Flow cytometry delivers a key value to detect differences between species and hybrids and to determine ploidy. In addition, DNA weight per nucleus appears to be related to various properties, such as ...the size of the cell and the nucleus, the duration of mitosis and meiosis and the generation time. The variation in DNA weight is also useful to analyze biodiversity, genome evolution and relationships between related taxa and recognizing ploidy-chimeras. Moreover, it is essential to know the size of a genome before one starts to determine the base sequences of DNA of a plant. To be able to measure the amount of DNA per nucleus, a standard that is genetically stable with constant genome size, easy to use and commonly available is recommended for flow cytometry. In this study, standards from selected perennial plants instead of annuals are recommended as these are more stable than individual seedlings and don’t need greenhouse facilities. Four different methods are used here to determine genome sizes or 2C-value (the amount of DNA per nucleus) for the standard values of perennial plants: 1. Eight selected standards are measured separately against four primary standards 2. Starting with the lowest two standards, each result is used cascade-wise as a standard for the next plant. 3/4. Combining six to nine standard plants in a single chopping event: 3. Calculating all standards against a single standard and 4. Calculate all plants cascade-wise. The last combination 3/4 was also used to compare the results from buffers of Bharathan, Galbraith, Otto and Doležel. The aim of this study was to present selected perennial plants to be useful in flow cytometry. Selected perennial plants have several advantages like permanent availability, surviving for weeks without watering and the absence of variation as is possible in seedlings of annuals. The obtained 2C-values of perennial plants, ranging from 2.7 to 70.5 pg, are presented as a valuable tool in the determination of genome sizes.
Agave americana
’Aureomarginata’ is presented as the preferred reference standard.
Nuclear genome size of conifers as measured by flow cytometry with propidium iodide was investigated, striving to collect at least a single species from each genus. 64 out of 67 genera and 172 ...species were measured. Of the 67 genera, 21 are reported here for the first time and the same is true for 76 species. This nearly doubles the number of measured genera and adds 50% to the number of analyzed species. Conifers have chromosome numbers in the range of n = (7)10–12(19). However, the nuclear DNA content (2C‐value) is shown here to range from 8.3 to 71.6 picogram. The largest genome contains roughly 6 × 1010 more base pairs than the smallest genome. Genome sizes are evaluated and compared with available taxonomic treatments. For the mainly (sub)tropical Podocarpaceae small genome sizes were found with a 2C‐value of only 8–28 pg, with 13.5 pg on average. For the Taxaceae 2C‐values from 23–60 pg were determined. Not surprisingly, the genus Pinus with 97 species (39 species measured here) has a broad range with 2C = 38–72 pg. A factor of 2 difference is also found in the Cupressaceae (136 species) with nuclear DNA contents in the range 18–35 pg. Apart from the allohexaploid Sequoia, ploidy plays a role only in Juniperus and some new polyploids are found. The data on genome size support conclusions on phylogenetic relationships obtained by DNA sequencing. Flow cytometry is applicable even to young plants or seeds for the monitoring of trade in endangered species.
ABSTRACT
Monoallelic PMS2 germline mutations cause 5%–15% of Lynch syndrome, a midlife cancer predisposition, whereas biallelic PMS2 mutations cause approximately 60% of constitutional mismatch ...repair deficiency (CMMRD), a rare childhood cancer syndrome. Recently improved DNA‐ and RNA‐based strategies are applied to overcome problematic PMS2 mutation analysis due to the presence of pseudogenes and frequent gene conversion events. Here, we determined PMS2 mutation detection yield and mutation spectrum in a nationwide cohort of 396 probands. Furthermore, we studied concordance between tumor IHC/MSI (immunohistochemistry/microsatellite instability) profile and mutation carrier state. Overall, we found 52 different pathogenic PMS2 variants explaining 121 Lynch syndrome and nine CMMRD patients. In vitro mismatch repair assays suggested pathogenicity for three missense variants. Ninety‐one PMS2 mutation carriers (70%) showed isolated loss of PMS2 in their tumors, for 31 (24%) no or inconclusive IHC was available, and eight carriers (6%) showed discordant IHC (presence of PMS2 or loss of both MLH1 and PMS2). Ten cases with isolated PMS2 loss (10%; 10/97) harbored MLH1 mutations. We confirmed that recently improved mutation analysis provides a high yield of PMS2 mutations in patients with isolated loss of PMS2 expression. Application of universal tumor prescreening methods will however miss some PMS2 germline mutation carriers.
We present a comprehensive overview of PMS2 mutations found in 121 Lynch syndrome and nine CMMRD patients from The Netherlands. PMS2 mutation analysis was performed with recently improved protocols circumventing interference of pseudogene sequences. Eight PMS2 mutation carriers (6%) showed discordant IHC whereas ten patients with isolated PMS2 loss in their tumors harbored an MLH1 mutation.
• Background and Aims Genome size (DNA C-value) data are key biodiversity characters of fundamental significance used in a wide variety of biological fields. Since 1976, Bennett and colleagues have ...made scattered published and unpublished genome size data more widely accessible by assembling them into user-friendly compilations. Initially these were published as hard copy lists, but since 1997 they have also been made available electronically (see the Plant DNA C-values database www.kew.org/cval/homepage.html). Nevertheless, at the Second Plant Genome Size Meeting in 2003, Bennett noted that as many as 1000 DNA C-value estimates were still unpublished and hence unavailable. Scientists were strongly encouraged to communicate such unpublished data. The present work combines the databasing experience of the Kew-based authors with the unpublished C-values produced by Zonneveld to make a large body of valuable genome size data available to the scientific community. • Methods C-values for angiosperm species, selected primarily for their horticultural interest, were estimated by flow cytometry using the fluorochrome propidium iodide. The data were compiled into a table whose form is similar to previously published lists of DNA amounts by Bennett and colleagues. • Key Results and Conclusions The present work contains C-values for 411 taxa including first values for 308 species not listed previously by Bennett and colleagues. Based on a recent estimate of the global published output of angiosperm DNA C-value data (i.e. 200 first C-value estimates per annum) the present work equals 1·5 years of average global published output; and constitutes over 12 % of the latest 5-year global target set by the Second Plant Genome Size Workshop (see www.kew.org/cval/workshopreport.html). Hopefully, the present example will encourage others to unveil further valuable data which otherwise may lie forever unpublished and unavailable for comparative analyses.
The taxonomy of all species of Narcissus (Amaryllidaceae), an important horticultural crop, has not been investigated recently. As a new approach, genome size was determined by flow cytometry with ...propidium iodide from 375 accessions. The somatic nuclear DNA contents (2C) were shown to range from 14 to 38 pg for the diploids. Narcissus assoanus and N. gaditanus are, based on their nuclear DNA content, removed from section Apodanthi and placed in a new section Juncifolii. The different ploidy levels and species involved were entangled for N . “fernandesii” s.l. and a new allotetraploid form is named here. Section Pseudonarcissus was much more heterogeneous in nuclear DNA content than expected. Sixty-five accessions of N. pseudonarcissus possessed, with 23.7 pg, similar amounts of DNA. However, several species from this section were clearly distinctive in nuclear DNA content. It runs from the diploid N. primigenius with 21.7 pg to the also diploid N. nevadensis with 38.2 pg. Also N. abscissus and N. moleroi are with about 26 pg clearly different from N. pseudonarcissus. For the first time, in 11 accessions, hexaploidy was found in N. pseudonarcissus ssp. bicolor. A new section Nevadensis with 30-39 pg of nuclear DNA was split off from the section Pseudonarcissus with now 21-27 pg. A nonoploid N. dubius with 96.3 pg has by far the highest amount of nuclear DNA and can be calculated to have the highest ploidy ever reported in Narcisssus. The total number of Narcissus species was determined as 36, nine more than in Flora Europaea and they were divided up in two subgenera and 11 sections. Flow cytometry is shown to produce easily obtainable and original systematic data that lead to new insights. Genome size or C-value turns out to be one of the most salient features to define the status of the species in the genus Narcissus.
For the first time, genome size was determined from a total of 343 wild collected plants from the succulent genera Haworthia and Astroloba (Asphodelaceae: Alooideae). Genome sizes (2C values) turned ...out to be rather close, especially within genus Haworthia s.s. To improve the accuracy of the results, in the end 2,368 measurements were made. The measured nuclear DNA contents provide a further basis for the separation of Haworthia s.l. into three genera. This resulted in 69 recognized species of the new genera Haworthia, Haworthiopsis and Tulista. The 2C values for the largest genus Haworthia (=Haworthia subgenus Haworthia) with 45 species varies only from 21.7 to 24.7 pg. An exception is some accessions of Haworthia nortieri (var. agnis) with up to 27.2 pg. The four varieties of H. nortieri are here elevated to species level and placed in a new section Nortierae Zonn. The genus Haworthiopsis (=Haworthia subgenus Hexangulares) are clearly divided in two sections, each with 10 species: section Coarctatae (25.2–27.6 pg) and Venosae (28.9–33.6 pg). The highest value so far for Haworthia s.l. has been H. limifolia which is hexaploid with 99.8 pg. The third genus Tulista (=Haworthia subgenus QueryRobustipedunculares) with only four species varies from 35.9 to 37.2 pg. Closely related with Tulista also with respect to genome size is the genus Astroloba (including Poelnitzia) with nine species and from 30.4 to 34.0 pg. The results also show that most, but not all varieties are correctly attributed to the nominate species. A few varieties have been reinstated as species of which two have been renamed in Haworthiopsis. Further details are discussed in the main text. The genome sizes were compared with the genome sizes of all species of Gasteria, Chortolirion and 83 Aloe species. Aloidendron (=Aloe section Aloidendron) with 24.5–37.4 pg, comes out as the most basal in the published cladogram for the Alooidae. It leads to the interesting suggestion that the amount of nuclear DNA of the two species in section Kumara (=Aloe section Kumara) namely K. plicatilis (17.6 pg) and K. haemanthifolia (16.2 pg) and species in Aloiampelos (=Aloe section Macrifoliae; (21.6 pg) have decreased strongly, which is a rare phenomenon.
To enhance classification of variants of uncertain significance (VUS) in the DNA mismatch repair (MMR) genes in the cancer predisposition Lynch syndrome, we developed the cell-free in vitro MMR ...activity (CIMRA) assay. Here, we calibrate and validate the assay, enabling its integration with in silico and clinical data.
Two sets of previously classified MLH1 and MSH2 variants were selected from a curated MMR gene database, and their biochemical activity determined by the CIMRA assay. The assay was calibrated by regression analysis followed by symmetric cross-validation and Bayesian integration with in silico predictions of pathogenicity. CIMRA assay reproducibility was assessed in four laboratories.
Concordance between the training runs met our prespecified validation criterion. The CIMRA assay alone correctly classified 65% of variants, with only 3% discordant classification. Bayesian integration with in silico predictions of pathogenicity increased the proportion of correctly classified variants to 87%, without changing the discordance rate. Interlaboratory results were highly reproducible.
The CIMRA assay accurately predicts pathogenic and benign MMR gene variants. Quantitative combination of assay results with in silico analysis correctly classified the majority of variants. Using this calibration, CIMRA assay results can be integrated into the diagnostic algorithm for MMR gene variants.
Nuclear genome size was determined to investigate the relationships between all 19 species of Araucaria de Jussieu. Species from the two other genera of Araucariaceae, Wollemia and Agathis, were also ...studied.The genome size of 17 out of the 19 species of Araucaria are reported here for the first time. All Araucariaceae have the same chromosome number 2n = 26. However, the nuclear DNA contents (2C value) for Araucaria range from 31.3 to 45.4 pg. There is a good correlation between genome size and division in sections, and geographical distribution.The two species from South America have 44.7 and 45.4 pg, the two species from Australia have 35.7 and 44.4 pg and the two species from New Guinea 34.7 and 40.4 pg. All 13 species of New Caledonia and the one from Norfolk Island have a similar, if not identical, amount of nuclear DNA of, on average, 31.9 pg. This corroborates the identical DNA rbcL sequences found for the New Caledonian araucarias. It suggests that the species from New Caledonia diversified more recently and it questions their status as separate species. Compared with this 31.9 pg a strong increase seems to have occurred in the genome size of the "mainland" araucarias. Genome sizes are evaluated and compared with available taxonomic treatments and extant geographic spreading. The nuclear DNA contents found within the sections are close, making it possible to assign an unknown plant to a section. A difference of 1 pg, which amounts to a difference of 978 Mbp, far exceeds a single character. Nuclear DNA content, as measured by flow cytometry, may conveniently be used to produce systematic data. It is applicable even with young plants or seeds for monitoring the trade in endangered species.
Genome sizes of 12 pines that produce edible nuts were investigated by flow cytometry with propidium iodide. Results were compared with the genome size and taste of 11 commercial samples of pine nuts ...to determine which species is the cause of a lingering bitter aftertaste (“pine nut syndrome”). Each nut sample was visually separated into two to six subsets. From a single nut, the embryo and the endosperm were measured. On the basis of nuclear DNA content, pine species could be matched with their nuts. Seven out of the 11 commercial samples contained only a single pine species: P. koraiensis Sieb.& Zucc., P. pinea L., P. armandii Zucc. ex Endl., or P. gerardiana Wall. ex Don, but the other four samples were a mix of two species. Tasting showed definitively that P. armandii is the origin of the bitter aftertaste. Nuclear DNA content can be measured using flow cytometry in less than 5 min, including the calculations. This makes it easy to identify the problem-causing nuts. With hindsight, it is now also possible to identify the species of four common edible pine nuts.
Nuclear DNA contents (2C‐value) are reported for 71 out of 76 accepted species of Zamia (Zamiaceae) using flow cytometry with propidium iodide. Nuclear DNA content in Zamia ranges between 33.7 and ...45.7 pg. Despite this small range, the largest genome contains roughly 1010 more base pairs than the smallest genome.
The results for Zamia point to two centers of biogeographic distribution: Mexico and Colombia. Nicaragua seems to be the biogeographic boundary for these two centres for Zamia. To the north, genome sizes of 33.7–38.0 pg (average 35.6 pg) are found and to the south (Costa Rica, Panama and South America) 41.2–45.7 pg (average 42.9 pg). Plants from the Caribbean islands (including Florida) have intermediate genome sizes with 37.3–40.9 pg (average 38.7 pg). Costa Rica and Panama are in a transition zone and its species can be divided into three subsections: four species with ‘Caribbean’ values of 38.4–39.5 pg (average 39.0 pg), six species with ‘South American’ values with 42.7–43.6 pg, (average 42.9 pg, and six species with intermediate values ranging between 40.1–41.0 pg (average 40.4 pg). The latter values are nearly absent in other areas, suggesting that they could be the products of (introgressive) hybridization. This study represents the first, nearly complete overview of the genome sizes of the genus Zamia and their relationship with biogeography.
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