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1.
Biol Lett ; 17(9): 20210293, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34520681

RESUMO

Fuelled by the ongoing genomic revolution, broadscale RNA expression surveys are fast replacing studies targeting one or a few genes to understand the molecular basis of behaviour. Yet, the timescale of RNA-sequencing experiments and the dynamics of neural gene activation are insufficient to drive real-time switches between behavioural states. Moreover, the spatial, functional and transcriptional complexity of the brain (the most commonly targeted tissue in studies of behaviour) further complicates inference. We argue that a Central Dogma-like 'back-to-basics' assumption that gene expression changes cause behaviour leaves some of the most important aspects of gene-behaviour relationships unexplored, including the roles of environmental influences, timing and feedback from behaviour-and the environmental shifts it causes-to neural gene expression. No perfect experimental solutions exist but we advocate that explicit consideration, exploration and discussion of these factors will pave the way toward a richer understanding of the complicated relationships between genes, environments, brain gene expression and behaviour over developmental and evolutionary timescales.


Assuntos
Genômica , Transcriptoma , Evolução Biológica , Perfilação da Expressão Gênica , Genoma
2.
Zool Res ; 42(5): 660-665, 2021 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-34472227

RESUMO

Flatheads are valuable commercial fish species endemic to the Indo-West Pacific. Due to their economic value and unique biological traits, such as metamorphosis and camouflage, they serve as ideal marine organisms for studies on demersal adaptation and evolution. The brown-spotted flathead (Platycephalus sp.1) is the most widely distributed in the northwestern Pacific. Despite the lack of a valid scientific name, it has been long recognized and exploited in the marine fisheries of China, Japan, and Korea. In the current study, we applied Illumina, PacBio, and Hi-C sequencing to assemble a chromosome-scale genome for this species. The assembled genome was 660.63 Mb long with a scaffold N50 of 28.65 Mb and 100% of the contigs were anchored onto 24 chromosomes. We predicted 22 743 protein-coding genes, 94.8% of which were functionally annotated. Comparative genomic analyses suggested that Platycephalus sp.1 diverged from its common ancestor with Gasterosteus aculeatus ~88.4 million years ago. The expanded gene families were significantly enriched in immune, biosynthetic, and metabolic pathways. Furthermore, three shared Gene Ontology terms and 377 common positively selected genes were identified between flathead and flatfish species, suggesting that these genes may contribute to demersal adaptation in flatheads. The assembled genomic data provide a valuable molecular resource for further research on the biological and adaptive evolution of flathead species.


Assuntos
Adaptação Fisiológica/genética , Cromossomos/genética , Peixes/genética , Genoma , Genômica/métodos , Animais , Oceano Pacífico , Filogenia
3.
Zool Res ; 42(5): 671-674, 2021 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-34490760

RESUMO

All extant species in the rodent family Spalacidae are subterranean and have evolved various traits for underground life. However, the phylogenomic relationships among its three subfamilies (Myospalacinae, Spalacinae, and Rhizomyinae) and the molecular basis underlying their adaptations to underground life remain poorly understood. Here, we inferred the phylogenomic relationships among these subfamilies based on de novo sequencing the genome of the hoary bamboo rat ( Rhizomys pruinosus). Analyses showed that ~50% of the identified 11 028 one-to-one orthologous protein-coding genes and the concatenated sequences of these orthologous genes strongly supported a sister relationship between Myospalacinae and Rhizomyinae. The three subfamilies diversified from each other within ~2 million years. Compared with the non-subterranean controls with similar divergence dates, the spalacids shared more convergent genes with the African subterranean mole-rats at the genomic scale due to more rapid protein sequence evolution. Furthermore, these convergent genes were enriched in the functional categories of carboxylic acid transport, vascular morphogenesis, and response to oxidative stress, which are closely associated with adaptations to the hypoxic-hypercapnic underground environment. Our study presents a well-supported phylogenomic relationship among the three subfamilies of Spalacidae and offers new insights into the molecular adaptations of spalacids living underground.


Assuntos
Adaptação Fisiológica/genética , Comportamento Animal/fisiologia , Evolução Molecular , Genômica , Roedores/genética , Animais , Genoma , Filogenia , Roedores/fisiologia , Especificidade da Espécie
4.
Curr Protoc ; 1(9): e252, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34506690

RESUMO

The creation of visualizations to interpret genomics data remains an important aspect of data science within computational biology. The GenVisR Bioconductor package was created to lower the entry point for publication-quality graphics and has remained a popular suite of tools within this domain. GenVisR supports visualizations covering a breadth of topics including functions to produce visual summaries of copy-number alterations, somatic variants, sequence quality metrics, and more. Recently, the GenVisR package has undergone significant updates to increase performance and functionality. To demonstrate the utility of GenVisR, we present protocols for use of the updated Waterfall() function to create a customizable Oncoprint-style plot of the mutational landscape of a tumor cohort. We explain the basics of installation, data import, configuration, plotting, clinical annotation, and customization. A companion online workshop describing the GenVisR library, Waterfall() function, and other genomic visualization tools is available at genviz.org. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generating a Waterfall() plot from original mutation data Basic Protocol 2: Adding clinical data to a Waterfall() plot Basic Protocol 3: Customizing mutation burden in Waterfall() plots Basic Protocol 4: Brief exploration of customizable options Support Protocol 1: Installing GenVisR.


Assuntos
Neoplasias , Software , Biologia Computacional , Genoma , Genômica , Humanos , Neoplasias/genética
5.
BMC Genomics ; 22(1): 665, 2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34521340

RESUMO

BACKGROUND: It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. RESULTS: Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls. CONCLUSIONS: The donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent.


Assuntos
Cromossomos Humanos Par 1 , Equidae , Animais , Cromossomos/genética , Cromossomos Humanos Par 5 , Equidae/genética , Genoma , Cavalos/genética , Humanos
6.
BMC Genomics ; 22(1): 673, 2021 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-34536998

RESUMO

BACKGROUND: Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and across species suggest that recombination is evolving adaptively. All studied insects with advanced eusociality have shown exceptionally high recombination rates, which may represent a prominent case of adaptive evolution of recombination. However, our understanding of the relationship between social evolution and recombination rates is incomplete, partly due to lacking empirical data. Here, we present a linkage map of the monandrous, advanced eusocial Brazilian stingless bee, Frieseomelitta varia, providing the first recombination analysis in the diverse Meliponini (Hymenoptera, Apidae). RESULTS: Our linkage map includes 1417 markers in 19 linkage groups. This map spans approximately 2580 centimorgans, and comparisons to the physical genome assembly indicate that it covers more than 75 % of the 275 Megabasepairs (Mbp) F. varia genome. Thus, our study results in a genome-wide recombination rate estimate of 9.3-12.5 centimorgan per Mbp. This value is higher than estimates from nonsocial insects and comparable to other highly social species, although it does not support our prediction that monandry and strong queen-worker caste divergence of F. varia lead to even higher recombination rates than other advanced eusocial species. CONCLUSIONS: Our study expands the association between elevated recombination and sociality in the order Hymenoptera and strengthens the support for the hypothesis that advanced social evolution in hymenopteran insects invariably selects for high genomic recombination rates.


Assuntos
Himenópteros , Animais , Abelhas/genética , Ligação Genética , Genoma , Recombinação Genética , Comportamento Social
7.
BMC Bioinformatics ; 22(Suppl 10): 394, 2021 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-34348661

RESUMO

BACKGROUND: Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family may enter the species tree from the outside. Moreover, within the genome, genes are often rearranged, causing them to move to new syntenic regions. RESULTS: We extend the DTL model to account for two events that commonly arise in the evolution of microbes: origin of a gene from outside the sampled species tree and rearrangement of gene syntenic regions. We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees to handle uncertainty in gene tree topologies. Finally, we describe preliminary experimental results from the integration of our algorithm into the existing xenoGI tool for reconstructing the histories of genomic islands in closely related bacteria. CONCLUSIONS: Reconciliation in the DTLOR model can offer new insights into the evolution of microbes that is not currently possible under the DTL model.


Assuntos
Evolução Molecular , Duplicação Gênica , Algoritmos , Genoma , Modelos Genéticos , Filogenia
8.
BMC Ecol Evol ; 21(1): 153, 2021 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-34348656

RESUMO

BACKGROUND: Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence. RESULTS: We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins. CONCLUSIONS: A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.


Assuntos
Eutérios , Placenta , Animais , Eutérios/genética , Feminino , Genoma/genética , Mamíferos/genética , Filogenia , Gravidez
9.
Trop Anim Health Prod ; 53(4): 432, 2021 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-34373940

RESUMO

The multiple sire system (MSS) is a common mating scheme in extensive beef production systems. However, MSS does not allow paternity identification and lead to inaccurate genetic predictions. The objective of this study was to investigate the implementation of single-step genomic BLUP (ssGBLUP) in different scenarios of uncertain paternity in the evaluation for 450-day adjusted liveweight (W450) and age at first calving (AFC) in a Nellore cattle population. To estimate the variance components using BLUP and ssGBLUP, the relationship matrix (A) with different proportions of animals with missing sires (MS) (scenarios 0, 25, 50, 75, and 100% of MS) was created. The genotyped animals with MS were randomly chosen, and ten replicates were performed for each scenario and trait. Five groups of animals were evaluated in each scenario: PHE, all animals with phenotypic records in the population; SIR, proven sires; GEN, genotyped animals; YNG, young animals without phenotypes and progeny; and YNGEN, young genotyped animals. The additive genetic variance decreased for both traits as the proportion of MS increased in the population when using the regular REML. When using the ssGBLUP, accuracies ranged from 0.13 to 0.47 for W450 and from 0.10 to 0.25 for AFC. For both traits, the prediction ability of the direct genomic value (DGV) decreased as the percentage of MS increased. These results emphasize that indirect prediction via DGV of young animals is more accurate when the SNP effects are derived from ssGBLUP with a reference population with known sires. The ssGBLUP could be applied in situations of uncertain paternity, especially when selecting young animals. This methodology is shown to be accurate, mainly in scenarios with a high percentage of MS.


Assuntos
Genoma , Modelos Genéticos , Animais , Bovinos/genética , Genômica , Genótipo , Linhagem , Fenótipo
10.
Zool Res ; 42(5): 606-613, 2021 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-34387416

RESUMO

The genus Tropidophorus consists of small semi-aquatic lizards that dwell in lowland forest steams (Barbour, 1921; Bauer & Jackman, 2008). Here, we designate the neotype and re-describe T. guangxiensis Wen, 1992 based on newly collected topotypic specimens. We also describe a new subspecies from Xuefeng Mountain, Hongjiang County, Hunan Province, central South China. Based on two mitochondrial genes (12S rRNA and 16S rRNA), the phylogenetic position of T. guangxiensis is allocated for the first time. Additionally, our data strongly support that the new subspecies is phylogenetically closely related to T. g. guangxiensis. We also present a morphological identification key for known species and subspecies of Tropidophorus in China.


Assuntos
Lagartos/anatomia & histologia , Lagartos/classificação , Animais , Classificação , DNA/genética , Feminino , Genoma , Masculino , Filogenia , Especificidade da Espécie
11.
DNA Res ; 28(4)2021 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-34387305

RESUMO

The crown-of-thorns starfish (COTS) is a coral predator that is widely distributed in Indo-Pacific Oceans. A previous phylogenetic study using partial mitochondrial sequences suggested that COTS had diverged into four distinct species, but a nuclear genome-based analysis to confirm this was not conducted. To address this, COTS species nuclear genome sequences were analysed here, sequencing Northern Indian Ocean (NIO) and Red Sea (RS) species genomes for the first time, followed by a comparative analysis with the Pacific Ocean (PO) species. Phylogenetic analysis and ADMIXTURE analysis revealed clear divergences between the three COTS species. Furthermore, within the PO species, the phylogenetic position of the Hawaiian sample was further away from the other Pacific-derived samples than expected based on the mitochondrial data, suggesting that it may be a PO subspecies. The pairwise sequentially Markovian coalescent model showed that the trajectories of the population size diverged by region during the Mid-Pleistocene transition when the sea-level was dramatically decreased, strongly suggesting that the three COTS species experienced allopatric speciation. Analysis of the orthologues indicated that there were remarkable genes with species-specific positive selection in the genomes of the PO and RS species, which suggested that there may be local adaptations in the COTS species.


Assuntos
Evolução Biológica , Genoma , Filogenia , Estrelas-do-Mar/genética , Animais , Genômica , Filogeografia , Análise de Sequência de DNA
12.
Nat Commun ; 12(1): 5091, 2021 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-34429415

RESUMO

Ten-eleven translocation (TET) proteins, the dioxygenase for DNA hydroxymethylation, are important players in nervous system development and diseases. However, their role in myelination and remyelination after injury remains elusive. Here, we identify a genome-wide and locus-specific DNA hydroxymethylation landscape shift during differentiation of oligodendrocyte-progenitor cells (OPC). Ablation of Tet1 results in stage-dependent defects in oligodendrocyte (OL) development and myelination in the mouse brain. The mice lacking Tet1 in the oligodendrocyte lineage develop behavioral deficiency. We also show that TET1 is required for remyelination in adulthood. Transcriptomic, genomic occupancy, and 5-hydroxymethylcytosine (5hmC) profiling reveal a critical TET1-regulated epigenetic program for oligodendrocyte differentiation that includes genes associated with myelination, cell division, and calcium transport. Tet1-deficient OPCs exhibit reduced calcium activity, increasing calcium activity rescues the differentiation defects in vitro. Deletion of a TET1-5hmC target gene, Itpr2, impairs the onset of OPC differentiation. Together, our results suggest that stage-specific TET1-mediated epigenetic programming and intracellular signaling are important for proper myelination and remyelination in mice.


Assuntos
Encéfalo/metabolismo , Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Camundongos Mutantes Neurológicos/metabolismo , Proteínas Proto-Oncogênicas/metabolismo , Remielinização/fisiologia , 5-Metilcitosina/análogos & derivados , Animais , Ciclo Celular , Diferenciação Celular , Metilação de DNA , Proteínas de Ligação a DNA/genética , Genoma , Camundongos , Camundongos Knockout , Oligodendroglia/metabolismo , Organogênese , Proteínas Proto-Oncogênicas/genética
13.
Nat Commun ; 12(1): 4737, 2021 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-34362910

RESUMO

Glucocorticoid hormones (GCs) - acting through hippocampal mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) - are critical to physiological regulation and behavioural adaptation. We conducted genome-wide MR and GR ChIP-seq and Ribo-Zero RNA-seq studies on rat hippocampus to elucidate MR- and GR-regulated genes under circadian variation or acute stress. In a subset of genes, these physiological conditions resulted in enhanced MR and/or GR binding to DNA sequences and associated transcriptional changes. Binding of MR at a substantial number of sites however remained unchanged. MR and GR binding occur at overlapping as well as distinct loci. Moreover, although the GC response element (GRE) was the predominant motif, the transcription factor recognition site composition within MR and GR binding peaks show marked differences. Pathway analysis uncovered that MR and GR regulate a substantial number of genes involved in synaptic/neuro-plasticity, cell morphology and development, behavior, and neuropsychiatric disorders. We find that MR, not GR, is the predominant receptor binding to >50 ciliary genes; and that MR function is linked to neuronal differentiation and ciliogenesis in human fetal neuronal progenitor cells. These results show that hippocampal MRs and GRs constitutively and dynamically regulate genomic activities underpinning neuronal plasticity and behavioral adaptation to changing environments.


Assuntos
Hipocampo/metabolismo , Plasticidade Neuronal/fisiologia , Receptores de Mineralocorticoides/genética , Receptores de Mineralocorticoides/metabolismo , Receptores de Esteroides/metabolismo , Animais , Regulação da Expressão Gênica , Genoma , Hipocampo/patologia , Humanos , Masculino , Ligação Proteica , RNA/metabolismo , Ratos , Ratos Wistar , Receptores de Glucocorticoides/genética , Receptores de Glucocorticoides/metabolismo , Elementos de Resposta , Fatores de Transcrição
14.
Nat Commun ; 12(1): 4765, 2021 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-34362925

RESUMO

Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an 'omics-based' framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as 'current threats' (Rank I; 3%) - already present among pathogens - and 'future threats' (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 'current threat' ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II ('future threats'). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana/efeitos dos fármacos , Farmacorresistência Bacteriana/genética , Bactérias/efeitos dos fármacos , Bactérias/genética , Bases de Dados Factuais , Microbioma Gastrointestinal/efeitos dos fármacos , Genes Bacterianos/efeitos dos fármacos , Genoma , Humanos , Metagenoma , Plasmídeos
15.
Nat Commun ; 12(1): 4790, 2021 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-34373465

RESUMO

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the most accurate models of biological systems include Expression and Thermodynamics FLux (ETFL), which efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable for E. coli. To adapt this model for Saccharomyces cerevisiae, we developed yETFL, in which we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the ability of yETFL to predict maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the presented formulation can be extended to a wide range of eukaryotic organisms to the benefit of academic and industrial research.


Assuntos
Genoma , Engenharia Metabólica , Redes e Vias Metabólicas , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Biomassa , Biotecnologia , Simulação por Computador , Escherichia coli/genética , Regulação Fúngica da Expressão Gênica , Glucose , Modelos Biológicos , Fenótipo , Termodinâmica
16.
Yi Chuan ; 43(8): 758-774, 2021 Aug 20.
Artigo em Chinês | MEDLINE | ID: mdl-34413016

RESUMO

CTCF (CCCTC-binding factor) is a zinc-finger protein which plays a vital role in the three-dimensional (3D) genome architecture. A pair of forward-reverse convergent CTCF binding sites (CBS elements) mediates long-distance DNA interactions to form chromatin loops with the assistance of the cohesin complex, while CBS elements at the chromatin domain boundaries show reverse-forward divergent patterns and function as insulators to discriminate against DNA interaction between chromatin domains. However, there are still many unresolved problems regarding CTCF-mediated insulation function. In order to study the connections between chromatin loops and the insulation function of CBS elements, we combinatorically inverted CBS elements at the HOXD locus by using CRISPR/Cas9 DNA-fragment editing methods in the HEK293T cell line and obtained five different kinds of single-cell CRISPR clones. By performing quantitative high-resolution chromosome conformation capture copy (QHR-4C) experiments, we found that boundary CBS inversions abolish original chromatin loops and establish new loops from the opposite direction, thus shifting the insulator boundary to the new divergent CTCF sites. Furthermore, tandem CBS elements block cohesin permeated from the opposite orientation to function as insulators. RNA-seq experiments showed that alterations of local three-dimensional genome architecture would further influence gene expression of the HOXD cluster. In conclusion, a pair of divergent CBS elements function as insulators by forming chromatin loops within chromatin domains to block cohesin sliding.


Assuntos
Cromatina , Genoma , Sítios de Ligação , Cromatina/genética , DNA , Células HEK293 , Humanos
17.
BMC Genomics ; 22(1): 625, 2021 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-34418978

RESUMO

BACKGROUND: Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS: In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS: Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.


Assuntos
Metagenômica , Projetos de Pesquisa , Animais , Genoma , Genômica , Humanos , Análise de Sequência de DNA
18.
Trop Anim Health Prod ; 53(4): 423, 2021 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-34333713

RESUMO

Most parts of Eritrea are classified as arid and semi-arid land (ASALs) which are characterised by dryness, high ambient temperatures and low precipitation. The country has three different environmental landscapes: highland, Western lowland and Eastern lowland agro-ecological zones (AEZs). The geophysical and biophysical characteristics of the AEZs vary. Indigenous cattle which are mainly kept in extensive production system have to cope with the adverse climatic conditions of these AEZs. They have to adapt to the harsh climate, poor feed quality and endemic diseases and parasites and reproduction challenges in the AEZs. The underlying genetic basis of the indigenous cattle adaption to the specific AEZs in Eritrea is limited. In this study, it is hypothesized that the indigenous cattle have evolved and developed unique adaptive characteristics because of being reared in specific ecological landscapes. This was tested using the landscape genomics and analysis of selection signatures to ascertain the genetic basis of their adaptability to the nutritional and environmental constraints that characterise the AEZ conditions. The study was carried out in three different environmental landscapes: highland, Eastern lowland and Western lowland AEZs. Blood samples were collected from a total of 188 indigenous cattle populations sampled from the three AEZs. DNA was extracted and genotyped using the genotype by sequencing (GBS) method. Analysis revealed the existence of medium to high genetic diversity between and within the indigenous cattle populations. Scanning of selection signatures revealed genomic regions under positive selection. The regions harboured genes (IFNAR2, CASR, AHSG, ATP1B3, AIRE, ROBO2, SCHIP1 and PARS2) of importance for facial morphology, locomotion, mineral homeostasis, immune system and skeletal and muscle system development. Findings pointed out the influence of AEZ landscapes on the genetic differentiation of indigenous cattle appearances probably due to selection driven by diverse climatic and biophysical conditions. The differentiation is orientated towards adaptive characteristics.


Assuntos
Adaptação Fisiológica , Genômica , Adaptação Fisiológica/genética , Animais , Bovinos/genética , Eritreia , Genoma , Genótipo , Polimorfismo de Nucleotídeo Único , Seleção Genética
19.
J Anim Sci ; 99(9)2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34378776

RESUMO

Accuracy of genomic predictions is an important component of the selection response. The objectives of this research were: 1) to investigate trends for prediction accuracies over time in a broiler population of accumulated phenotypes, genotypes, and pedigrees and 2) to test if data from distant generations are useful to maintain prediction accuracies in selection candidates. The data contained 820K phenotypes for a growth trait (GT), 200K for two feed efficiency traits (FE1 and FE2), and 42K for a carcass yield trait (CY). The pedigree included 1,252,619 birds hatched over 7 years, of which 154,318 from the last 4 years were genotyped. Training populations were constructed adding 1 year of data sequentially, persistency of accuracy over time was evaluated using predictions from birds hatched in the three generations following or in the years after the training populations. In the first generation, before genotypes became available for the training populations (first 3 years of data), accuracies remained almost stable with successive additions of phenotypes and pedigree to the accumulated dataset. The inclusion of 1 year of genotypes in addition to 4 years of phenotypes and pedigree in the training population led to increases in accuracy of 54% for GT, 76% for FE1, 110% for CY, and 38% for FE2; on average, 74% of the increase was due to genomics. Prediction accuracies declined faster without than with genomic information in the training populations. When genotypes were unavailable, the average decline in prediction accuracy across traits was 41% from the first to the second generation of validation, and 51% from the second to the third generation of validation. When genotypes were available, the average decline across traits was 14% from the first to the second generation of validation, and 3% from the second to the third generation of validation. Prediction accuracies in the last three generations were the same when the training population included 5 or 2 years of data, and a decrease of ~7% was observed when the training population included only 1 year of data. Training sets including genomic information provided an increase in accuracy and persistence of genomic predictions compared with training sets without genomic data. The two most recent years of pedigree, phenotypic, and genomic data were sufficient to maintain prediction accuracies in selection candidates. Similar conclusions were obtained using validation populations per year.


Assuntos
Galinhas , Modelos Genéticos , Animais , Galinhas/genética , Genoma , Genômica , Genótipo , Fenótipo , Polimorfismo de Nucleotídeo Único
20.
Theriogenology ; 173: 269-278, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34403972

RESUMO

With continuous improvement of sow litter size, breeders are gradually paying more attention to the quality of litter traits that directly impact the production efficiency of pig companies, such as the rate of piglets born alive (RBA) and the rate of healthy births (RHB). The objectives of this study are to dissect the genetic basis of litter traits in pig and to identify valuable genes and genetic markers, especially pleiotropic, for pig breeding. Herein, 1140 Duroc pigs and 2046 reproduction records, 5 litter traits, including the number of healthy births (NHB), number of deformed fetuses (NDF), number of stillborn (NSB), RBA, and RHB, were used in this study. Subsequently, a genome-wide association study (GWAS) was performed for the five litter traits in the first two parities from two Duroc populations. A total of 76 significantly related SNPs and 10 potential candidate genes (CAV1, DAB2, FGF12, FHOD3, DYNC2H1, GRHL1, TCTN3, PYROXD2, MMP8, MMP13, and PGR) were detected, including 13 pleiotropic SNPs that affected more than one litter trait. Finally, the functional enrichment analysis of functional genes that were closest to these significant SNPs indicated that most of the significant pathways were associated with hormone secretion and embryo and organ development. This study advances our understanding of the genetic mechanisms of litter traits, especially the survival rate of piglets born, and provides an opportunity to increase the quality of litter using marker-assisted selection or genomic selection in pigs.


Assuntos
Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Animais , Feminino , Genoma , Estudo de Associação Genômica Ampla/veterinária , Tamanho da Ninhada de Vivíparos/genética , Fenótipo , Gravidez , Suínos/genética
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