Flow cytometry and cytogenetic tools in eucalypts: genome size variation × karyotype stability

Carvalho, Guilherme Mendes Almeida; Carvalho, Carlos Roberto; Soares, Fernanda Aparecida Ferrari

doi:10.1007/s11295-017-1186-0

Cited by 10 publications

(14 citation statements)

References 53 publications

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“…We verified inter- and intraspecific variations of GC% for the diploid and polyploid species. Although variations occurred, the overall mean 38.92% CG in Psidium is close to the mean value of 38.06% obtained by means of 22 diploid Eucalyptus species and three of the genus Corymbia , also species of the Myrtaceae family 37 .…”

Section: Discussionsupporting

confidence: 79%

“…Solanum lycopersicum L., 1753, ‘Stupické’ was used as internal standard (2C = 2.00 pg) 10 . 2 cm 2 leaf fragment from each Psidium germplasm and from the S. lycopersicum were simultaneously chopped 43 for about 30 s in a Petri dish containing 0.5 mL OTTO-I 44 modified for species of the Myrtaceae family (0.1 M citric acid, 0.5% Tween 20, 50 µg mL -1 RNAse, 2 mM dithiothreitol, and 7% polyethylene glycol 2000 – PEG) 37 .After adding 0.5 mL of the same buffer, the resulted suspensions were incubated for 3 min, filtered on a 30 μm diameter nylon filter (Partec) in a 2.0 mL microtube, and centrifuged at 100 x g for 5 min. The supernatant was discarded and 100 μL of the same buffer was added to the pellet, which was homogenized in vortex and incubated for 10 min.…”

Section: Methodsmentioning

confidence: 99%

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Genomic and epigenomic variation in Psidium species and their outcome under the yield and composition of essential oils

Silva

Soares

Clarindo

et al. 2023

Sci Rep

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Diploid and polyploid species derived from the euploid series x = 11 occur in the genus Psidium, as well as intraspecific cytotypes. Euploidy in the genus can alter the gene copy number, resulting in several “omics” variations. We revisited the euploidy, reported genomic (nuclear 2C value, GC%, and copy number of secondary metabolism genes) and epigenomic (5-mC%) differences in Psidium, and related them to essential oil yield and composition. Mean 2C values ranged from 0.90 pg (P. guajava) to 7.40 pg (P. gaudichaudianum). 2C value is intraspecifically varied in P. cattleyanum and P. gaudichaudianum, evidencing cytotypes that can be formed from euploid (non-reduced) and/or aneuploid reproductive cells. GC% ranged from 34.33% (P. guineense) to 48.95% (P. myrtoides), and intraspecific variations occurred even for species without 2C value intraspecific variation. Essential oil yield increased in relation to 2C value and to GC%. We showed that P. guajava (diploid) possesses two and P. guineense (tetraploid) four copies of the one specific TPS gene, as well as eight and sixteen copies respectively of the conserved regions that occur in eight TPS genes. We provide a wide “omics'' characterization of Psidium and show the outcome of the genome and epigenome variation in secondary metabolism.

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Section: Discussionsupporting

confidence: 79%

Section: Methodsmentioning

confidence: 99%

Genomic and epigenomic variation in Psidium species and their outcome under the yield and composition of essential oils

Silva

Soares

Clarindo

et al. 2023

Sci Rep

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“…Nevertheless, as for the secondary constriction, we also found a divergence regarding the chromosome with the fluorescent signal, being chromosome 5 in this study and chromosome 3 in Ribeiro et al (2016). Distinct authors have reported the remarkable homogeneity among the karyotypes of Eucalyptus species and even between Eucalyptus and Corymbia a closely related genus (Matsumoto et al 2000, Oudjehih and Abdellah 2006, Carvalho et al 2017. Therefore, the differences regarding the location of secondary constrictions and 5S rDNA in the karyotypes of E. dunnii and the six species analyzed by Ribeiro et al (2016) are most likely a result of variations on the methodologies applied for chromosome classification.…”

Section: Discussionsupporting

confidence: 44%

“…It is worth mentioning that the classification of E. dunnii chromosomes in this study was divergent from the classification proposed by Ribeiro et al (2016) for other species of the genus. In our analysis, the E. dunnii chromosome carrying the secondary constriction was classified as number 6 in the karyotype, in accordance with E. botryoides, E. baileyana, E. microcorys and Corymbia intermedia (Carvalho et al 2017), and with C. citriodora (Carvalho and Carvalho 2016). Such divergence regarding the position of the chromosome with secondary constriction on the karyogram may occur because some authors may or may not consider the secondary constriction and satellite during the chromosome size measurement.…”

Section: Discussionmentioning

confidence: 86%

Physical Mapping of 5S rDNA in <i>Eucalyptus dunnii</i> Maiden and <i>Zea mays</i> L. by PRINS

et al. 2019

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The in situ detection of specific DNA sequences by fluorescence in situ hybridization (FISH) is a widely used tool for physical mapping, which is important to understand genome structure and organization. For species with small chromosomes, detection of the position of marker sequences is useful to aid chromosome identification and classification. Primed in situ labeling (PRINS) comprises an alternative to FISH, but its specificity and sensitivity may be influenced by species-specific factors, as chromosome length and chromatin structure. To overcome these obstacles, we designed a reproducible PRINS protocol for physical mapping of 5S rDNA in Eucalyptus dunnii Maiden and Zea mays L. Slides containing mitotic metaphases were submitted to one cycle of PRINS using 5S rDNA primers. Clear signals for 5S rDNA were observed in metaphase chromosomes of both species. In E. dunnii, 5S rDNA was mapped on the pericentromeric region of the short arm of chromosome 5. For Z. mays, the signal was detected in the terminal region of the long arm of chromosome 2. Although chromosome structure may influence the PRINS resolution, a high signal/background ratio was obtained for both species. In Z. mays, clear 5S rDNA signals were obtained by PRINS and FISH. Nonetheless, the former was superior regarding the time required for signal detection. Therefore, PRINS has the potential to aid plant genome studies by allowing fast detection of repetitive sequences, even in species with small chromosomes. Moreover, this is the first report of specific sequence mapping in Eucalyptus by PRINS, contributing to physical mapping progress in this genus.

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“…Genome size is the total amount of DNA in the nucleus of an organism that is measured either in picograms (1 pg = 10 −12 g) or megabase pairs (Mbp, with 1 pg = 978 Mbp) [8,9]. Flow cytometry has become the method of choice for genome size determination as it can analyse thousands of particles per second, requires small tissue samples, and finally produced high accuracy and resolution data [10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Nuclear Genome Size Determination Of Christia Vespertilionis Via Flow Cytometry

Midin

Fikri

Zailani

2020

Acta Chemica Malaysia

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AbstractChristia vespertilionis (butterfly wing plant) is an ornamental plant originated from South East Asia with reported usage in traditional medicine practice and potential as an anticancer and antitumor. This research aims to estimate the genome size of C. vespertilionis via flow cytometry (FCM) method. The research was conducted with the optimisation of nuclear suspension preparation followed by the genome size estimation. Two chopping techniques [manual chopping (MC) and BDTM Medimachine (MM)] and two lysis buffers (Otto and LBO1) were tested. Otto buffer with manual chopping was found to be the most suitable method, generated fine DNA peak with minimum debris background, and coefficient of variation (CV) value less than 3%. Five replicates of the FCM analysis were made for the genome size determination. The estimated genome size of C. vespertilionis was found to be 3.22 pg by using Glycine max cv. Polanka (2C=2.5pg) as an external reference standard. Further comparison with other Christia species was not possible due to the lack of data on genome size. The genome size data of C. vespertilionis can be useful for future morphology and genetics studies of Christia species.

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Flow cytometry and cytogenetic tools in eucalypts: genome size variation × karyotype stability

Cited by 10 publications

References 53 publications

Genomic and epigenomic variation in Psidium species and their outcome under the yield and composition of essential oils

Genomic and epigenomic variation in Psidium species and their outcome under the yield and composition of essential oils

Physical Mapping of 5S rDNA in <i>Eucalyptus dunnii</i> Maiden and <i>Zea mays</i> L. by PRINS

Nuclear Genome Size Determination Of Christia Vespertilionis Via Flow Cytometry

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