Genome size and genomic <scp>GC</scp> content evolution in the miniature genome‐sized family Lentibulariaceae

Veleba, Adam; Bureš, Petr; Adamec, Lubomír; Šmarda, Petr; Lipnerová, Ivana; Horová, Lucie

doi:10.1111/nph.12790

Cited by 45 publications

(62 citation statements)

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“…4) corroborates previous findings from geophytic (bulbous) plants (16) and suggests that this relationship may hold across the diversity of plants. The positive correlation between GC content and genome size observed for monocot species with small to medium genome sizes reflects a general trend observed in many plant genera (18,41) as well as bacterial and animal genomes (6,22,42). In plants, this correlation might arise simply from the fact that genome growth predominantly arises from increases in the amount of LTR retrotransposons that dominate most plant genomes (43,44).…”

Section: Resultssupporting

confidence: 58%

“…The DNA base composition is also frequently discussed in relation to the evolution of the isochore structure in humans and other homeothermic (warm-blooded) vertebrates (i.e., birds and mammals) (8-10). In contrast, considerably less attention has been paid to the biological relevance of genomic GC content variation in plants (11), with genomic GC contents known only for a limited amount of the total phylogenetic diversity (11)(12)(13)(14)(15)(16)(17)(18).One important feature of the GC base pair is its higher thermal stability compared with the AT base pair, a feature that arises from the stronger stacking interaction between GC bases and the presence of a triple compared with a double hydrogen bond between the paired bases (19). In turn, these interactions seem to be important in conferring stability to higher order structures of DNA and RNA transcripts (11,20).…”

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Ecological and evolutionary significance of genomic GC content diversity in monocots

Šmarda

Bureš

Horová

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Genomic DNA base composition (GC content) is predicted to significantly affect genome functioning and species ecology. Although several hypotheses have been put forward to address the biological impact of GC content variation in microbial and vertebrate organisms, the biological significance of GC content diversity in plants remains unclear because of a lack of sufficiently robust genomic data. Using flow cytometry, we report genomic GC contents for 239 species representing 70 of 78 monocot families and compare them with genomic characters, a suite of life history traits and climatic niche data using phylogeny-based statistics. GC content of monocots varied between 33.6% and 48.9%, with several groups exceeding the GC content known for any other vascular plant group, highlighting their unusual genome architecture and organization. GC content showed a quadratic relationship with genome size, with the decreases in GC content in larger genomes possibly being a consequence of the higher biochemical costs of GC base synthesis. Dramatic decreases in GC content were observed in species with holocentric chromosomes, whereas increased GC content was documented in species able to grow in seasonally cold and/or dry climates, possibly indicating an advantage of GC-rich DNA during cell freezing and desiccation. We also show that genomic adaptations associated with changing GC content might have played a significant role in the evolution of the Earth's contemporary biota, such as the rise of grass-dominated biomes during the mid-Tertiary. One of the major selective advantages of GC-rich DNA is hypothesized to be facilitating more complex gene regulation.plant genome | genome size evolution | Poaceae | phylogenetic regression | geographical stratification D eep insights into the genomic architecture of model plants are rapidly accumulating, especially because of advances being made in high-throughput next generation and third generation sequencing techniques (1). However, the genomic constitution of the vast majority of nonmodel plants still remains unknown (2), impeding our understanding of the relationship between particular genomic architectures and evolutionary fitness in various environments. One of the important qualitative aspects of genomic architecture is the genomic nucleotide composition, which is usually expressed as the proportion of guanine and cytosine bases in the DNA molecule (GC content). In prokaryotes, the GC content is a well-studied and widely used character in taxonomy (3), and numerous studies have shown both the impact of GC content on microbial ecology and the influence of the environment in shaping the DNA base composition of microbial communities (4-7). The DNA base composition is also frequently discussed in relation to the evolution of the isochore structure in humans and other homeothermic (warm-blooded) vertebrates (i.e., birds and mammals) (8-10). In contrast, considerably less attention has been paid to the biological relevance of genomic GC content variation in plants (11), with genomic GC co...

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Section: Resultssupporting

confidence: 58%

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confidence: 99%

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confidence: 99%

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Ecological and evolutionary significance of genomic GC content diversity in monocots

Šmarda

Bureš

Horová

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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271

212

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“…U. gibba is of particular interest given the previous publication of an ∼82-Mb short-read assembly (10), which revealed that its genome gained and deleted gene duplicates significantly faster than those of other genomes (11). Given that the U. gibba genome likely descended via considerable shrinkage from an ancestral genome up to 1.5 Gb in size (12), duplicates that survived deletion during its evolutionary history arguably evolved under greater purifying selection pressure compared with the more expansive genomes of most angiosperms. Therefore, we hypothesized that the deletion-prone genome of U. gibba could be particularly illustrative regarding…”

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Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Lan

Renner

Ibarra-Laclette

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.

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“…Casper [7] divided the genus into three subgenera and 15 sections, but his taxonomy resulted artificial in several cases [8]. Compared with other families, a good molecular phylogenetic knowledge is available in literature for Lentibulariaceae [2, 9, 10, 11] and for its three genera: Pinguicula , Genlisea [12] and Utricularia [13]. …”

Section: Introductionmentioning

confidence: 99%

Disentangling Phylogenetic Relationships in a Hotspot of Diversity: The Butterworts (Pinguicula L., Lentibulariaceae) Endemic to Italy

et al. 2016

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The genus Pinguicula (Lentibulariaceae) consists of about 100 carnivorous species, also known as butterworts. Eleven taxa are endemic to Italy, which represents a biodiversity hotspot for butterworts in Europe. The aim of our study was to provide a phylogenetic framework for the Italian endemics, in order to: a) investigate the relationships between species in this group; b) evaluate their actual taxonomic value. To achieve this, we analysed all the taxa endemic to Italy, along with several other species, by means of ITS nrDNA analysis. Our results clarify the relationships between Italian endemics and other Pinguicula taxa identifying a basal polytomy defined by five clades. All of the Italian endemics (with the exception of P. lavalvae) fall within a single large clade, which includes P. vulgaris and allied species. Among them, P. poldinii represents the most isolated lineage. Other taxa show strong molecular similarities and form a single subclade, although their taxonomic ranks can be retained. Pinguicula lattanziae sp. nov., seemingly endemic to Liguria (NW Italy), is also described.

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Genome size and genomic GC content evolution in the miniature genome‐sized family Lentibulariaceae

Cited by 45 publications

References 32 publications

Ecological and evolutionary significance of genomic GC content diversity in monocots

Ecological and evolutionary significance of genomic GC content diversity in monocots

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Disentangling Phylogenetic Relationships in a Hotspot of Diversity: The Butterworts (Pinguicula L., Lentibulariaceae) Endemic to Italy

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