scholarly journals The scaling of genome size and cell size limits maximum rates of photosynthesis with implications for ecological strategies

2019 ◽  
Author(s):  
Adam B. Roddy ◽  
Guillaume Théroux-Rancourt ◽  
Tito Abbo ◽  
Joseph W. Benedetti ◽  
Craig R. Brodersen ◽  
...  
Keyword(s):  
Genome Size ◽  
Cell Size ◽  
Maximum Rate ◽  
Strong Predictor ◽  
Plant Ecology ◽  
Carbon Gain ◽  
Genome Size Evolution ◽  
Order Constraint ◽  
Rate Of Photosynthesis ◽  
Packing Densities

AbstractA central challenge in plant ecology is to define the major axes of plant functional variation with direct consequences for fitness. Central to the three main components of plant fitness (growth, survival, and reproduction) is the rate of metabolic conversion of CO2 into carbon that can be allocated to various structures and functions. Here we (1) argue that a primary constraint on the maximum rate of photosynthesis per unit leaf area is the size and packing density of cells and (2) show that variation in genome size is a strong predictor of cell sizes, packing densities, and the maximum rate of photosynthesis across terrestrial vascular plants. Regardless of the genic content associated with variation in genome size, the simple biophysical constraints of encapsulating the genome define the lower limit of cell size and the upper limit of cell packing densities, as well as the range of possible cell sizes and densities. Genome size, therefore, acts as a first-order constraint on carbon gain and is predicted to define the upper limits of allocation to growth, reproduction, and defense. The strong effects of genome size on metabolism, therefore, have broad implications for plant biogeography and for other theories of plant ecology, and suggest that selection on metabolism may have a role in genome size evolution.

scholarly journals Genome size is a strong predictor of cell size and stomatal density in angiosperms

2008 ◽  
Vol 179 (4) ◽  
pp. 975-986 ◽  
Author(s):  
Jeremy M. Beaulieu ◽  
Ilia J. Leitch ◽  
Sunil Patel ◽  
Arjun Pendharkar ◽  
Charles A. Knight
Keyword(s):  
Genome Size ◽  
Cell Size ◽  
Stomatal Density ◽  
Strong Predictor

Cell size does not always correspond to genome size: Phylogenetic analysis in geckos questions optimal DNA theories of genome size evolution

Zoology ◽  
2008 ◽  
Vol 111 (5) ◽  
pp. 377-384 ◽  
Author(s):  
Zuzana Starostová ◽  
Lukáš Kratochvíl ◽  
Martin Flajšhans
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Size ◽  
Cell Size ◽  
Genome Size Evolution ◽  
Size Evolution

Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing

Genome ◽  
2014 ◽  
Vol 57 (10) ◽  
pp. 555-566 ◽  
Author(s):  
Thomas A. Henry ◽  
Jillian D. Bainard ◽  
Steven G. Newmaster
Keyword(s):  
Comparative Analysis ◽  
Genome Size ◽  
Cell Size ◽  
Dna Content ◽  
Habitat Type ◽  
Principal Component ◽  
Genome Size Variation ◽  
Ecological Traits ◽  
Spore Size ◽  
Genome Size Evolution

Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.

PATTERNS OF GENOME SIZE EVOLUTION IN TETRAODONTIFORM FISHES

Evolution ◽  
2001 ◽  
Vol 55 (11) ◽  
pp. 2363 ◽  
Author(s):  
Elizabeth L. Brainerd ◽  
Sandra S. Slutz ◽  
Edward K. Hall ◽  
Randall W. Phillis
Keyword(s):  
Genome Size ◽  
Genome Size Evolution ◽  
Size Evolution

scholarly journals Maize centromeric chromatin scales with changes in genome size

Genetics ◽  
2021 ◽  
Vol 217 (4) ◽  
Author(s):  
Na Wang ◽  
Jianing Liu ◽  
William A Ricci ◽  
Jonathan I Gent ◽  
R Kelly Dawe
Keyword(s):  
Genome Size ◽  
Cell Size ◽  
Histone H3 ◽  
Limiting Factors ◽  
Positive Relationships ◽  
Satellite Sequence ◽  
Centromeric Chromatin ◽  
Protein Levels ◽  
Centromeric Satellite

Abstract Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.

Polyploidization and Genome Size Evolution in Australian Billy Buttons (Craspedia, Asteraceae: Gnaphalieae)

2017 ◽  
Vol 178 (5) ◽  
pp. 352-361 ◽  
Author(s):  
Meghan Castelli ◽  
Cathy H. Miller ◽  
Alexander N. Schmidt-Lebuhn
Keyword(s):  
Genome Size ◽  
Genome Size Evolution ◽  
Size Evolution

scholarly journals Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
C. P. Stelzer ◽  
J. Blommaert ◽  
A. M. Waldvogel ◽  
M. Pichler ◽  
B. Hecox-Lea ◽  
...  
Keyword(s):  
Genome Size ◽  
Satellite Dna ◽  
Gc Content ◽  
Size Variation ◽  
Isolated Populations ◽  
Genome Size Variation ◽  
Variable Regions ◽  
Geographic Population ◽  
Genome Size Evolution ◽  
Size Evolution

Abstract Background Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied—despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population. Results Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Conclusions By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

scholarly journals The hidden elasticity of avian and mammalian genomes

2016 ◽  
Author(s):  
Aurélie Kapusta ◽  
Alexander Suh ◽  
Cédric Feschotte
Keyword(s):  
Genome Size ◽  
Interspecific Variation ◽  
Size Spectrum ◽  
Computational Pipeline ◽  
Substantial Variation ◽  
Avian Evolution ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Mammalian Genomes ◽  
Dna Loss

AbstractGenome size in mammals and birds shows remarkably little interspecific variation compared to other taxa. Yet, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been co-variation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size homeostasis. To test this model, we develop a computational pipeline to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 million years (My) in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extent across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified ‘accordion’ model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.

scholarly journals An enormous Paris polyphylla genome sheds light on genome size evolution and polyphyllin biogenesis

2020 ◽  
Author(s):  
Jing Li ◽  
Meiqi Lv ◽  
Lei Du ◽  
A Yunga ◽  
Shijie Hao ◽  
...  
Keyword(s):  
Genome Size ◽  
Single Molecule ◽  
Repetitive Sequences ◽  
Plant Genome ◽  
Growth Stages ◽  
Evolutionary Trend ◽  
Rna Seq ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Paris Polyphylla

AbstractThe monocot family Melanthiaceae with varying genome sizes in a range of 230-fold is an ideal model to study the genome size fluctuation in plants. Its family member Paris genus demonstrates an evolutionary trend of bearing huge genomes characterized by an average c-value of 49.22 pg. Here, we report a 70.18 Gb genome assembly out of the 82.55 Gb genome of Paris polyphylla var. yunnanensis (PPY), which represents the biggest sequenced genome to date. We annotate 69.53% repetitive sequences in this genome and 62.50% of which are long-terminal repeat (LTR) transposable elements. Further evolution analysis indicates that the giant genome likely results from the joint effect of common and species-specific expansion of different LTR superfamilies, which might contribute to the environment adaptation after speciation. Moreover, we identify the candidate pathway genes for the biogenesis of polyphyllins, the PPY-specific medicinal saponins, by complementary approaches including genome mining, comprehensive analysis of 31 next-generation RNA-seq data and 55.23 Gb single-molecule circular consensus sequencing (CCS) RNA-seq reads, and correlation of the transcriptome and phytochemical data of five different tissues at four growth stages. This study not only provides significant insights into plant genome size evolution, but also paves the way for the following polyphyllin synthetic biology.

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