Phylogenetic Insights Into the Pace and Pattern of Plant Genome Size Evolution

2008 ◽  
pp. 57-68 ◽  
Author(s):  
C.E. Grover ◽  
J.S. Hawkins ◽  
J.F. Wendel
Keyword(s):  
Genome Size ◽  
Plant Genome ◽  
Genome Size Evolution ◽  
Size Evolution

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.

Repeated big bangs and the expanding universe: Directionality in plant genome size evolution

Plant Science ◽  
2008 ◽  
Vol 174 (6) ◽  
pp. 557-562 ◽  
Author(s):  
Jennifer S. Hawkins ◽  
Corrinne E. Grover ◽  
Jonathan F. Wendel
Keyword(s):  
Genome Size ◽  
Plant Genome ◽  
Expanding Universe ◽  
Genome Size Evolution ◽  
Size Evolution

scholarly journals Environmental pressures on stomatal size may drive plant genome size evolution: evidence from a natural experiment with Cape geophytes

2020 ◽  
Vol 126 (2) ◽  
pp. 323-330 ◽  
Author(s):  
Pavel Veselý ◽  
Petr Šmarda ◽  
Petr Bureš ◽  
Charles Stirton ◽  
A Muthama Muasya ◽  
...  
Keyword(s):  
Genome Size ◽  
Stomatal Density ◽  
Guard Cells ◽  
Plant Genome ◽  
Fossil Plants ◽  
Environmental Pressures ◽  
Stomatal Size ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Species Pairs

Abstract Background and Aims The idea that genome (size) evolution in eukaryotes could be driven by environmental factors is still vigorously debated. In extant plants, genome size correlates positively with stomatal size, leading to the idea that conditions enabling the existence of large stomata in fossil plants also supported growth of their genome size. We test this inductive assumption in drought-adapted, prostrate-leaved Cape (South Africa) geophytes where, compared with their upright-leaved geophytic ancestors, stomata develop in a favourably humid microclimate formed underneath their leaves. Methods Stomatal parameters (leaf cuticle imprints) and genome size (flow cytometry) were measured in 16 closely related geophytic species pairs from seven plant families. In each pair, representing a different genus, we contrasted a prostrate-leaved species with its upright-leaved phylogenetic relative, the latter whose stomata are exposed to the ambient arid climate. Key Results Except for one, all prostrate-leaves species had larger stomata, and in 13 of 16 pairs they also had larger genomes than their upright-leaved relatives. Stomatal density and theoretical maximum conductance were less in prostrate-leaved species with small guard cells (<1 pL) but showed no systematic difference in species pairs with larger guard cells (>1 pL). Giant stomata were observed in the prostrate-leaved Satyrium bicorne (89–137 µm long), despite its relatively small genome (2C = 9 Gbp). Conclusions Our results imply that climate, through selection on stomatal size, might be able to drive genome size evolution in plants. The data support the idea that plants from ‘greenhouse’ geological periods with large stomata might have generally had larger genome sizes when compared with extant plants, though this might not have been solely due to higher atmospheric CO2 in these periods but could also have been due to humid conditions prevailing at fossil deposit sites.

Recent progress in plant genome size evolution

2009 ◽  
Vol 31 (5) ◽  
pp. 464-470
Author(s):  
Jian-Jun CHEN ◽  
Ying WANG
Keyword(s):  
Genome Size ◽  
Recent Progress ◽  
Plant Genome ◽  
Genome Size Evolution ◽  
Size Evolution

scholarly journals A ROLE FOR NONADAPTIVE PROCESSES IN PLANT GENOME SIZE EVOLUTION?

Evolution ◽  
2010 ◽  
Author(s):  
Kenneth D. Whitney ◽  
Eric J. Baack ◽  
James L. Hamrick ◽  
Mary Jo W. Godt ◽  
Brian C. Barringer ◽  
...  
Keyword(s):  
Genome Size ◽  
Plant Genome ◽  
Genome Size Evolution ◽  
Size Evolution

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.

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