scholarly journals Variation and Evolution of Genome Size in Gymnosperms

2021 ◽  
Vol 70 (1) ◽  
pp. 156-169
Author(s):  
Deepak Ohri
Keyword(s):  
Transposable Elements ◽  
Genome Size ◽  
Narrow Range ◽  
Ltr Retrotransposons ◽  
General Survey ◽  
Efficient Mechanism ◽  
Repeat Sequences ◽  
Adaptive Value ◽  
Epigenetic Machinery ◽  
Large Genomes

Abstract Gymnosperms show a significantly higher mean (1C=18.16, 1Cx=16.80) and a narrow range (16.89-fold) of genome sizes as compared with angiosperms. Among the 12 families the largest ranges of 1C values is shown by Ephedraceae (4.73-fold) and Cupressaceae (4.45-fold) which are partly due to polyploidy as 1Cx values vary 2.41 and 1.37-fold respectively. In rest of the families which have only diploid taxa the range of 1C values is from 1.18-fold (Cycadaeae) to 4.36-fold (Podocarpaceae). The question is how gymnosperms acquired such big genome sizes despite the rarity of recent instances of polyploidy. A general survey of different families and genera shows that gymnosperms have experienced both increase and decrease in their genome size during evolution. Various genomic components which have accounted for these large genomes have been discussed. The major contributors are the transposable elements particularly LTR-retrotransposons comprising of Ty3gypsy, Ty1copia and gymny superfamilies which are most widespread. The genomes of gymnosperms have been acquiring diverse LTR-RTs in their long evolution in the absence of any efficient mechanism of their elimination. The epigenetic machinery which silences these large tracts of repeat sequences into the stretches of heterochromatin and the adaptive value of these silenced repeat sequences need further investigation.

scholarly journals MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Juan Manuel Crescente ◽  
Diego Zavallo ◽  
Marcelo Helguera ◽  
Leonardo Sebastián Vanzetti
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Large Genomes

scholarly journals Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis

Gigabyte ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Rui Zhang ◽  
Chang Li ◽  
Mengjun Yu ◽  
Xiaoyun Huang ◽  
Mengqi Zhang ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Phylogenetic Tree ◽  
Genome Size ◽  
Genome Assembly ◽  
Teleost Fish ◽  
Common Ancestor ◽  
Biological Features ◽  
Repeat Sequences ◽  
Genomic Resource ◽  
Chromosome Level

The humpback puffer, Tetraodon palembangensis, is a poisonous freshwater pufferfish species mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). The humpback puffer has many interesting biological features, such as inactivity, tetrodotoxin production and body expansion. Here, we report the first chromosome-level genome assembly of the humpback puffer. The genome size is 362 Mb, with a contig N50 value of ∼1.78 Mb and a scaffold N50 value of ∼15.8 Mb. Based on this genome assembly, ∼61.5 Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and the function of 90.01% of these genes could be predicted. Finally, a phylogenetic tree of ten teleost fish species was constructed. This analysis suggests that the humpback puffer and T. nigroviridis share a common ancestor 18.1 million years ago (MYA), and diverged from T. rubripes 45.8 MYA. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance.

APOBEC3 proteins: major players in intracellular defence against LINE-1-mediated retrotransposition

2007 ◽  
Vol 35 (3) ◽  
pp. 637-642 ◽  
Author(s):  
G.G. Schumann
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats ◽  
Genetic Disorders ◽  
Single Copy ◽  
Long Terminal Repeat Retrotransposons ◽  
Variable Number ◽  
Ltr Retrotransposons ◽  
Negative Effects ◽  
Processed Pseudogenes ◽  
Retrotransposon Activity

Mammalian genomes are littered with enormous numbers of transposable elements interspersed within and between single-copy endogenous genes. The only presently spreading class of human transposable elements comprises non-LTR (long terminal repeat) retrotransposons, which cover approx. 34% of the human genome. Non-LTR retrotransposons include the widespread autonomous LINEs (long interspersed nuclear elements) and non-autonomous elements such as processed pseudogenes, SVAs [named after SINE (short interspersed nuclear element), VNTR (variable number of tandem repeats) and Alu] and SINEs. Mobilization of these elements affects the host genome, can be deleterious to the host cell, and cause genetic disorders and cancer. In order to limit negative effects of retrotransposition, host genomes have adopted several strategies to curb the proliferation of transposable elements. Recent studies have demonstrated that members of the human APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypeptide 3) protein family inhibit the mobilization of the non-LTR retrotransposons LINE-1 and Alu significantly and participate in the intracellular defence against retrotransposition by mechanisms unknown to date. The striking coincidence between the expansion of the APOBEC3 gene cluster and the abrupt decline in retrotransposon activity in primates raises the possibility that these genes may have been expanded to prevent genomic instability caused by endogenous retroelements.

scholarly journals Evolution and diversity of transposable elements in fish genomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Feng Shao ◽  
Minjin Han ◽  
Zuogang Peng
Keyword(s):  
Species Diversity ◽  
Transposable Elements ◽  
Long Terminal Repeat ◽  
Genome Size ◽  
Fish Species ◽  
Significant Variation ◽  
Genomic Sequences ◽  
Fish Genome ◽  
Long Interspersed Nuclear Elements ◽  
Fish Species Diversity

Abstract Transposable elements (TEs) are genomic sequences that can move, multiply, and often form sizable fractions of vertebrate genomes. Fish belong to a unique group of vertebrates, since their karyotypes and genome sizes are more diverse and complex, with probably higher diversity and evolution specificity of TE. To investigate the characteristics of fish TEs, we compared the mobilomes of 39 species, and observed significant variation of TE content in fish (from 5% in pufferfish to 56% in zebrafish), along with a positive correlation between fish genome size and TE content. In different classification hierarchies, retrotransposons (class), long terminal repeat (order), as well as Helitron, Maverick, Kolobok, CMC, DIRS, P, I, L1, L2, and 5S (superfamily) were all positively correlated with fish genome size. Consistent with previous studies, our data suggested fish genomes to not always be dominated by DNA transposons; long interspersed nuclear elements are also prominent in many species. This study suggests CR1 distribution in fish genomes to be obviously regular, and provides new clues concerning important events in vertebrate evolution. Altogether, our results highlight the importance of TEs in the structure and evolution of fish genomes and suggest fish species diversity to parallel transposon content diversification.

scholarly journals The Mobilome of Reptiles: Evolution, Structure, and Function

2019 ◽  
Vol 157 (1-2) ◽  
pp. 21-33 ◽  
Author(s):  
Stéphane Boissinot ◽  
Yann Bourgeois ◽  
Joseph D. Manthey ◽  
Robert P. Ruggiero
Keyword(s):  
Gene Flow ◽  
Transposable Elements ◽  
Genome Size ◽  
Local Adaptation ◽  
Size Structure ◽  
Structure And Function ◽  
Genomic Diversity ◽  
Genomic Features ◽  
And Function

Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

scholarly journals Transposons, Genome Size, and Evolutionary Insights in Animals

2015 ◽  
Vol 147 (4) ◽  
pp. 217-239 ◽  
Author(s):  
Adriana Canapa ◽  
Marco Barucca ◽  
Maria A. Biscotti ◽  
Mariko Forconi ◽  
Ettore Olmo
Keyword(s):  
Natural Selection ◽  
Transposable Elements ◽  
Genome Size ◽  
Small Rnas ◽  
Evolutionary History ◽  
Animal Species ◽  
Current Situation ◽  
Environmental Stressors ◽  
Functional Parameters ◽  
The Relationship

The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.

scholarly journals GA-repeats on mammalian X chromosomes support Ohno’s hypothesis of dosage compensation by transcriptional upregulation

2018 ◽  
Author(s):  
Edridge D’Souza ◽  
Elizaveta Hosage ◽  
Kathryn Weinand ◽  
Steve Gisselbrecht ◽  
Vicky Markstein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Binding Sites ◽  
Convergent Evolution ◽  
Fruit Fly ◽  
Dosage Compensation Complex ◽  
X Chromosomes ◽  
Repeat Sequences

ABSTRACTOver 50 years ago, Susumo Ohno proposed that dosage compensation in mammals would require upregulation of gene expression on the single active X chromosome, a mechanism which to date is best understood in the fruit fly Drosophila melanogaster. Here, we report that the GA-repeat sequences that recruit the conserved MSL dosage compensation complex to the Drosophila X chromosome are also enriched across mammalian X chromosomes, providing genomic support for the Ohno hypothesis. We show that mammalian GA-repeats derive in part from transposable elements, suggesting a mechanism whereby unrelated X chromosomes from dipterans to mammals accumulate binding sites for the MSL dosage compensation complex through convergent evolution, driven by their propensity to accumulate transposable elements.

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