animal genomes
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2021 ◽  
Author(s):  
Richard Meisel

This article reviews and discusses ecological factors that affect sex chromosome evolution. Sex chromosomes are common features of animal genomes, and are often the location where master sex determination genes are found. Many important aspects of sex chromosome evolution are thought to be driven by sex-specific selection pressures, such as sexual antagonism and sexual selection. Sex-specific selection affects both the formation of sex chromosomes from autosomes and differences in the evolutionary trajectories between sex chromosomes and autosomes. Most population genetic models are agnostic as to whether the sex-specific selection pressures arise from intrinsic features of organismal biology or extrinsic factors that depend on environment. Here, I review the evidence that extrinsic, or ecological, factors are important determinants of sex-specific selection pressures that shape sex chromosome evolution.


2021 ◽  
Author(s):  
Michele Gabriele ◽  
Hugo B Brandão ◽  
Simon Grosse-Holz ◽  
Asmita Jha ◽  
Gina M Dailey ◽  
...  

Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF and cohesin, but whether these loops are stable or dynamic is unknown. Here, we directly visualize chromatin looping at the Fbn2 TAD in mouse embryonic stem cells using super-resolution live-cell imaging and quantify looping dynamics by Bayesian inference. Our results are consistent with cohesin-mediated loop extrusion in cells, and with CTCF both stopping and stabilizing cohesin. Surprisingly, the Fbn2 loop is both rare and dynamic, with a looped fraction of ~3-6.5% and a median loop lifetime of ~10-30 minutes. Instead of a stable loop, our results establish a highly dynamic view of TADs and loops where the Fbn2 TAD exists predominantly in a partially extruded conformation. This dynamic and quantitative view of TADs may facilitate a mechanistic understanding of their functions.


2021 ◽  
Vol 12 ◽  
Author(s):  
Amanda Jane Chamberlain ◽  
Hans H. Cheng ◽  
Elisabetta Giuffra ◽  
Christa Kuehn ◽  
Christopher K. Tuggle ◽  
...  

Author(s):  
Jessica Schultz ◽  
Paul Hebert

Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. The number of NUMTs meeting four length criteria (>150 bp, >300 bp, >450 bp, >600 bp) was determined, and they were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 389 NUMTs <100 bp were detected, with an average of 2.49 per species (range = 0–50) and a mean length of 336 bp +/- 208 bp. Among NUMTs lacking diagnostic features, 52.5% were ≤300 bp, 63.9% were ≤450 bp, and 76.2% were ≤600 bp. Studies examing 150 bp amplicons inflate the OTU count by 1.57x compared to the true species count and increase perceived intraspecific variation at COI by 1.19x (when sequence variants with >2% sequence divergence are recognized as different OTUs). There was a weak positive correlation between genome size and NUMT count but no variation among phyla, trophic groups or life history traits. While bioinformatic advances will improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.


2021 ◽  
Author(s):  
Tereza Clarence ◽  
Nicolas Robert ◽  
Fatih Sarigol ◽  
Xiao Fu ◽  
Paul Bates ◽  
...  

Abstract Animal genomes are organized into chromosomes that are remarkably conserved in their gene content, forming distinct evolutionary units (macrosynteny). We developed a novel three-dimensional chromosomal modelling approach to show that syntenic signals are reflected in conserved three-dimensional networks, encompassed within interaction spheres. We show evidence for evolutionary constraints that could not be surmised by genomic sequence alone, thereby underlining the importance of three-, rather than just two-, dimensional organization.


eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Jordan Yupeng Xiao ◽  
Antonina Hafner ◽  
Alistair N Boettiger

Animal genomes are organized into topologically associated domains (TADs). TADs are thought to contribute to gene regulation by facilitating enhancer-promoter (E-P) contacts within a TAD preventing these contacts across TAD borders. However, the absolute difference in contact frequency across TAD boundaries is usually less than two-fold, even though disruptions of TAD borders can change gene expression by ten-fold. Existing models fail to explain this hypersensitive response. Here, we propose a futile cycle model of enhancer-mediated regulation that can exhibit hypersensitivity through bistability and hysteresis. Consistent with recent experiments, this regulation does not exhibit strong correlation between enhancer-promoter contact and promoter activity, even though regulation occurs through contact. Through mathematical analysis and stochastic simulation, we show that this system can create an illusion of enhancer-promoter biochemical specificity and explain the importance of weak TAD boundaries. It also offers a mechanism to reconcile apparently contradictory results from recent global TAD disruption with local TAD boundary deletion experiments. Together, these analyses advance our understanding of cis-regulatory contacts in controlling gene expression, and suggest new experimental directions.


Author(s):  
Juan J. Tena ◽  
José M. Santos-Pereira

Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as structural scaffolds for the establishment of regulatory landscapes (RLs). In this review, we discuss recent advances in the connection between TADs and gene regulation, their relationship with gene RLs and their dynamics during development and differentiation. Moreover, we describe how restructuring TADs may lead to pathological conditions, which explains their high evolutionary conservation, but at the same time it provides a substrate for the emergence of evolutionary innovations that lay at the origin of vertebrates and other phylogenetic clades.


2021 ◽  
Vol 12 ◽  
Author(s):  
Peter W. Harrison ◽  
Alexey Sokolov ◽  
Akshatha Nayak ◽  
Jun Fan ◽  
Daniel Zerbino ◽  
...  

The Functional Annotation of ANimal Genomes (FAANG) project is a worldwide coordinated action creating high-quality functional annotation of farmed and companion animal genomes. The generation of a rich genome-to-phenome resource and supporting informatic infrastructure advances the scope of comparative genomics and furthers the understanding of functional elements. The project also provides terrestrial and aquatic animal agriculture community powerful resources for supporting improvements to farmed animal production, disease resistance, and genetic diversity. The FAANG Data Portal (https://data.faang.org) ensures Findable, Accessible, Interoperable and Reusable (FAIR) open access to the wealth of sample, sequencing, and analysis data produced by an ever-growing number of FAANG consortia. It is developed and maintained by the FAANG Data Coordination Centre (DCC) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). FAANG projects produce a standardised set of multi-omic assays with resulting data placed into a range of specialised open data archives. To ensure this data is easily findable and accessible by the community, the portal automatically identifies and collates all submitted FAANG data into a single easily searchable resource. The Data Portal supports direct download from the multiple underlying archives to enable seamless access to all FAANG data from within the portal itself. The portal provides a range of predefined filters, powerful predictive search, and a catalogue of sampling and analysis protocols and automatically identifies publications associated with any dataset. To ensure all FAANG data submissions are high-quality, the portal includes powerful contextual metadata validation and data submissions brokering to the underlying EMBL-EBI archives. The portal will incorporate extensive new technical infrastructure to effectively deliver and standardise FAANG's shift to single-cellomics, cell atlases, pangenomes, and novel phenotypic prediction models. The Data Portal plays a key role for FAANG by supporting high-quality functional annotation of animal genomes, through open FAIR sharing of data, complete with standardised rich metadata. Future Data Portal features developed by the DCC will support new technological developments for continued improvement for FAANG projects.


2021 ◽  
Vol 12 ◽  
Author(s):  
Sichong Peng ◽  
Rebecca Bellone ◽  
Jessica L. Petersen ◽  
Theodore S. Kalbfleisch ◽  
Carrie J. Finno

An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin to characterize tissue specificity of genome function for prioritized tissues have been performed. Due to the logistics of tissue collection and storage, extracting nuclei from a large number of tissues for ATAC-seq at the time of collection is not always practical. To assess the feasibility of using stored frozen tissues for ATAC-seq and to provide a guideline for the equine FAANG project, we compared ATAC-seq results from nuclei isolated from frozen tissue to cryopreserved nuclei (CN) isolated at the time of tissue harvest in liver, a highly cellular homogenous tissue, and lamina, a relatively acellular tissue unique to the horse. We identified 20,000–33,000 accessible chromatin regions in lamina and 22–61,000 in liver, with consistently more peaks identified using CN isolated at time of tissue collection. Our results suggest that frozen tissues are an acceptable substitute when CN are not available. For more challenging tissues such as lamina, nuclei extraction at the time of tissue collection is still preferred for optimal results. Therefore, tissue type and accessibility to intact nuclei should be considered when designing ATAC-seq experiments.


2021 ◽  
Author(s):  
Moataz Dowaidar

Shadow enhancers' objective seems to be to establish robust growth patterns, independent of genetic or environmental stress. Multiple enhancers give more ability to encode intricate biological functions. Shadow enhancers are more conserved than other enhancers after being identified in the genome. Most shadow enhancer knockout research was undertaken in lab conditions that do not reflect natural scenarios. Many interactions across shadow enhancers (whether synergistic or repressive) are comparable to interactions inside a single enhancer between TF-binding sites. Because the length of DNA that can function as an enhancer is likely to be limited, multiple enhancers can be useful in regulating gene expression in complex ways.Despite its widespread presence in animal genomes, the evolutionary origins of shadow enhancies remain unknown.Most alterations in genome-wide association studies are projected to alter enhancer sequences. Patient-wide genome sequencing showed an increasing number of unusual non-coding mutations that change developmental genes and are linked to disease. It is possible that disease-causing non-Coding mutations preferentially impact genes without shadow enhancers or increase enhancer activity not dampened by the availability of enhancers. Alternatively, shadow enhancer changes may have some impact on target gene expression, which may be amplified by other mutations or the environment.


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