Nuclear genome size variation in fleshy-fruited Neotropical Myrtaceae

The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet ( Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea , Saintpaulia, and Streptocarpus , all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia , a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%–26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine–cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon ( Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ∼633 × 106 base pairs, which is approximately 40% of the previously published estimate.

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Chromosome and nuclear DNA study on Luzula - a genus with holokinetic chromosomes

Genome ◽

10.1139/g03-121 ◽

2004 ◽

Vol 47 (2) ◽

pp. 246-256 ◽

Cited By ~ 18

Author(s):

Elzbieta Kuta ◽

Borut Bohanec ◽

Ewa Dubas ◽

Liliana Vizintin ◽

Leslaw Przywara

Keyword(s):

Genome Size ◽

Nuclear Dna ◽

Size Variation ◽

Nuclear Genome ◽

Dna Amount ◽

Genome Size Variation ◽

Chromosome Fusion ◽

Holokinetic Chromosomes ◽

Nuclear Dna Amount ◽

Leaf Tissues

Chromosomes and nuclear DNA amount were analyzed in leaf tissues of Luzula nivea, Luzula luzuloides, and Luzula multiflora. Intra- and interspecific karyological variability was stated. Chromosome numbers in diploids ranged 2n = 8-24 in L. nivea and L. luzuloides and 2n = 12-84 in hexaploid L. multiflora. Karyological variability resulted mainly from chromosome fission (agmatoploidy) and aneusomaty; chromosome fusion (symploidy) and polyploidy were also involved. Flow cytometric determination of nuclear genome size using propidium iodide staining gave values of 1.584 pg in L. luzuloides, 1.566 pg in L. nivea, and 3.034 pg in L. multiflora. Variability in relative nuclear genome size within species was measured by 4',6-diamidino-2-phenylindole staining. In contrast with previous reports, variability was fairly small and ranged from 1.796 to 1.864 pg in L. luzuloides, from 1.783 to 1.847 pg and from 1.737 to 1.808 pg in two populations (S and F) of L. nivea, respectively, and from 3.125 to 3.271 pg in L. multiflora. An intraplant (interleaf) genome size variation was also observed and its possible causes are discussed.Key words: Luzula, holokinetic chromosomes, agmatoploidy, symploidy, polyploidy, nuclear DNA amount, intraplant genome size variability, flow cytometry.

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Nuclear genome size variation in the allopolyploid Onosma arenaria – O. pseudoarenaria species group: methodological issues and revised data

Botany ◽

10.1139/cjb-2017-0164 ◽

2018 ◽

Vol 96 (6) ◽

pp. 397-410 ◽

Cited By ~ 2

Author(s):

V. Kolarčik ◽

V. Kocová ◽

D. Caković ◽

T. Kačmárová ◽

J. Piovár ◽

...

Keyword(s):

Genome Size ◽

Size Variation ◽

Nuclear Genome ◽

Taxonomic Revision ◽

Balkan Peninsula ◽

Species Group ◽

Genome Size Variation ◽

Size Groups ◽

Internal Standardization ◽

Size Estimates

We used flow cytometry (FCM) to investigate genome size variation in two polymorphic allopolyploids, Onosma arenaria Waldst. and Kit. and O. pseudoarenaria Schur, in Central Europe and the Balkan Peninsula. An intercalating DNA stain, propidium iodide (PI), and internal standardization were used. Our data showed that cytosolic compounds may be present in FCM samples and could inhibit, or more frequently promote, PI intercalation. In the absence of PI intercalation interference, leaf-based genome size estimates were observed to be lower than seed-based ones in O. pseudoarenaria, whereas no difference was recorded in O. arenaria. In incubation tests, genome size values frequently increase after a longer staining period. For final genome size measurements, we applied the FCM protocol based on seed material using a ∼150 min incubation period, and provide evidence of mean genome size variation among populations of both species. Two and four natural genome size groups were revealed in O. arenaria and O. pseudoarenaria respectively. Group mean genome sizes varied considerably in both O. arenaria (5.36–5.76 pg) and O. pseudoarenaria (5.98–6.58 pg). This extensive genome size variation is attributed to unexplored taxonomic heterogenity in both taxa. Future taxonomic revision of the group may be supported with genome size measurements obtained using an appropriately standardized methodology.

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Ploidy tug-of-war: evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen

10.1101/084467 ◽

2016 ◽

Author(s):

Aleeza C. Gerstein ◽

Heekyung Lim ◽

Judith Berman ◽

Meleah A. Hickman

Keyword(s):

Genome Size ◽

Fungal Pathogen ◽

Size Variation ◽

Nuclear Genome ◽

Complete Medium ◽

Genome Size Variation ◽

Ploidy Levels ◽

Human Fungal Pathogen ◽

Original Genome ◽

Phosphorus Depletion

AbstractVariation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is selected over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term ‘ploidy drive’. We evolved haploid, diploid, and polyploid strains of the human fungal pathogen Candida albicans under three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive. Strains generally maintained or acquired smaller genome sizes in minimal medium and under phosphorus depletion compared to in a complete medium, while mostly maintained or acquired increased genome sizes under nitrogen depletion. Surprisingly, improvements in fitness often ran counter to changes in total nuclear genome size; in a number of scenarios lines that maintained their original genome size often increased in fitness more than lines that converged towards diploidy. Combined, this work demonstrates a role for both the environment and genotype in determination of the rate of ploidy drive, and highlights questions that remain about the force(s) that cause genome size variation.

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Documenting Intraspecfic Genome Size Variation in Soybean

Crop Science ◽

10.2135/cropsci2004.0261 ◽

2004 ◽

Vol 44 (1) ◽

pp. 261 ◽

Cited By ~ 6

Author(s):

A. Lane Rayburn ◽

D. P. Biradar ◽

R. L. Nelson ◽

R. McCloskey ◽

K. M. Yeater

Keyword(s):

Genome Size ◽

Size Variation ◽

Genome Size Variation

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Genome size variation in deep-sea amphipods

Royal Society Open Science ◽

10.1098/rsos.170862 ◽

2017 ◽

Vol 4 (9) ◽

pp. 170862 ◽

Cited By ~ 3

Author(s):

H. Ritchie ◽

A. J. Jamieson ◽

S. B. Piertney

Keyword(s):

Life History ◽

Genome Size ◽

Deep Sea ◽

Research Effort ◽

Life History Strategy ◽

Size Variation ◽

Genome Size Variation ◽

New Hebrides ◽

Contrast Analysis ◽

Independent Contrast

Genome size varies considerably across taxa, and extensive research effort has gone into understanding whether variation can be explained by differences in key ecological and life-history traits among species. The extreme environmental conditions that characterize the deep sea have been hypothesized to promote large genome sizes in eukaryotes. Here we test this supposition by examining genome sizes among 13 species of deep-sea amphipods from the Mariana, Kermadec and New Hebrides trenches. Genome sizes were estimated using flow cytometry and found to vary nine-fold, ranging from 4.06 pg (4.04 Gb) in Paralicella caperesca to 34.79 pg (34.02 Gb) in Alicella gigantea . Phylogenetic independent contrast analysis identified a relationship between genome size and maximum body size, though this was largely driven by those species that display size gigantism. There was a distinct shift in the genome size trait diversification rate in the supergiant amphipod A. gigantea relative to the rest of the group. The variation in genome size observed is striking and argues against genome size being driven by a common evolutionary history, ecological niche and life-history strategy in deep-sea amphipods.

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Patterns of genome size variation in snapping shrimp

Genome ◽

10.1139/gen-2015-0206 ◽

2016 ◽

Vol 59 (6) ◽

pp. 393-402 ◽

Cited By ~ 19

Author(s):

Nicholas W. Jeffery ◽

Kristin Hultgren ◽

Solomon Tin Chi Chak ◽

T. Ryan Gregory ◽

Dustin R. Rubenstein

Keyword(s):

Genome Size ◽

Phylogenetic Signal ◽

Size Variation ◽

Diverse Group ◽

Chromosome Size ◽

Genome Size Variation ◽

Large Genome ◽

Large Genome Size ◽

Single Genus ◽

Geographic Regions

Although crustaceans vary extensively in genome size, little is known about how genome size may affect the ecology and evolution of species in this diverse group, in part due to the lack of large genome size datasets. Here we investigate interspecific, intraspecific, and intracolony variation in genome size in 39 species of Synalpheus shrimps, representing one of the largest genome size datasets for a single genus within crustaceans. We find that genome size ranges approximately 4-fold across Synalpheus with little phylogenetic signal, and is not related to body size. In a subset of these species, genome size is related to chromosome size, but not to chromosome number, suggesting that despite large genomes, these species are not polyploid. Interestingly, there appears to be 35% intraspecific genome size variation in Synalpheus idios among geographic regions, and up to 30% variation in Synalpheus duffyi genome size within the same colony.

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