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opennotspecifiedJun 2015View details →

FIGURE 3 in Molecular, chromosomal and morphological characters reveal a new diploid species in the Smilax china complex (Smilacaceae)

FIGURE 3. Morphology and karyotype of Smilax microdontus sp. nov.. A. Inflorescence & male flowers; B. Leaf blade (dry), showing pale green color abaxially and minutely serrulate blade margin; C. The chromosomes of population mYXS (mitotic metaphase); D. Habit, showing the sub-erect stem and flowers in May; E. red fruits in October. Bars represent 1 cm.

opennotspecifiedMar 2024View details →

FIGURE S1 in Two new diploid species of Isoetes (Isoetaceae: Lycopodiopsida) from Southeastern China based on morphological and molecular evidence

FIGURE S1. Spore morphology of Isoetes in China. (A) I. changleensis (B) I. yuhangensis (C) I. taiwanensis (cited from Liu et al. 2008). (D) I. sinensis (cited from Liu et al. 2008). (E) I. baodongii (cite from Lu et al. 2021). (F) I. longpingii (cite from Shu et al. 2022). (G) I. xiangfei (cite from Shu et al. 2022). (H) I. orientalis (cited from Liu et al. 2008). (I) I. yunguiensis (cited from Liu et al. 2008). (J) I. hypsophila (cited from Li et al. 2019). (K) I. shangrilaensis (cited from Li et al. 2019). Scale bars: A1–A3 = 100 μm; A4–A5 = 5 μm; B1–B3 = 100 μm; B4–B5 = 5 μm; C1–C3 = 150 μm; C4 = 12 μm; C5 = 8.6 μm; D1–D3 = 150 μm; D4–D5 = 10 μm; E1–E2 = 100 μm; E3–E4 = 10 μm; F1–F2 = 100 μm; F3–F4 = 10 μm; G1–G2 = 100 μm; G3–G4 = 10 μm; H1–H2 = 75 μm; H3–H4 = 4 μm; I1,I3 = 176 μm; I2 = 136 μm; I4–I5 = 10 μm; J1–J3 = 200 μm; J4–J5 = 10 μm; K1–K3 = 200 μm; K4–K5 = 10 μm.

FIGURE 1 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 1. Map of sample sites of Pannonian populations of Odontarrhena tortuosa under study. Population codes follow Table 1. Taxa (O. tortuosa subsp. heterophylla and O. tortuosa subsp. tortuosa), ploidy levels and the type of substrate are indicated by symbol colours and shapes.

FIGURE 4 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 4. Canonical discriminant analysis (CDA 1) of 329 individuals of Odontarrhena tortuosa based on 27 morphological characters and three predefined groups corresponding to populations from three geographic regions differing in the type of substrate: (1) sand dunes in southwestern Slovakia, central Hungary and northern Serbia (tetraploid populations 24GRE, 244ORK, 471MCL, 473UZO, 539KIS, 540KSH), (2) sandy and rocky screes in central Hungary (diploid populations 13PIL, 447TOK, 537DOR, 538CSI), (3) calcareous rocks in eastern Slovakia (diploid populations 201JBV, 552KRV, 553HRH). 95 % isodensity circles are depicted. Population codes follow Table 1. For total canonical structure, see Table 5.

FIGURE 5 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 5. Canonical discriminant analyses (CDA) of 329 individuals of Odontarrhena tortuosa based on 27 morphological characters. A. CDA 2 with diploids (black) and tetraploids (white) as two predefined groups, B. CDA 3 with O. tortuosa subsp. tortuosa (white) and O. tortuosa subsp. heterophylla (black) as two predefined groups. For total canonical structure, see Table 5.

FIGURE 3 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 3. Principal coordinate analysis (PCoA) of 13 populations of Odontarrhena tortuosa based on 27 morphological characters and population means. The first three components explain 46.3%, 18.5% and 10.1% of the variation, respectively. Different colours and symbols are used to mark the two ploidy levels, two subspecies and populations from three regions differing in the type of substrate: diploids of O. tortuosa subsp. heterophylla from rocks of the Slovak Karst and Vihorlat Mts in eastern Slovakia (black squares), diploids of O. tortuosa subsp. tortuosa from habitats with sandy and rocky screes in the Gerecse, Pilis and Buda Mts in the northern part of central Hungary (black circles), and tetraploids of O. tortuosa subsp. tortuosa from sand dunes in southwestern Slovakia, central Hungary and northern Serbia (white circles).

FIGURE 2 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 2. Monoploid relative genome size variation of Pannonian populations of Odontarrhena tortuosa sorted into groups based on three criteria: ploidy level (A), assignment to a subspecies (B) and the type of substrate (C). Boxes define the 25th and 75th percentiles, vertical lines within boxes indicate medians, and whiskers extend from minimum to maximum values.

opennotspecifiedJan 2018View details →

FIGURE 2 in Allium monophyllum (Amaryllidaceae) is a diploid species

FIGURE 2. Diploid idiogram of Allium monophyllum, based on the data of Table 1. Chromosomes #15 and #16 showing satellites are shown in the second row. Measures are in μm.

opennotspecifiedMar 2024View details →

TABLE 1 in Two new diploid species of Isoetes (Isoetaceae: Lycopodiopsida) from Southeastern China based on morphological and molecular evidence

TABLE 1. Comparative accounts on the morphology of megaspores and microspores of Isoetes species in China.<table><tbody><tr><th></th><th>I. changleensis</th><th>I. yuhangensis</th><th>I. baodongii</th><th>I. sinensis</th><th>I. longpingii</th><th>I. xiangfei</th><th>I. orientalis</th><th>I. taiwanensis</th><th>I. yunguiensis</th><th>I. hypsophila</th><th>I. shangrilaensis</th></tr></tbody><tbody><tr><th>Megaspore diameter (μm)</th><td>246–314</td><td>270–324</td><td>390–510</td><td>317–424</td><td>310–410</td><td>390–450</td><td>350–460</td><td>280–340</td><td>340–430</td><td>361–510</td><td>207–273</td></tr><tr><th>Mean megaspore size (μm)</th><td>284</td><td>302</td><td>450</td><td>378</td><td>350</td><td>430</td><td>420</td><td>312</td><td>390</td><td>450</td><td>245</td></tr><tr><th>Ornamentation of megaspores</th></tr><tr><th>proximal surface</th><td>tuberculate</td><td>rugulate</td><td>echinate-cristate</td><td>echinate</td><td>tuberculate-cristate</td><td>cristate-reticulate</td><td>cristate-reticulate</td><td>tuberculate</td><td>cristate-reticulate</td><td>levigate</td><td>levigate</td></tr><tr><th>Equatorial surface (girdle)</th><td>rugulate</td><td>smooth</td><td>/</td><td>loss</td><td>/</td><td>/</td><td>/</td><td>smooth</td><td>loss</td><td>loss</td><td>smooth</td></tr><tr><th>distal surface</th><td>rugulate</td><td>rugulate</td><td>echinate-cristate</td><td>echinate-cristate</td><td>tuberculate-cristate</td><td>cristate-reticulate</td><td>cristate-reticulate</td><td>tuberculate-cristate</td><td>cristate-reticulate</td><td>levigate</td><td>tuberculate-rugulate</td></tr><tr><th>Range microspore size (μm)</th><td>14–20</td><td>16–26</td><td>22–27</td><td>20–29</td><td>27–30</td><td>26–28</td><td>20–38</td><td>20–28</td><td>20–25</td><td>19–25</td><td>11–24</td></tr><tr><th>Mean microspore size (μm)</th><td>18</td><td>21</td><td>25</td><td>25</td><td>29</td><td>27</td><td>34</td><td>24</td><td>22</td><td>22</td><td>19</td></tr><tr><th>Ornamentation of microspores</th><td>blunt-tipped echinate</td><td>sharp-tipped echinate</td><td>echinate</td><td>echinate</td><td>echinate</td><td>echinate</td><td>echinate-tuberculate</td><td>echinate</td><td>levigate-granulate</td><td>rugulate</td><td>echinate-cristate</td></tr><tr><th>Chromosome number</th><td>22</td><td>22</td><td>22</td><td>44</td><td>44</td><td>44</td><td>66</td><td>22</td><td>22</td><td>22</td><td>22</td></tr><tr><th>Data Source</th><td>this study</td><td>this study</td><td>Lu et al. 2021</td><td>Liu et al. 2008</td><td>Shu et al. 2022</td><td>Shu et al. 2022</td><td>Liu et al. 2008</td><td>Liu et al. 2008</td><td>Liu et al. 2008</td><td>Li et al. 2019</td><td>Li et al. 2019 Shu et al. 2022</td></tr></tbody></table>Note:/ represents no data.

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Effects of temperature treatments on cytosine-methylation profiles of diploid and tetraploid plants of the alpine species Ranunculus kuepferi (Ranunculaceae)

The current dataset refers to the DNA methylation patterns of diploid and tetraploid individuals of Ranunculus kuepferi, obtained with the method of methylation-sensitive AFLPs (MS-AFLPs). The individuals of Ranunculus kuepferi were collected from several locations throughout the distribution of the species in the Alps, transferred to the old Botanical Garden of Göttingen and placed into two climate chambers MC1000E (Snijders Scientific, Tilburg, Netherlands), where the temperature treatment experiments took place. In the first chamber a cold treatment was applied (+7°C day/+2°C night; frost treatment: -1°C cold shocks for three nights per week), while in the second chamber a warm treatment was applied (+15° day/+10°C night). The plants were shifted from one treatment to the other one after the end of the 2016 flowering period and leaf material was collected during the flowering period of 2016 and 2017. This material went through the respective lab procedures in order to obtain the genome-wide patterns of epigenetic variation via MS-AFLPs. The analysis of the electropherograms was conducted with Peakscanner v.2 and fragment scoring was performed with RawGeno 2.0-1 R package. These fragment scoring binary matrices are presented here.

opencc-zeroJun 2021View details →

FIGURE 4 in A new diploid species of Leucanthemum (Asteraceae, Anthemideae) from Liguria (northwestern Italy)

FIGURE 4. Leucanthemum ligusticum sp. nov. Examples of metaphasic plates and relative haploid idiograms, from Ponte di Lagoscuro (A, D), Rocche di Valletti (B, E) and Rocchetta di Vara (C, F). Scale bars of metaphasic plates = 10 µm; scale bars of haploid idiograms = 1 µm.

FIGURE 3 in A new diploid species of Leucanthemum (Asteraceae, Anthemideae) from Liguria (northwestern Italy)

FIGURE 3. Leucanthemum ligusticum sp. nov. Known geographical distribution in eastern Liguria (northwestern Italy Italy).

FIGURE 2 in A new diploid species of Leucanthemum (Asteraceae, Anthemideae) from Liguria (northwestern Italy)

FIGURE 2. Leucanthemum ligusticum sp. nov. Variability of basal leaves in individuals from Ponte di Lagoscuro (A), Rocche di Valletti (B), Rocchetta di Vara (C). Variability of cauline leaves, upper ones (sx) to lower ones (dx), from Ponte di Lagoscuro (D), Rocche di Valletti (E), Rocchetta di Vara (F). Scale bars: 10 cm.

FIGURE 1 in A new diploid species of Leucanthemum (Asteraceae, Anthemideae) from Liguria (northwestern Italy)

FIGURE 1. Leucanthemum ligusticum sp. nov. General view of the plant (A); closeup of a capitulum in top view (B) and bottom view (C).

opennotspecifiedNov 2013View details →

FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 in Taxonomic identity of the Iranian diploid Triticum as evidenced by nrDNA ITS analysis

FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 sequences inferred by the Neighbor-Joining method using the Kimura 2- parameter model; all bootstrap values over 50% are shown. Sequences obtained from the NCBI are marked with the sequence accession numbers. Aegilops tauschii sequence was defined as an outgroup in the analysis. Clades 1 and 2 are associated with Triticum monococcum s. lat. and T. urartu, respectively.

opennotspecifiedNov 2013View details →

FIGURE 2 in Taxonomic identity of the Iranian diploid Triticum as evidenced by nrDNA ITS analysis

FIGURE 2. Distribution map of Triticum monococcum subsp. aegilopoides (□) and Triticum urartu (■) in Iran.

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Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species

Despite their suitability for studying evolution, many conifer species have large and repetitive giga-genomes (16-31Gbp) that create hurdles to producing high coverage SNP datasets that capture diversity from across the entirety of the genome. Due in part to multiple ancient whole genome duplication events, gene family expansion and subsequent evolution within Pinaceae, false diversity from the misalignment of paralog copies creates further challenges in accurately and reproducibly inferring evolutionary history from sequence data. Here, we leverage the cost-saving benefits of pool-seq and exome-capture to discover SNPs in two conifer species, Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco, Pinaceae) and jack pine (Pinus banksiana Lamb., Pinaceae). We show, using minimal baseline filtering, that allele frequencies estimated from pooled individuals show a strong positive correlation with those estimated by sequencing the same population as individuals (r > 0.948), on par with such comparisons made in model organisms. Further, we highlight the utility of haploid megagametophyte tissue for identifying sites that are likely due to misaligned paralogs. Together with additional minor filtering, we show that it is possible to remove many of the loci with large frequency estimate discrepancies between individual and pooled sequencing approaches, improving the correlation further (r > 0.973). Our work addresses bioinformatic challenges in non-model organisms with large and complex genomes, highlights the use of megagametophyte tissue for the identification of paralog sites, and suggests the combination of pool-seq and exome capture to be robust for further evolutionary hypothesis testing in these systems.

opencc-zeroDec 2020View details →

opennotspecifiedDec 2014View details →

FIGURE 3. P in A new diploid butterwort species (Pinguicula, Lentibulariaceae) from Sardinia

FIGURE 3. P. sehuensis sp. nov., mitotic metaphase plate showing 2n = 16 chromosomes. Scale bar = 10 μm.

opennotspecifiedDec 2014View details →

FIGURE 4 in Stemodia diplohyptoides (Plantaginaceae, Gratiolae): a new diploid species from South America

FIGURE 4. Mitotic chromosomes in species of Stemodia. A. S. diplohyptoides, 2n=2x=22. B. S. hyptoides, 2n=4x=44. Bar= 2 μm. (A, Sosa et al. 123 CTES; B, Sosa 272 CTES).