Giovana Augusta Torres

Repeatless and Repeat-Based Centromeres in Potato: Implications for Centromere Evolution

The authors used a genome-wide approach to identify the DNA sequences associated with the centromeres of potato chromosomes. Five potato centromeres are composed of single- or low-copy sequences, including active genes; six centromeres contain almost exclusively satellite repeats. The results have implications for evolution of repeat-based centromeres from repeatless centromeres. Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats. By contrast, most newly formed centromeres (neocentromeres) do not contain satellite repeats and instead include DNA sequences representative of the genome. An unknown question in centromere evolution is how satellite repeat-based centromeres evolve from neocentromeres. We conducted a genome-wide characterization of sequences associated with CENH3 nucleosomes in potato (Solanum tuberosum). Five potato centromeres (Cen4, Cen6, Cen10, Cen11, and Cen12) consisted primarily of single- or low-copy DNA sequences. No satellite repeats were identified in these five centromeres. At least one transcribed gene was associated with CENH3 nucleosomes. Thus, these five centromeres structurally resemble neocentromeres. By contrast, six potato centromeres (Cen1, Cen2, Cen3, Cen5, Cen7, and Cen8) contained megabase-sized satellite repeat arrays that are unique to individual centromeres. The satellite repeat arrays likely span the entire functional cores of these six centromeres. At least four of the centromeric repeats were amplified from retrotransposon-related sequences and were not detected in Solanum species closely related to potato. The presence of two distinct types of centromeres, coupled with the boom-and-bust cycles of centromeric satellite repeats in Solanum species, suggests that repeat-based centromeres can rapidly evolve from neocentromeres by de novo amplification and insertion of satellite repeats in the CENH3 domains.

Organization and evolution of subtelomeric satellite repeats in the potato genome.

Subtelomeric domains immediately adjacent to telomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes. A common feature associated with subtelomeric regions in different eukaryotes is the presence of long arrays of tandemly repeated satellite sequences. However, studies on molecular organization and evolution of subtelomeric repeats are rare. We isolated two subtelomeric repeats, CL14 and CL34, from potato (Solanum tuberosum). The CL14 and CL34 repeats are organized as independent long arrays, up to 1-3 Mb, of 182 bp and 339 bp monomers, respectively. The CL14 and CL34 repeat arrays are directly connected with the telomeric repeats at some chromosomal ends. The CL14 repeat was detected at the subtelomeric regions among highly diverged Solanum species, including tomato (Solanum lycopersicum). In contrast, CL34 was only found in potato and its closely related species. Interestingly, the CL34 repeat array was always proximal to the telomeres when both CL14 and CL34 were found at the same chromosomal end. In addition, the CL34 repeat family showed more sequence variability among monomers compared with the CL14 repeat family. We conclude that the CL34 repeat family emerged recently from the subtelomeric regions of potato chromosomes and is rapidly evolving. These results provide further evidence that subtelomeric domains are among the most dynamic regions in eukaryotic genomes.

Boom-Bust Turnovers of Megabase-Sized Centromeric DNA in Solanum Species: Rapid Evolution of DNA Sequences Associated with Centromeres

This work compares the sequences of five homoeologous centromeres in two closely related species, revealing rapid divergence of centromeric sequences. The results support the idea that centromeric satellite repeats undergo boom-bust cycles before a favorable repeat is fixed in the population. Centromeres are composed of long arrays of satellite repeats in most multicellular eukaryotes investigated to date. The satellite repeat–based centromeres are believed to have evolved from “neocentromeres” that originally contained only single- or low-copy sequences. However, the emergence and evolution of the satellite repeats in centromeres has been elusive. Potato (Solanum tuberosum) provides a model system for studying centromere evolution because each of its 12 centromeres contains distinct DNA sequences, allowing comparative analysis of homoeologous centromeres from related species. We conducted genome-wide analysis of the centromeric sequences in Solanum verrucosum, a wild species closely related to potato. Unambiguous homoeologous centromeric sequences were detected in only a single centromere (Cen9) between the two species. Four centromeres (Cen2, Cen4, Cen7, and Cen10) in S. verrucosum contained distinct satellite repeats that were amplified from retrotransposon-related sequences. Strikingly, the same four centromeres in potato contain either different satellite repeats (Cen2 and Cen7) or exclusively single- and low-copy sequences (Cen4 and Cen10). Our sequence comparison of five homoeologous centromeres in two Solanum species reveals rapid divergence of centromeric sequences among closely related species. We propose that centromeric satellite repeats undergo boom-bust cycles before a favorable repeat is fixed in the population.

Interstitial telomeric repeats are enriched in the centromeres of chromosomes in Solanum species.

Interstitial telomeric repeats (ITRs) were reported in a number of animal and plant species. Most ITRs are organized as short tandem arrays and are likely evolutionary relics derived from chromosomal rearrangements and DNA repairs. However, megabase-sized ITR arrays were reported in Solanum species. Here, we report a fluorescence in situ hybridization (FISH) survey of ITRs in all representative diploid Solanum species, including potato, tomato, and eggplant. FISH revealed massive amplification of ITRs in the centromeric regions of chromosomes from the Solanum species containing the B and P genomes. A significant proportion of the ITR FISH signals was mapped within the primary constrictions of the pachytene chromosomes of Solanum pinnatisectum (B genome). In addition, some ITR sites overlapped with St49, a satellite repeat enriched in centromeric DNA sequences associated with CENH3 nucleosomes, in both A and B genome Solanum species. These results show that some ITR subfamilies have been amplified and invaded in the functional centromeres of chromosomes in Solanum species.

Functional repetitive sequences and fragile sites in chromosomes of Lolium perenne L.

Lolium perenne is considered a high-quality forage widely used in temperate regions to meet the shortage of forage during the winter. In this species, some peculiarities related to cytogenetic aspects have already been described, as the variability in number and position of 45S ribosomal DNA (rDNA) sites and the expression of fragile sites, which require further studies to support the understanding of their causes and consequences. In this way, this study aimed to evaluate the relationship between the expression of fragile sites and functional repetitive sequences (rDNA and telomeric) in chromosomes of diploid and polyploid cultivars of L. perenne. The techniques of FISH, Ag-NOR and fluorescence banding were used to assess the distribution of sites of 45S rDNA, 5S, telomeric sequences, and the transcriptional activity of the 45S ribosomal genes and the distribution of AT- and/or GC-rich sequences in L. perenne, respectively. There was variability in the number and location of 45S rDNA sites, which was not observed for 5S rDNA sites. One of the genotypes showed two 45S rDNA sites on the same chromosome, located in different chromosome arms. Breaks and gaps were found in 45S rDNA sites in most metaphases evaluated for both cultivars. Telomeric sequences were not detected at the end of the chromosomal fragments corresponding to the location of breaks at 45S sites. Apparently, the transcriptional activity was modified in fragile sites. Variation in the number and size of nucleoli, nucleolar fusions and dissociations were observed. All CMA+ bands were colocalized with the 45S sites.

Chromosome banding and essential oils composition of Brazilian accessions of Lippia alba (Verbenaceae)

The essential oil components and a karyotypic analysis of five Lippia alba (Verbenaceae) accessions from Brazil were performed with the objective of investigating the variation among different populations. The chemistry analysis allowed the grouping of the accessions in two main chemotypes: neral chemotype (LaCat, LaJF and LaRJ) and linalool chemotype (LaGua and LaVC). However, large karyotypic differences, verified by different chromosome banding techniques, were not detected. The results presented the same chromosome number for all accessions (2n = 30) with 10 metacentric chromosomes and 5 submetacentric. The chromosome banding showed great blocks of constitutive heterochromatin (C-bands) around the centromeric region, which was rich in AT bases (DAPI+), while the CMA bands were observed only in terminal regions of six chromosomes. Through Ag-NOR techniques, only two active pairs of NORs were detected on the three pairs of secondary constrictions (the NOR activity is discussed). This work relates the pattern of heterochromatin for Lippia alba for the first time.

Chromosome number and meiosis in populations of Senna species (Caesalpinioideae – Fabaceae) from Southeast Brazil

Senna Mill. is one of the most representative genera of Caesalpinioideae, with wide geographical distribution. Some species have been cytogenetically characterized, but there is no information on population level. Therefore, the present work had the objective of characterizing and comparing chromosomal number and meiotic behavior of 39 accessions belonging to 11 species of Senna Mill. from southern Minas Gerais state, Brazil. Meiotic preparations were obtained by cell suspension technique and stained with 10% Giemsa solution. All meiotic phases were analyzed and the meiotic index was obtained. The species showed different chromosome numbers (n = 12, 13, 14, and 28). Meiotic behavior of four species is described for the first time. The chromosomal numbers reported for most species coincide with those described for populations from either Southern Brazil or from state of Pará. Intraspecific variation for chromosome number was observed in S. rugosa (G. Don) H. S. Irwin & Barneby (n = 14 and n = 28). This variation along with multivalent occurrence suggests polyploidization as an important event in the evolution of this species, as described for many others, mainly in Caesalpinioideae. Most of the analyzed species showed regular meiotic behavior, despite the occurrence of some irregularities.

Abnormal meiotic behavior in three species of Crotalaria.

O objetivo deste trabalho foi comparar o comportamento meiotico e a viabilidade dos graos de polen de tres especies de Crotalaria. A analise meiotica foi realizada por meio da tecnica de secagem ao ar. A viabilidade dos graos de polen foi avaliada por testes de coloracao (corante de Alexander, cloreto de tetrazolio e diacetato de fluoresceina) e por teste de germinacao em solucao de sacarose. Foram observados oito bivalentes, confirmando relatos previos em populacoes de outras regioes do Brasil e de outros paises. As tres especies apresentaram comportamento meiotico irregular: em Crotalaria micans, citomixia e pareamento irregular na diacinese; em C. spectabilis, pareamento irregular no diploteno; e em C. zanzibarica, nucleo fortemente condensado nas fases de leptoteno e zigoteno. A viabilidade dos graos de polen das tres especies e baixa, o que pode estar associado as irregularidades do comportamento meiotico.

Comparative oligo-FISH Mapping: An Efficient and Powerful Methodology to Reveal Karyotypic and Chromosomal Evolution

Development of a eukaryotic karyotype relies on identification of individual chromosomes in the species, which has been accomplished only in a limited... Developing the karyotype of a eukaryotic species relies on identification of individual chromosomes, which has been a major challenge for most nonmodel plant and animal species. We developed a novel chromosome identification system by selecting and labeling oligonucleotides (oligos) located in specific regions on every chromosome. We selected a set of 54,672 oligos (45 nt) based on single copy DNA sequences in the potato genome. These oligos generated 26 distinct FISH signals that can be used as a “bar code” or “banding pattern” to uniquely label each of the 12 chromosomes from both diploid and polyploid (4× and 6×) potato species. Remarkably, the same bar code can be used to identify the 12 homeologous chromosomes among distantly related Solanum species, including tomato and eggplant. Accurate karyotypes based on individually identified chromosomes were established in six Solanum species that have diverged for >15 MY. These six species have maintained a similar karyotype; however, modifications to the FISH signal bar code led to the discovery of two reciprocal chromosomal translocations in Solanum etuberosum and S. caripense. We also validated these translocations by oligo-based chromosome painting. We demonstrate that the oligo-based FISH techniques are powerful new tools for chromosome identification and karyotyping research, especially for nonmodel plant species.

Relationship between pollen morphology and chromosome numbers in Brazilian species of Lippia L. (Verbenaceae)

The pollen morphology and exine structure of 17 species of Lippia L. were investigated in this work using light and scanning electron microscopy. Among the species studied, 14 showed tricolporate pollen grains, two had tri- and tetracolporate pollen grains and a single species exhibited, only tetracolporate pollen. The amb ranged from triangular to square, and the shape varied from oblate-spheroidal to prolate-spheroidal. Three different types of exine ornamentation were observed: psilate, scabrate and perforate. In addition to morphological data, we found positive association between the chromosome numbers and size of pollen grains, and also between the length and width of the colpi. The results indicate that the characteristics of pollen grains in Lippia may be used as an additional taxonomic character of the genus.