Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge DOI Creative Commons
Abderrahmane Eleiwa, Jesús Nadal, Ester Vilaprinyó

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Aug. 22, 2024

The red-legged partridge Alectoris rufa plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation management. Here we sequence, assemble, annotate highly contiguous nearly complete version genome. This assembly encompasses 96.9% avian genes flagged as essential BUSCO aves_odb10 dataset. Moreover, pinpointed RNA protein-coding genes, 95% which had functional annotations. Notably, observed significant chromosome rearrangements comparison to quail (Coturnix japonica) chicken (Gallus gallus). In addition, comparative phylogenetic analysis these genomes suggests that A. C. japonica diverged roughly 20 million years ago their common ancestor from G. gallus 35 ago. Our represents advancement towards reference genome rufa, facilitating genomics, providing valuable resource future research efforts partridge.

Language: Английский

FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research DOI Creative Commons
Feng Shao,

Minzhi Zeng,

Xiaofei Xu

et al.

Database, Journal Year: 2024, Volume and Issue: 2024

Published: Jan. 1, 2024

We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over past 5 years, 1.0 has gained approximately 10 000 users, accumulating more than 450 interactions. With unveiling extensive fish genome data and increasing emphasis on TE research, needs extend richness functions. To achieve above goals, we introduced 33 new species 2.0, encompassing a wide array belonging 48 orders. make updated database functional, added browser visualize positional relationship between TEs genes estimated insertion time different species. In conclusion, released database, designed assist researchers future study functions promote progress biological theories related TEs. Database URL: https://www.fishtedb.com/.

Language: Английский

Citations

5
Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library DOI Creative Commons
Jeferson A. Durán-Fuentes, Maximiliano M. Maronna, Octavio M. Palacios‐Gimenez

et al.

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: May 13, 2025

Genomic repetitive DNA sequences (Repeatomes, REPs) are widespread in eukaryotes, influencing biological form and function. In Cnidaria, an early-diverging animal lineage, these remain largely uncharacterized. This study investigates sea anemone REPs (Cnidaria: Actiniaria) a phylogenetic context. We sequenced assembled de novo the genome of Actinostella flosculifera analyzed total 38 nuclear genomes to create first ActiniariaREP library (Actiniaria-REPlib). compared Actiniaria-REPlib with Repbase RepeatModeler2 libraries, used dnaPipeTE annotate from genomic short-read datasets 36 species for divergence landscapes. Our annotated mitochondrial genomes, including 27 newly ones. re-annotated ~92% unknown initial library, finding that 6.4-30.6% were transposons, 2.1-11.6% retrotransposons, 1-28.4% tandem repeat sequences, 1.2-7% unclassifiable sequences. recovered 9.4x more REP actiniarian than Dfam 10.4x Repbase. It yielded 79,903 TE consensus (74,643 known, 5,260 unknown), 7,697 (3,742 3,944 unknown) Repbae (763 known). significantly enhances characterization DNA, assembling re-annotating identifying diverse elements. vastly outperforms existing databases, recovering providing comprehensive resource future evolutionary studies Actiniaria.

Language: Английский

Citations

0
Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution DOI Creative Commons
C. Dittrich, Franz Hoelzl, Steve Smith

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(6)

Published: May 15, 2024

Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display greatest variation in genome size, making them ideal models explore causes consequences However, high-quality assemblies for have, until recently, been rare. Here, we generate a assembly dyeing poison frog, Dendrobates tinctorius. We compare publicly available frog genomes find evidence both large-scale conserved synteny widespread rearrangements between lineages. Comparing orthologs annotated these revealed strong correlation gene size. To cause gene-size variation, quantified location relative features that accumulation introns has played role evolution D. tinctorius, while estimates insertion times suggest many events recent species-specific. Finally, carry out population-scale mobile-element sequencing show diversity abundance can complicate genotyping from repetitive element sequence anchors. Our results have clearly large Future studies needed fully understand dynamics optimize primer or bait design cost-effective population-level species with large, genomes.

Language: Английский

Citations

2
Genome-wide analysis of histone modifications can contribute to the identification of candidate cis-regulatory regions in the threespine stickleback fish DOI Creative Commons
Genta Okude, Yo Y. Yamasaki, Atsushi Toyoda

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: July 11, 2024

Abstract Background Cis -regulatory mutations often underlie phenotypic evolution. However, because identifying the locations of promoters and enhancers in non-coding regions is challenging, we have fewer examples identified causative cis that naturally occurring variations than amino acid-altering mutations. Because elements epigenetic marks specific histone modifications, can detect by mapping analyzing them. Here, investigated modifications chromatin accessibility with cleavage under targets tagmentation (CUT&Tag) assay for transposase-accessible chromatin-sequencing (ATAC-seq). Results Using threespine stickleback ( Gasterosteus aculeatus ) as a model, confirmed genes which nearby showed active marks, such H3K4me1, H3K4me3, high accessibility, were highly expressed. In contrast, expression levels repressive H3K27me3, reduced, suggesting our analysis protocols overall worked well. Genomic peaks higher nucleotide diversity within between populations. By comparing gene gills marine stream ecotypes, several insertions deletions (indels) transposable element fragments candidate regions. Conclusions Thus, help identify accelerate identification underlying variations.

Language: Английский

Citations

1
An almost chromosome-level assembly and annotation of theAlectoris rufagenome DOI Open Access
Abderrahmane Eleiwa, Jesús Nadal, Ester Vilaprinyó

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 11, 2024

The red-legged partridge, Alectoris rufa (n=38 chromosomes) plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation management. Here we sequence, assemble, annotate highly contiguous nearly complete version it genome (115 scaffolds, L90=23). This assembly contains 96.9% (8078 out 8332) orthologous genes from BUSCO aves_odb10 dataset single copy genes. We identify RNA protein genes, 95% which with functional annotation. near-chromosome level revealed significant chromosome rearrangements compared to quail ( Coturnix japonica ) chicken Gallus gallus ), suggesting that A. C. diverged 21 M-years ago their common ancestor G. 37 ago. reported step towards reference , contributing facilitate comparative avian genomics, providing valuable resource future research efforts partridge.

Language: Английский

Citations

0
Genetic basis and expression of ventral colour in polymorphic common lizards DOI Creative Commons
Hans Recknagel, Henrique G. Leitão, Kathryn R. Elmer

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(5)

Published: Jan. 24, 2024

Colour is an important visual cue that can correlate with sex, behaviour, life history or ecological strategies, and has evolved divergently convergently across animal lineages. Its genetic basis in non-model organisms rarely known, but such information vital for determining the drivers mechanisms of colour evolution. Leveraging admixture a rare contact zone between oviparous viviparous common lizards (Zootoca vivipara), we show females (N = 558) two otherwise morphologically indistinguishable reproductive modes differ their ventral colouration (from pale to vibrant yellow) intensity melanic patterning. We find no association female investment, evidence selection on colour. Using combination mapping transcriptomic evidence, identified candidate genes associated differentiation, DGAT2 PMEL. These are known be involved carotenoid metabolism melanin synthesis respectively. Ventral spots were genomic regions, including SNP close protein tyrosine phosphatase (PTP) genes. genome re-sequencing data, our results fixed coding mutations cannot account differences colouration. Taken together, findings evolution its associations lizard lineages variable. A potential mechanism explaining flexibility may lizards, also squamates, predominantly driven by regulatory variation.

Language: Английский

Citations

0
Effects of Arboviral Infections on Transposable Element Transcript Levels in Aedes aegypti DOI Creative Commons
Chloé Garambois, Matthieu Boulesteix, Marie Fablet

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(5)

Published: May 1, 2024

Abstract Transposable elements are mobile repeated sequences found in all genomes. controlled by RNA interference pathways most organisms, and this control involves the PIWI-interacting pathway small interfering pathway, which is also known to be first line of antiviral defense invertebrates. Using Drosophila, we recently showed that viral infections result modulation transposable element transcript levels through repertoire. The Aedes aegypti mosquito particular interest because almost half its genome made elements, it described as a major vector viruses (such dengue [DENV], Zika [ZIKV], chikungunya [CHIKV] arboviruses). Moreover, mosquitoes unique among insects involved somatic response, addition genes expanded genome. For these reasons, studied impacts on A. samples. We retrieved public datasets corresponding RNA-seq data obtained from DENV, ZIKV, CHIKV various tissues. transcripts moderately modulated following infection direction varies greatly across tissues viruses. These results highlight need for an in-depth investigation tightly intertwined interactions between

Language: Английский

Citations

0
Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge DOI Creative Commons
Abderrahmane Eleiwa, Jesús Nadal, Ester Vilaprinyó

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Aug. 22, 2024

The red-legged partridge Alectoris rufa plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation management. Here we sequence, assemble, annotate highly contiguous nearly complete version genome. This assembly encompasses 96.9% avian genes flagged as essential BUSCO aves_odb10 dataset. Moreover, pinpointed RNA protein-coding genes, 95% which had functional annotations. Notably, observed significant chromosome rearrangements comparison to quail (Coturnix japonica) chicken (Gallus gallus). In addition, comparative phylogenetic analysis these genomes suggests that A. C. japonica diverged roughly 20 million years ago their common ancestor from G. gallus 35 ago. Our represents advancement towards reference genome rufa, facilitating genomics, providing valuable resource future research efforts partridge.

Language: Английский

Citations

0