Genome Size Evolution of the Extant Lycophytes and Ferns

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.

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The hidden elasticity of avian and mammalian genomes

10.1101/081307 ◽

2016 ◽

Cited By ~ 1

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.

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

10.1101/2020.06.01.126920 ◽

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

Genome ◽

10.1139/gen-2016-0166 ◽

2017 ◽

Vol 60 (4) ◽

pp. 285-292 ◽

Cited By ~ 2

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.

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Cytogenetics and Genome Size Evolution in Illicium L.

HortScience ◽

10.21273/hortsci12922-18 ◽

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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Genome Size Evolution and Dynamics in Iris, with Special Focus on the Section Oncocyclus

Plants ◽

10.3390/plants9121687 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1687

Author(s):

Nour Abdel Samad ◽

Oriane Hidalgo ◽

Elie Saliba ◽

Sonja Siljak-Yakovlev ◽

Kit Strange ◽

...

Keyword(s):

Genome Size ◽

Eastern Mediterranean ◽

Eastern Mediterranean Region ◽

Evolutionary Model ◽

Distinct Species ◽

Special Focus ◽

Plant Groups ◽

Genome Size Evolution ◽

Size Evolution ◽

Phylogenetic Framework

Insights into genome size dynamics and its evolutionary impact remain limited by the lack of data for many plant groups. One of these is the genus Iris, of which only 53 out of c. 260 species have available genome sizes. In this study, we estimated the C-values for 41 species and subspecies of Iris mainly from the Eastern Mediterranean region. We constructed a phylogenetic framework to shed light on the distribution of genome sizes across subgenera and sections of Iris. Finally, we tested evolutionary models to explore the mode and tempo of genome size evolution during the radiation of section Oncocyclus. Iris as a whole displayed a great variety of C-values; however, they were unequally distributed across the subgenera and sections, suggesting that lineage-specific patterns of genome size diversification have taken place within the genus. The evolutionary model that best fitted our data was the speciational model, as changes in genome size appeared to be mainly associated with speciation events. These results suggest that genome size dynamics may have contributed to the radiation of Oncocyclus irises. In addition, our phylogenetic analysis provided evidence that supports the segregation of the Lebanese population currently attributed to Iris persica as a distinct species.

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CLASSIFICATION OF LIFE BY THE MECHANISM OF GENOME SIZE EVOLUTION

Modern Physics Letters B ◽

10.1142/s0217984909021624 ◽

2009 ◽

Vol 23 (30) ◽

pp. 3563-3580 ◽

Cited By ~ 4

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.

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