scholarly journals Large genomic variants reveal unexplored intraspecific diversity in Brassica rapa genomes

2020 ◽  
Author(s):  
Julien Boutte ◽  
Loeiz Maillet ◽  
Thomas Chaussepied ◽  
Sébastien Letort ◽  
Jean-Marc Aury ◽  
...  
Keyword(s):  
Genome Size ◽  
Brassica Rapa ◽  
Core Collection ◽  
Size Variation ◽  
Intraspecific Diversity ◽  
Phenotypic Traits ◽  
Genome Size Variation ◽  
F1 Hybrid ◽  
Genomic Variants ◽  
Long Read

ABSTRACTTraditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Using two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection.We explored the structural consequences of the presence of large repeated sequences in B. rapa ‘Z1’ genome versus the B. rapa ‘Chiifu’ genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09 and A10 are due to large insertions and inversions when comparing B. rapa ‘Z1’ and B. rapa ‘Chiifu’ at the origin of important length differences in some chromosomes. For instance, lengths of ‘Z1’ and ‘Chiifu’ A06 chromosomes were estimated in silico to be 55Mb and 29Mb, respectively. To validate these observations, we compared using fluorescent in-situ hybridization (FISH) the two A06 chromosomes present in a F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of ‘Z1’ compared to ‘Chiifu’. Alternatively, using a Copy Number Variation approach, we were able to quantify the presence of a higher number of rDNA and Gypsy elements in ‘Z1’ genome compared to ‘Chiifu’ on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions.This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.

scholarly journals Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa

2020 ◽  
Vol 11 ◽  
Author(s):  
Julien Boutte ◽  
Loeiz Maillet ◽  
Thomas Chaussepied ◽  
Sébastien Letort ◽  
Jean-Marc Aury ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Size ◽  
Brassica Rapa ◽  
Size Variation ◽  
Intraspecific Diversity ◽  
Genome Size Variation

scholarly journals On the Tempo of Genome Size Evolution in Angiosperms

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Jeremy M. Beaulieu ◽  
Stephen A. Smith ◽  
Ilia J. Leitch
Keyword(s):  
Life History ◽  
Genome Size ◽  
Large Scale ◽  
Growth Form ◽  
Size Variation ◽  
Threshold Effect ◽  
Phenotypic Traits ◽  
Genome Size Variation ◽  
Genome Size Evolution ◽  
Size Evolution

Broadly sampled phylogenies have uncovered extreme deviations from a molecular clock with the rates of molecular substitution varying dramatically within/among lineages. While growth form, a proxy for life history, is strongly correlated with molecular rate heterogeneity, its influence on trait evolution has yet to be examined. Here, we explore genome size evolution in relation to growth form by combining recent advances in large-scale phylogeny construction with model-based phylogenetic comparative methods. We construct phylogenies for Monocotyledonae (monocots) and Fabaceae (legumes), including all species with genome size information, and assess whether rates of genome size evolution depend on growth form. We found that the rates of genome size evolution for woody lineages were consistently an order of magnitude slower than those of herbaceous lineages. Our findings also suggest that growth form constrains genome size evolution, not through consequences associated with the phenotype, but instead through the influence of life history attributes on the tempo of evolution. Consequences associated with life history now extend to genomic evolution and may shed light on the frequently observed threshold effect of genome size variation on higher phenotypic traits.

Documenting Intraspecfic Genome Size Variation in Soybean

Crop Science ◽  
2004 ◽  
Vol 44 (1) ◽  
pp. 261 ◽  
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

scholarly journals Genome size variation in deep-sea amphipods

2017 ◽  
Vol 4 (9) ◽  
pp. 170862 ◽  
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.

scholarly journals Patterns of genome size variation in snapping shrimp

Genome ◽  
2016 ◽  
Vol 59 (6) ◽  
pp. 393-402 ◽  
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.

scholarly journals Genome size variation in gymnosperms under different growth conditions

Caryologia ◽  
2015 ◽  
Vol 68 (2) ◽  
pp. 92-96 ◽  
Author(s):  
Oriane Hidalgo ◽  
Joan Vallès ◽  
Angel Romo ◽  
Miguel-Ángel Canela ◽  
Teresa Garnatje
Keyword(s):  
Genome Size ◽  
Size Variation ◽  
Growth Conditions ◽  
Genome Size Variation

Nuclear genome size variation in fleshy-fruited Neotropical Myrtaceae

2008 ◽  
Vol 276 (3-4) ◽  
pp. 209-217 ◽  
Author(s):  
Itayguara Ribeiro da Costa ◽  
Marcelo Carnier Dornelas ◽  
Eliana Regina Forni-Martins
Keyword(s):  
Genome Size ◽  
Size Variation ◽  
Nuclear Genome ◽  
Genome Size Variation

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 Miscanthus: Inter- and Intraspecific Genome Size Variation Among M. × Giganteus, M. Sinensis, M. Sacchariflorus Accessions

2015 ◽  
Vol 57 (1) ◽  
pp. 104-113
Author(s):  
Sandra Cichorz ◽  
Maria Gośka ◽  
Monika Rewers
Keyword(s):  
Genome Size ◽  
Dna Content ◽  
Nuclear Dna ◽  
Size Variation ◽  
Nuclear Dna Content ◽  
Interspecific Variation ◽  
Genome Size Variation ◽  
2C Dna Content ◽  
Cytological Characteristics ◽  
Stomatal Length

AbstractSinceM. sinensisAnderss.,M. sacchariflorus(Maxim.) Hack. andM. ×giganteusJ.M.Greef & Deuter ex Hodk. and Renvoize have considerably the highest potential for biomass production amongMiscanthusAnderss. species, there is an urgent need to broaden the knowledge about cytological characteristics required for their improvement. In this study our objectives were to assess the genome size variation among eighteenMiscanthusaccessions, as well as estimation of the monoploid genome size (2C and Cx) of theM. sinensiscultivars, which have not been analyzed yet. The characterization of threeMiscanthusspecies was performed with the use of flow cytometry and analysis of the stomatal length. The triploid (2n = 3x = 57)M. sinensis‘Goliath’ andM. ×giganteusclones possessed the highest 2C DNA content (8.34 pg and 7.43 pg, respectively). The intermediate 2C-values were found in the nuclei of the diploid (2n = 2x = 38)M. sinensisaccessions (5.52–5.72 pg), whereas they were the lowest in the diploid (2n = 2x = 38)M. sacchariflorusecotypes (4.58–4.59 pg). The presented study revealed interspecific variation of nuclear DNA content (P<0.01) and therefore allowed for recognition of particular taxa, inter- and intraspecific hybrids and prediction of potential parental components. Moreover, intraspecific genome size variation (P<0.01) was observed inM. sinensiscultivars at 3.62%. The values of the stomatal size obtained for the triploidM. ×giganteus‘Great Britain’ (mean 30.70 μm) or ‘Canada’ (mean 29.67 μm) and diploidM. sinensis‘Graziella’ (mean 29.96 μm) did not differ significantly, therefore this parameter is not recommended for ploidy estimation.

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