scholarly journals The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Francisco J. Herraiz ◽  
José Blanca ◽  
Pello Ziarsolo ◽  
Pietro Gramazio ◽  
Mariola Plazas ◽  
...  
Keyword(s):  
Related Species ◽  
De Novo ◽  
Comprehensive Analysis ◽  
De Novo Transcriptome ◽  
Closely Related Species ◽  
Solanum Muricatum

scholarly journals Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

2021 ◽  
Author(s):  
Ching-Ho Chang ◽  
Lauren E. Gregory ◽  
Kathleen E. Gordon ◽  
Colin D. Meiklejohn ◽  
Amanda M. Larracuente
Keyword(s):  
Positive Selection ◽  
Y Chromosome ◽  
Related Species ◽  
De Novo ◽  
Gene Families ◽  
Chromosome Organization ◽  
End Joining ◽  
Sexual Antagonism ◽  
Closely Related Species ◽  
Y Chromosomes

AbstractY chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposable elements, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism generally contributes to the convergent evolution of Y chromosome organization.

scholarly journals Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251655
Author(s):  
Maurizio Mascarello ◽  
Mario Amalfi ◽  
Pieter Asselman ◽  
Erik Smets ◽  
Olivier J. Hardy ◽  
...  
Keyword(s):  
Related Species ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Microscopic Analysis ◽  
Comparative Genomic ◽  
Timber Species ◽  
Illegal Logging ◽  
Closely Related Species ◽  
Genome Skimming ◽  
The Tropics

Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the tropics. Several laws and regulations have been set up to combat illegal timber trade. Despite significant enforcement efforts of these regulations, illegal logging continues to be a serious problem and impacts for the functioning of the forest ecosystem and global biodiversity in the tropics. Microscopic analysis of wood samples and the use of conventional plant DNA barcodes often do not allow to distinguish closely-related species. The use of novel molecular technologies could make an important contribution for the identification of tree species. In this study, we used high-throughput sequencing technologies and bioinformatics tools to obtain the complete de-novo chloroplast genome of 62 commercial African timber species using the genome skimming method. Then, we performed a comparative genomic analysis that revealed new candidate genetic regions for the discrimination of closely-related species. We concluded that genome skimming is a promising method for the development of plant genetic markers to combat illegal logging activities supporting CITES, FLEGT and the EU Timber Regulation.

scholarly journals Divergence and introgression among the virilis group of Drosophila

2022 ◽  
Author(s):  
Leeban Yusuf ◽  
Venera Tyukmaeva ◽  
Anneli Hoikkala ◽  
Michael G Ritchie
Keyword(s):  
Gene Flow ◽  
Related Species ◽  
De Novo ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Sexual Isolation ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Closely Related Species ◽  
Virilis Group

Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains around a dozen species that are geographically widespread and show varying levels of pre-zygotic and post-zygotic isolation. Here, we utilize de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and much more recent gene flow between closely-related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and may be related to the evolution of sexual isolation. We suggest that gene flow between closely-related species has potentially had an impact on lineage-specific adaptation and the evolution of reproductive barriers. Our results show how ancient and recent introgression confuse phylogenetic reconstruction, and suggest that shared variation can facilitate adaptation and speciation.

scholarly journals Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Ching-Ho Chang ◽  
Lauren E Gregory ◽  
Kathleen E Gordon ◽  
Colin D Meiklejohn ◽  
Amanda M Larracuente
Keyword(s):  
Positive Selection ◽  
Y Chromosome ◽  
Related Species ◽  
De Novo ◽  
Gene Families ◽  
Chromosome Organization ◽  
End Joining ◽  
Sexual Antagonism ◽  
Closely Related Species ◽  
Y Chromosomes

Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism contributes to the convergent evolution of Y chromosome organization across organisms.

scholarly journals Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Cécile Lorrain ◽  
Alice Feurtey ◽  
Mareike Möller ◽  
Janine Haueisen ◽  
Eva Stukenbrock
Keyword(s):  
Transposable Elements ◽  
Related Species ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
De Novo ◽  
Zymoseptoria Tritici ◽  
Closely Related Species ◽  
Fungal Plant Pathogens ◽  
Wide Range ◽  
The Impact

Abstract Transposable elements (TEs) impact genome plasticity, architecture, and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defense mechanisms that can counter-balance TE expansion and spread. Closely related species can harbor drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here, we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and repeat-induced point mutation signatures in 26 genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The 26 genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation, and with effectors in all Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.

scholarly journals Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defences

2020 ◽  
Author(s):  
Cécile Lorrain ◽  
Alice Feurtey ◽  
Mareike Möller ◽  
Janine Haueisen ◽  
Eva Stukenbrock
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Related Species ◽  
Plant Pathogens ◽  
De Novo ◽  
Zymoseptoria Tritici ◽  
Closely Related Species ◽  
Fungal Plant Pathogens ◽  
Wide Range ◽  
The Impact

AbstractTransposable elements (TEs) impact genome plasticity, architecture and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defence mechanisms that can counter-balance TE expansion and spread. Closely related species can harbour drastically different TE repertoires, suggesting variation in the efficacy of genome defences. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and Repeat-Induced Point mutation signatures in thirteen genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The thirteen genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with distinct genome compartments in all Zymoseptoria species, including chromosomal rearrangements, genes showing presence/absence variation and effectors. European Z. tritici isolates have reduced signatures of Repeat-Induced Point mutations compared to Iranian isolates and closely related species. Our study supports the hypothesis that ongoing but moderate TE mobility in Zymoseptoria species shapes pathogen genome evolution.

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