Genome size and developmental parameters in the homeothermic vertebrates

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 833-838 ◽  
Author(s):  
T Ryan Gregory
Keyword(s):  
Body Size ◽  
Metabolic Rate ◽  
Genome Size ◽  
Developmental Rate ◽  
Large Dataset ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Developmental Parameters ◽  
C Value ◽  
Organismal Complexity

Although unrelated to any intuitive notions of organismal complexity, haploid genome sizes (C values) are correlated with a variety of cellular and organismal parameters in different taxa. In some cases, these relationships are universal — notably, genome size correlates positively with cell size in each of the vertebrate classes. Other relationships are apparently relevant only in particular groups. For example, although genome size is inversely correlated with metabolic rate in both mammals and birds, no such relationship is found in amphibians. More recently, it has been suggested that developmental rate and (or) longevity are related to genome size in birds. In the present study, a large dataset was used to examine possible relationships between genome size and various developmental parameters in both birds and mammals. In neither group does development appear to be of relevance to genome size evolution (except perhaps indirectly in birds through the intermediation of body size and (or) within the rodents), a situation very different from that found in amphibians. These findings make it clear that genome size evolution cannot be understood without reference to the particular biology of the organisms under study.Key words: body size, C-value enigma, C-value paradox, fledging, gestation, growth, incubation, lactation, metabolism.

scholarly journals CLASSIFICATION OF LIFE BY THE MECHANISM OF GENOME SIZE EVOLUTION

2009 ◽  
Vol 23 (30) ◽  
pp. 3563-3580 ◽  
Author(s):  
DIRSON JIAN LI ◽  
SHENGLI ZHANG
Keyword(s):  
Genome Size ◽  
Phylogenetic Trees ◽  
Living System ◽  
Protein Length ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
C Value ◽  
Stable Characteristic ◽  
Main Component

We find that the global relationships among species should be of circular phylogeny, which is quite different from common sense based on phylogenetic trees. A domain can be defined by a distinct phylogenetic circle, which is a global and stable characteristic of the living system. The mechanism in genome size evolution has been clarified; hence the main component questions on C-value enigma can be explained. We find the intrinsic relationship between genome size evolution and protein length evolution; that is the genome size and non-coding DNA ratio can be calculated based on protein length distributions.

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

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.

scholarly journals Genome size drives morphological evolution in organ-specific ways

2021 ◽  
Author(s):  
Michael W Itgen ◽  
Dustin S Siegel ◽  
Stanley K Sessions ◽  
Rachel Lockridge Mueller
Keyword(s):  
Body Size ◽  
Genome Size ◽  
Cell Size ◽  
Structural Changes ◽  
Morphological Evolution ◽  
Empty Space ◽  
Developmental Rate ◽  
Cellular Interactions ◽  
Structure Changes ◽  
Organ Specific

Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through its effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested the effects of genome size and body size evolution on heart and liver morphology using nine species of the salamander genus Plethodon (genome sizes 29.3-67 Gb). Our results show that whole organ size is determined by body size, whereas tissue structure changes dramatically with evolutionary increases in genome size. In the heart, increased genome size is correlated with a reduction of myocardia in the ventricle, yielding proportionally less force-producing mass and more empty space. In the liver, increased genome size is correlated with fewer and larger vascular structures, positioning hepatocytes farther from the circulatory vessels that transport key metabolites. Although these structural changes should have obvious impacts on organ function, their effects on organismal performance and fitness are likely negligible because low metabolic rates in salamanders relax selective pressure on key metabolic organ performance. Overall, this study reveals the effects of large genome and cell size on the developmental systems producing the heart and liver.

scholarly journals The dynamic evolutionary history of genome size in North American woodland salamanders

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 285-292 ◽  
Author(s):  
Catherine E. Newman ◽  
T. Ryan Gregory ◽  
Christopher C. Austin
Keyword(s):  
Genome Size ◽  
Evolutionary History ◽  
Future Studies ◽  
Plethodontid Salamanders ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
History Of ◽  
Large Genome Size ◽  
Uncertain Future ◽  
Phylogeographic Study

The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5–20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.

scholarly journals Cytogenetics and Genome Size Evolution in Illicium L.

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 620-623
Author(s):  
Thomas G. Ranney ◽  
Connor F. Ryan ◽  
Lauren E. Deans ◽  
Nathan P. Lynch
Keyword(s):  
North America ◽  
Plant Breeding ◽  
Genome Size ◽  
Chromosome Numbers ◽  
Phylogenetic Analyses ◽  
Basal Angiosperm ◽  
Ploidy Levels ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Improvement Programs

Illicium is an ancient genus and member of the earliest diverging angiosperms known as the Amborellales, Nymphaeales, and Austrobaileyales (ANA) grade. These adaptable, broadleaf evergreen shrubs, including ≈40 species distributed throughout Asia and North America, are valued for diverse culinary, medicinal, and ornamental applications. The study of cytogenetics of Illicium can clarify various discrepancies and further elucidate chromosome numbers, ploidy, and chromosome and genome size evolution in this basal angiosperm lineage and provide basic information to guide plant breeding and improvement programs. The objectives of this study were to use flow cytometry and traditional cytology to determine chromosome numbers, ploidy levels, and relative genome sizes of cultivated Illicium. Of the 29 taxa sampled, including ≈11 species and one hybrid, 2C DNA contents ranged from 24.5 pg for Illicium lanceolatum to 27.9 pg for Illicium aff. majus. The genome sizes of Illicium species are considerably higher than other ANA grade lineages indicating that Illicium went through considerable genome expansion compared with sister lineages. The New World sect. Cymbostemon had a slightly lower mean 2C genome size of 25.1 pg compared with the Old World sect. Illicium at 25.9 pg, providing further support for recognizing these taxonomic sections. All taxa appeared to be diploid and 2n = 2x = 28, except for Illicium floridanum and Illicium mexicanum which were found to be 2n = 2x = 26, most likely resulting from dysploid reduction after divergence into North America. The base chromosome number of x = 14 for most Illicium species suggests that Illicium are ancient paleotetraploids that underwent a whole genome duplication derived from an ancestral base of x = 7. Information on cytogenetics, coupled with phylogenetic analyses, identifies some limitations, but also considerable potential for the development of plant breeding and improvement programs with this genus.

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