Cytogenetic characterization through FISH of 5S and 35S ribosomal RNA genes in eight Cheirolophus species from continent and Canary Islands revealed an unusually high number of 35S predominantly at terminal position, together with a single interstitial 5S rDNA locus in all the studied taxa. Such an abundance of 35S rDNA signals is unique among Centaureinae and predates Cheirolophus arrival in Canary Islands. The possible link of the rDNA profile with radiation process is discussed through a comparison with two other case studies, the closely related Rhaponticum group and the genus Centaurea.

Plant rDNA database: ribosomal DNA loci information goes online

Number, position and structure of the 5S and 18S-5.8S-26S ribosomal DNA (rDNA) loci are important species characteristics. In recent decades, we have witnessed accumulation of rDNA data, and there is a need to compile, store and analyse this information, and to make it accessible to a broader scientific community. An online resource, accessible at www.plantrdnadatabase.com , has been developed to accomplish these goals. Current knowledge regarding chromosomal rDNA sites is provided for more than 1,000 plant species (including more than 1,400 different accessions). The data comes from fluorescent in situ hybridisation experiments (FISH) from more than 300 publications. Additional information is also displayed, such as ploidy level, mutual arrangement of rRNA genes, genome size and life cycle. The webpage is intuitive and user-friendly, including different search options, and currently holds information published (or in press) up until January 2011; frequent updates are planned. We expect this database to be used for data-mining, analysing rDNAs from different angles, unit organisation, distribution, evolution and linkage of rDNA patterns with phylogenetic relationships.

Telomere and 45S rDNA sequences are structurally linked on the chromosomes in Chrysanthemum segetum L

Some reports have shown that nucleolar organizer regions are located at the telomeric region and have a structural connection with telomeres at the cellular level in many organisms. In this study, we found that all 45S ribosomal DNA (rDNA) signals were located at telomeric regions on the chromosomes in Chrysanthemum segetum L., and the 45S rDNA showed distinct signal patterns on different metaphase chromosome spreads. The bicolor fluorescence in situ hybridization experiment on the extended fibers revealed that telomere repeats were structurally connected with or interspersed into rDNA sequences. The close cytological structure relation between rDNA and telomere sequences led us to use PCR with combinations of the telomere primer and the rDNA primer to obtain some fragments, which were flanked by different rDNA and telomere primer sequences. One representative clone CHS2 contains closely connected rDNA and telomere sequences, suggesting that the telomere sequence invaded into the conserved rDNA sequence. In addition, the sequences of some PCR clones were flanked by the single telomeric primer sequence or the rDNA primer sequence. These results suggested that homologous recombination occurred between tandem repeat units of rDNA sequences or telomere repeats at the chromosome terminus.

Heterochromatin patterns and ribosomal DNA loci distribution in diploid and polyploid Crotalaria species (Leguminosae, Papilionoideae), and inferences on karyotype evolution

Most Crotalaria species display a symmetric karyotype with 2n = 16, but 2n = 14 is found in Chrysocalycinae subsection Incanae and 2n = 32 in American species of the section Calycinae. Seven species of the sections Chrysocalycinae, Calycinae, and Crotalaria were analyzed for the identification of heterochromatin types with GC- and AT-specific fluorochromes and chromosomal location of ribosomal DNA loci using fluorescent in situ hybridization (FISH). A major 45S rDNA locus was observed on chromosome 1 in all the species, and a variable number of minor ones were revealed. Only one 5S rDNA locus was observed in the species investigated. Chromomycin A(3) (CMA) revealed CMA(+) bands colocalized with most rDNA loci, small bands unrelated to ribosomal DNA on two chromosome pairs in Crotalaria incana, and CMA(+) centromeric bands that were quenched by distamycin A were detected in species of Calycinae and Crotalaria sections. DAPI(+) bands were detected in C. incana. The results support the species relationships based on flower specialization and were useful for providing insight into mechanisms of karyotype evolution. The heterochromatin types revealed by fluorochromes suggest the occurrence of rearrangements in repetitive DNA families in these heterochromatic blocks during species diversification. This DNA sequence turnover and the variability in number/position of rDNA sites could be interpreted as resulting from unequal crossing over and (or) transposition events. The occurrence of only one 5S rDNA locus and the smaller chromosome size in the polyploids suggest that DNA sequence losses took place following polyploidization events.

A molecular phylogenetic approach to western North America endemic Artemisia and allies (Asteraceae): untangling the sagebrushes

PREMISE OF THE STUDY

Artemisia subgenus Tridentatae plants characterize the North American Intermountain West. These are landscape-dominant constituents of important ecological communities and habitats for endemic wildlife. Together with allied species and genera (Picrothamnus and Sphaeromeria), they make up an intricate series of taxa whose limits are uncertain, likely the result of reticulate evolution. The objectives of this study were to resolve relations among Tridentatae species and their near relatives by delimiting the phylogenetic positions of subgenus Tridentatae species with particular reference to its New World geographic placement and to provide explanations for the relations of allied species and genera with the subgenus with an assessment of their current taxonomic placement.

METHODS

Bayesian inference and maximum parsimony analysis were based on 168 newly generated sequences (including the nuclear ITS and ETS and the plastid trnS(UGA)-trnfM(CAU) and trnS(GCU)-trnC(GCA)) and 338 previously published sequences (ITS and ETS). Genome size by flow cytometry of species from Sphaeromeria was also determined.

KEY RESULTS

The results support an expanded concept and reconfiguration of Tridentatae to accommodate additional endemic North American Artemisia species. The monotypic Picrothamnus and all Sphaeromeria species appear nested within subgenus Tridentatae clade.

CONCLUSIONS

A redefinition of subgenus Tridentatae to include other western North American endemics is supported. We propose a new circumscription of the subgenus and divide it into three sections: Tridentatae, Filifoliae, and Nebulosae. The position of the circumboreal and other North American species suggests that subgenus Artemisia is the ancestral stock for the New World endemics, including those native to South America.