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1.
PLoS Biol ; 18(9): e3000636, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32991578

RESUMO

The Myriapoda, composed of millipedes and centipedes, is a fascinating but poorly understood branch of life, including species with a highly unusual body plan and a range of unique adaptations to their environment. Here, we sequenced and assembled 2 chromosomal-level genomes of the millipedes Helicorthomorpha holstii (assembly size = 182 Mb; shortest scaffold/contig length needed to cover 50% of the genome [N50] = 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (assembly size = 449 Mb, N50 = 26.78 Mb mainly on 17 pseudomolecules). Unique genomic features, patterns of gene regulation, and defence systems in millipedes, not observed in other arthropods, are revealed. Both repeat content and intron size are major contributors to the observed differences in millipede genome size. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute (AGO) proteins for loading small RNAs are duplicated in both millipedes, but unlike in insects, an AGO duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs-including species-specific microRNA arm switching-providing differential gene regulation is also obtained. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules found in centipedes. We identify sets of genes associated with the ozadene that play roles in chemical defence as well as antimicrobial activity. Macro-synteny analyses revealed highly conserved genomic blocks between the 2 millipedes and deuterostomes. Collectively, our analyses of millipede genomes reveal that a series of unique adaptations have occurred in this major lineage of arthropod diversity. The 2 high-quality millipede genomes provided here shed new light on the conserved and lineage-specific features of millipedes and centipedes. These findings demonstrate the importance of the consideration of both centipede and millipede genomes-and in particular the reconstruction of the myriapod ancestral situation-for future research to improve understanding of arthropod evolution, and animal evolutionary genomics more widely.


Assuntos
Adaptação Biológica/genética , Artrópodes , Evolução Molecular , Genoma/genética , Animais , Artrópodes/classificação , Artrópodes/genética , Sequência de Bases , Elementos de DNA Transponíveis/genética , Genes Homeobox , Genoma de Inseto , Insetos/classificação , Insetos/genética , MicroRNAs/genética , Filogenia , Sintenia
2.
PLoS One ; 15(8): e0238256, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32866176

RESUMO

In recent years, the binary definition of sex is being challenged by repetitive reports about individuals with ambiguous sexual identity from various animal groups. This has created an urge to decode the molecular mechanism underlying sexual development. However, sexual ambiguities are extremely uncommon in nature, limiting their experimental value. Here, we report the establishment of a genetically modified clone of Daphnia magna from which intersex daphniids can be readily generated. By mutating the conserved central sex determining factor Doublesex1, body-wide feminization of male daphniid could be achieved. Comparative transcriptomic analysis also revealed a genetic network correlated with Doublesex1 activity which may account for the establishment of sexual identity in D. magna. We found that Dsx1 repressed genes related to growth and promoted genes related to signaling. We infer that different intersex phenotypes are the results of fluctuation in activity of these Dsx1 downstream factors. Our results demonstrated that the D. magna genome is capable of expressing sex in a continuous array, supporting the idea that sex is actually a spectrum.


Assuntos
Daphnia/genética , Daphnia/fisiologia , Transtornos do Desenvolvimento Sexual/genética , Redes Reguladoras de Genes/genética , Desenvolvimento Sexual/genética , Sequência de Aminoácidos , Animais , Genoma/genética , Fenótipo , Transcriptoma/genética
3.
Nat Commun ; 11(1): 4739, 2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32958756

RESUMO

More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.


Assuntos
Búfalos/genética , Bovinos/genética , Domesticação , Genoma/genética , Animais , Cruzamento , Búfalos/classificação , Bovinos/classificação , Evolução Molecular , Loci Gênicos/genética , Variação Genética , Fenótipo , Filogeografia , Seleção Genética
4.
PLoS Genet ; 16(8): e1008995, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32833967

RESUMO

Pan-genomic open reading frames (ORFs) potentially carry protein-coding gene or coding variant information in a population. In this study, we suggest that pan-genomic ORFs are promising to be utilized in estimation of heritability and genomic prediction. A Saccharomyces cerevisiae dataset with whole-genome SNPs, pan-genomic ORFs, and the copy numbers of those ORFs is used to test the effectiveness of ORF data as a predictor in three prediction models for 35 traits. Our results show that the ORF-based heritability can capture more genetic effects than SNP-based heritability for all traits. Compared to SNP-based genomic prediction (GBLUP), pan-genomic ORF-based genomic prediction (OBLUP) is distinctly more accurate for all traits, and the predictive abilities on average are more than doubled across all traits. For four traits, the copy number of ORF-based prediction(CBLUP) is more accurate than OBLUP. When using different numbers of isolates in training sets in ORF-based prediction, the predictive abilities for all traits increased as more isolates are added in the training sets, suggesting that with very large training sets the prediction accuracy will be in the range of the square root of the heritability. We conclude that pan-genomic ORFs have the potential to be a supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction.


Assuntos
Genoma/genética , Genômica , Fases de Leitura Aberta/genética , Locos de Características Quantitativas/genética , Animais , Cruzamento , Estudo de Associação Genômica Ampla , Genótipo , Fenótipo , Polimorfismo de Nucleotídeo Único/genética
5.
PLoS One ; 15(8): e0236515, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32764757

RESUMO

With the increasing availability of high quality genomic data, there is opportunity to deeply explore the genealogical relationships of different gene loci between closely related species. In this study, we utilized genomes of Xenopus laevis (XLA, a tetraploid species with (L) and (S) sub-genomes) and X. tropicalis (XTR, a diploid species) to investigate whether synonymous substitution rates among orthologous or homoeologous genes displayed any heterogeneity. From over 1500 orthologous/homoeologous genes collected, we calculated proportion of synonymous substitutions between genomes/sub-genomes (k) and found variation within and between chromosomes. Within most chromosomes, we identified higher k with distance from the centromere, likely attributed to higher substitution rates and recombination in these regions. Using maximum likelihood methods, we identified further evidence supporting rate heterogeneity, and estimated species divergence times and ancestral population sizes. Estimated species divergence times (XLA.L-XLA.S: ~25.5 mya; XLA-XTR: ~33.0 mya) were slightly younger compared to a past study, attributed to consideration of population size in our study. Meanwhile, we found very large estimated population size in the ancestral populations of the two species (NA = 2.55 x 106). Local hybridization and population structure, which have not yet been well elucidated in frogs, may be a contributing factor to these possible large population sizes.


Assuntos
Evolução Molecular , Genoma/genética , Mutação Silenciosa/genética , Xenopus laevis/genética , Animais , Cromossomos , Heterogeneidade Genética , Hibridização Genética , Hibridização in Situ Fluorescente , Filogenia
6.
Anim Sci J ; 91(1): e13432, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32779330

RESUMO

The objective of this study was to assess the effect of genotyped bulls with different numbers of phenotyped progenies on quantitative trait loci (QTL) detection and genomic evaluation using a simulated cattle population. Twelve generations (G1-G12) were simulated from the base generation (G0). The recent population had different effective population sizes, heritability, and number of QTL. G0-G4 were used for pedigree information. A total of 300 genotyped bulls from G5-G10 were randomly selected. Their progenies were generated in G6-G11 with different numbers of progeny per bull. Scenarios were considered according to the number of progenies and whether the genotypes were possessed by the bulls or the progenies. A genome-wide association study and genomic evaluation were performed with a single-step genomic best linear unbiased prediction method to calculate the power of QTL detection and the genomic estimated breeding value (GEBV). We found that genotyped bulls could be available for QTL detection depending on conditions. Additionally, using a reference population, including genotyped bulls, which had more progeny phenotypes, enabled a more accurate prediction of GEBV. However, it is desirable to have more than 4,500 individuals consisting of both genotypes and phenotypes for practical genomic evaluation.


Assuntos
Bovinos/genética , Genoma/genética , Fenótipo , Locos de Características Quantitativas/genética , Animais , Genômica , Masculino
7.
Nature ; 584(7821): 403-409, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32760000

RESUMO

The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2-is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.


Assuntos
Evolução Molecular , Genoma/genética , Filogenia , Répteis/genética , Animais , Conservação dos Recursos Naturais/tendências , Feminino , Genética Populacional , Lagartos/genética , Masculino , Anotação de Sequência Molecular , Nova Zelândia , Caracteres Sexuais , Serpentes/genética , Sintenia
8.
Nucleic Acids Res ; 48(15): 8320-8331, 2020 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-32749457

RESUMO

The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.


Assuntos
Genoma/genética , Anotação de Sequência Molecular , RNA-Seq/métodos , Transcriptoma/genética , Processamento Alternativo/genética , Animais , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Ratos , Sequenciamento Completo do Exoma
9.
PLoS One ; 15(8): e0238108, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32853264

RESUMO

Somatic structural variants are an important contributor to cancer development and evolution. Accurate detection of these complex variants from whole genome sequencing data is influenced by a multitude of parameters. However, there are currently no tools for guiding study design nor are there applications that could predict the performance of somatic structural variant detection. To address this gap, we developed Shiny-SoSV, a user-friendly web-based calculator for determining the impact of common variables on the sensitivity, precision and F1 score of somatic structural variant detection, including choice of variant detection tool, sequencing depth of coverage, variant allele fraction, and variant breakpoint resolution. Using simulation studies, we determined singular and combinatoric effects of these variables, modelled the results using a generalised additive model, allowing structural variant detection performance to be predicted for any combination of predictors. Shiny-SoSV provides an interactive and visual platform for users to easily compare individual and combined impact of different parameters. It predicts the performance of a proposed study design, on somatic structural variant detection, prior to the commencement of benchwork. Shiny-SoSV is freely available at https://hcpcg.shinyapps.io/Shiny-SoSV with accompanying user's guide and example use-cases.


Assuntos
Biologia Computacional/métodos , Variação Genética/genética , Algoritmos , Carcinogênese/genética , Genoma/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Internet , Neoplasias/genética , Software
10.
BMC Bioinformatics ; 21(1): 285, 2020 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-32631227

RESUMO

BACKGROUND: The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly. RESULTS: We propose OPTICALKERMIT which directly integrates genome wide optical maps into contig assembly. We show how genome wide optical maps can be used to localize reads on the genome and then we adapt the Kermit method, which originally incorporated genetic linkage maps to the miniasm assembler, to use this information in contig assembly. Our experimental results show that incorporating genome wide optical maps to the contig assembly of miniasm increases NGA50 while the number of misassemblies decreases or stays the same. Furthermore, when compared to the Canu assembler, OPTICALKERMIT produces an assembly with almost three times higher NGA50 with a lower number of misassemblies on real A. thaliana reads. CONCLUSIONS: OPTICALKERMIT successfully incorporates optical mapping data directly to contig assembly of eukaryotic genomes. Our results show that this is a promising approach to improve the contiguity of genome assemblies.


Assuntos
Genoma/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Imagens com Corantes Sensíveis à Voltagem/métodos , Humanos
11.
PLoS Genet ; 16(7): e1008828, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32609721

RESUMO

Homologous recombination (HR) has an intimate relationship with genome replication, both during repair of DNA lesions that might prevent DNA synthesis and in tackling stalls to the replication fork. Recent studies led us to ask if HR might have a more central role in replicating the genome of Leishmania, a eukaryotic parasite. Conflicting evidence has emerged regarding whether or not HR genes are essential, and genome-wide mapping has provided evidence for an unorthodox organisation of DNA replication initiation sites, termed origins. To answer this question, we have employed a combined CRISPR/Cas9 and DiCre approach to rapidly generate and assess the effect of conditional ablation of RAD51 and three RAD51-related proteins in Leishmania major. Using this approach, we demonstrate that loss of any of these HR factors is not immediately lethal but in each case growth slows with time and leads to DNA damage and accumulation of cells with aberrant DNA content. Despite these similarities, we show that only loss of RAD51 or RAD51-3 impairs DNA synthesis and causes elevated levels of genome-wide mutation. Furthermore, we show that these two HR factors act in distinct ways, since ablation of RAD51, but not RAD51-3, has a profound effect on DNA replication, causing loss of initiation at the major origins and increased DNA synthesis at subtelomeres. Our work clarifies questions regarding the importance of HR to survival of Leishmania and reveals an unanticipated, central role for RAD51 in the programme of genome replication in a microbial eukaryote.


Assuntos
Recombinação Homóloga/genética , Leishmania major/genética , Leishmaniose Cutânea/genética , Rad51 Recombinase/genética , Sistemas CRISPR-Cas/genética , Dano ao DNA/genética , Reparo do DNA/genética , Replicação do DNA/genética , Técnicas de Inativação de Genes , Genoma/genética , Humanos , Leishmania major/patogenicidade , Leishmaniose Cutânea/parasitologia
12.
RNA ; 26(10): 1464-1480, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32631843

RESUMO

Many eukaryotes use RNA processing, including alternative splicing, to express multiple gene products from the same gene. The budding yeast Saccharomyces cerevisiae has been successfully used to study the mechanism of splicing and the splicing machinery, but alternative splicing in yeast is relatively rare and has not been extensively studied. Alternative splicing of SKI7/HBS1 is widely conserved, but yeast and a few other eukaryotes have replaced this one alternatively spliced gene with a pair of duplicated, unspliced genes as part of a whole genome doubling (WGD). We show that other examples of alternative splicing known to have functional consequences are widely conserved within Saccharomycotina. A common mechanism by which alternative splicing has disappeared is by replacement of an alternatively spliced gene with duplicate unspliced genes. This loss of alternative splicing does not always take place soon after duplication, but can take place after sufficient time has elapsed for speciation. Saccharomycetaceae that diverged before WGD use alternative splicing more frequently than S. cerevisiae, suggesting that WGD is a major reason for infrequent alternative splicing in yeast. We anticipate that WGDs in other lineages may have had the same effect. Having observed that two functionally distinct splice-isoforms are often replaced by duplicated genes allowed us to reverse the reasoning. We thereby identify several splice isoforms that are likely to produce two functionally distinct proteins because we find them replaced by duplicated genes in related species. We also identify some alternative splicing events that are not conserved in closely related species and unlikely to produce functionally distinct proteins.


Assuntos
Processamento Alternativo/genética , Proteoma/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Saccharomycetales/genética , Proteínas Adaptadoras de Transdução de Sinal/genética , Evolução Molecular , Duplicação Gênica/genética , Genoma/genética , Isoformas de Proteínas/genética
13.
Proc Natl Acad Sci U S A ; 117(31): 18880-18890, 2020 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-32694208

RESUMO

Genomic instability contributes to tumorigenesis through the amplification and deletion of cancer driver genes. DNA copy number (CN) profiling of ensembles of tumors allows a thermodynamic analysis of the profile for each tumor. The free energy of the distribution of CNs is found to be a monotonically increasing function of the average chromosomal ploidy. The dependence is universal across several cancer types. Surprisal analysis distinguishes two main known subgroups: tumors with cells that have or have not undergone whole-genome duplication (WGD). The analysis uncovers that CN states having a narrower distribution are energetically more favorable toward the WGD transition. Surprisal analysis also determines the deviations from a fully stable-state distribution. These deviations reflect constraints imposed by tumor fitness selection pressures. The results point to CN changes that are more common in high-ploidy tumors and thus support altered selection pressures upon WGD.


Assuntos
Dosagem de Genes/genética , Instabilidade Genômica/genética , Neoplasias/genética , Variações do Número de Cópias de DNA/genética , Genoma/genética , Humanos , Ploidias , Termodinâmica
14.
Nucleic Acids Res ; 48(15): 8431-8444, 2020 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-32667642

RESUMO

Genome-wide passive DNA demethylation in cleavage-stage mouse embryos is related to the cytoplasmic localization of the maintenance methyltransferase DNMT1. However, recent studies provided evidences of the nuclear localization of DNMT1 and its contribution to the maintenance of methylation levels of imprinted regions and other genomic loci in early embryos. Using the DNA adenine methylase identification method, we identified Dnmt1-binding regions in four- and eight-cell embryos. The unbiased distribution of Dnmt1 peaks in the genic regions (promoters and CpG islands) as well as the absence of a correlation between the Dnmt1 peaks and the expression levels of the peak-associated genes refutes the active participation of Dnmt1 in the transcriptional regulation of genes in the early developmental period. Instead, Dnmt1 was found to associate with genomic retroelements in a greatly biased fashion, particularly with the LINE1 (long interspersed nuclear elements) and ERVK (endogenous retrovirus type K) sequences. Transcriptomic analysis revealed that the transcripts of the Dnmt1-enriched retroelements were overrepresented in Dnmt1 knockdown embryos. Finally, methyl-CpG-binding domain sequencing proved that the Dnmt1-enriched retroelements, which were densely methylated in wild-type embryos, became demethylated in the Dnmt1-depleted embryos. Our results indicate that Dnmt1 is involved in the repression of retroelements through DNA methylation in early mouse development.


Assuntos
DNA (Citosina-5-)-Metiltransferase 1/genética , Metilação de DNA/genética , Desenvolvimento Embrionário/genética , Genômica , Retroelementos/genética , Animais , Ilhas de CpG/genética , Proteínas de Ligação a DNA/genética , Embrião de Mamíferos , Perfilação da Expressão Gênica , Genoma/genética , Impressão Genômica/genética , Camundongos , Fatores de Transcrição/genética
15.
Mol Genet Genomics ; 295(6): 1339-1353, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32601732

RESUMO

Transposable elements (TEs) are mobile DNA sequences that are able to move from one genomic location to another. These selfish elements are known as genomic parasites, since they hijack the host molecular machinery to generate new copies of themselves. The mobilization of TEs can be seen as a natural mutagen because new TE copies can insert into different loci and impact host genomic structure through different mechanisms. Although our knowledge about TEs is improving with new genomes available, there is still very limited data about the mobilome of species from the Coleoptera order, the most diverse order of insects, including species from the Scarabaeidae family. Therefore, the main goal of this study was to characterize the mobilome of D. (Luederwaldtinia) schiffleri, based on low-coverage genome sequencing, and reconstruct their evolutionary history. We used a combination of four different approaches for TE characterization and maximum likelihood phylogenetic analysis to study their evolution. We found a large and diverse mobilome composed of 38 TE superfamilies, 20 DNA transposon and 18 retrotransposons, accounting for 21% of the genome. Moreover, we found a number of incongruences between the TE and host phylogenetic trees in three DNA transposon TE superfamilies, which represents five TE families, suggesting possible horizontal transfer events between highly divergent taxa. In summary, we found an abundant and diverse mobilome and a number of horizontal transfer events that have shaped the evolutionary history of this species.


Assuntos
Besouros/genética , Elementos de DNA Transponíveis/genética , Evolução Molecular , Transferência Genética Horizontal , Genoma/genética , Filogenia , Animais
16.
Nucleic Acids Res ; 48(15): 8349-8359, 2020 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-32621610

RESUMO

Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG islands (iCGIs) and their corresponding host genes exhibit dynamic epigenetic and gene expression patterns during development and between different tissues. We hypothesise that iCGI-associated H3K36me3, DNA methylation and transcription can influence host gene AS and/or APA. We investigate H3K36me3 and find that this histone mark is not a major regulator of AS or APA in our model system. Genomewide, we identify over 4000 host genes that harbour an iCGI in the mammalian genome, including both previously annotated and novel iCGI/host gene pairs. The transcriptional activity of these iCGIs is tissue- and developmental stage-specific and, for the first time, we demonstrate that the premature termination of host gene transcripts upstream of iCGIs is closely correlated with the level of iCGI transcription in a DNA-methylation independent manner. These studies suggest that iCGI transcription, rather than H3K36me3 or DNA methylation, interfere with host gene transcription and pre-mRNA processing genomewide and contributes to the spatiotemporal diversification of both the transcriptome and proteome.


Assuntos
Epigênese Genética , Processamento de Proteína Pós-Traducional/genética , Precursores de RNA/genética , Transcrição Genética , Animais , Diferenciação Celular/genética , Cromatina/genética , Ilhas de CpG/genética , Metilação de DNA/genética , Genoma/genética , Código das Histonas/genética , Humanos , Regiões Promotoras Genéticas , Pseudogenes/genética , Precursores de RNA/metabolismo
17.
Nat Commun ; 11(1): 3320, 2020 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-32620776

RESUMO

Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer insights into the genetic diversity and gene functions in benthic diatoms.


Assuntos
Adaptação Fisiológica/genética , Diatomáceas/genética , Ecossistema , Evolução Molecular , Genoma/genética , Diatomáceas/classificação , Diatomáceas/metabolismo , Água Doce , Tamanho do Genoma , Genômica/métodos , Polimorfismo de Nucleotídeo Único , Água do Mar , Especificidade da Espécie , Transcriptoma/genética
18.
Nat Commun ; 11(1): 2722, 2020 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-32483172

RESUMO

Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. Our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity. Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development.


Assuntos
Diferenciação Celular/genética , Elementos Facilitadores Genéticos/genética , Regulação da Expressão Gênica no Desenvolvimento , Genoma/genética , Regiões Promotoras Genéticas/genética , Células-Tronco/metabolismo , Animais , Células Cultivadas , Cromatina/genética , Cromossomos de Mamíferos/genética , Feminino , Perfilação da Expressão Gênica/métodos , Células-Tronco Hematopoéticas/citologia , Células-Tronco Hematopoéticas/metabolismo , Camundongos , Camundongos Endogâmicos C57BL , Células-Tronco Embrionárias Murinas/citologia , Células-Tronco Embrionárias Murinas/metabolismo , Células-Tronco/citologia
19.
PLoS One ; 15(6): e0234504, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32542006

RESUMO

The continual loss of threatened biodiversity is occurring at an accelerated pace. High-throughput sequencing technologies are now providing opportunities to address this issue by aiding in the generation of molecular data for many understudied species of high conservation interest. Our overall goal of this study was to begin building the genomic resources to continue investigations and conservation of the Spot-Tailed Earless lizard. Here we leverage the power of high-throughput sequencing to generate the liver transcriptome for the Northern Spot-Tailed Earless Lizard (Holbrookia lacerata) and Southern Spot-Tailed Earless Lizard (Holbrookia subcaudalis), which have declined in abundance in the past decades, and their sister species, the Common Lesser Earless Lizard (Holbrookia maculata). Our efforts produced high quality and robust transcriptome assemblies validated by 1) quantifying the number of processed reads represented in the transcriptome assembly and 2) quantifying the number of highly conserved single-copy orthologs that are present in our transcript set using the BUSCO pipeline. We found 1,361 1-to-1 orthologs among the three Holbrookia species, Anolis carolinensis, and Sceloporus undulatus. We carried out dN/dS selection tests using a branch-sites model and identified a dozen genes that experienced positive selection in the Holbrookia lineage with functions in development, immunity, and metabolism. Our single-copy orthologous sequences additionally revealed significant pairwise sequence divergence (~.73%) between the Northern H. lacerata and Southern H. subcaudalis that further supports the recent elevation of the Southern Spot-Tailed Earless Lizard to full species.


Assuntos
Biodiversidade , Lagartos/genética , Seleção Genética/genética , Transcriptoma/genética , Animais , Genoma/genética , Sequenciamento de Nucleotídeos em Larga Escala , Lagartos/crescimento & desenvolvimento , Filogenia , Análise de Sequência de RNA , Sequenciamento Completo do Exoma
20.
Nature ; 582(7811): 283-288, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32499657

RESUMO

Mobile genetic elements threaten genome integrity in all organisms. RDE-3 (also known as MUT-2) is a ribonucleotidyltransferase that is required for transposon silencing and RNA interference in Caenorhabditis elegans1-4. When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3' termini of these RNAs (designated poly(UG) or pUG tails)5. Here we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNA interference, as well as to transposon RNAs. RNA fragments attached to pUG tails with more than 16 perfectly alternating 3' U and G nucleotides become gene-silencing agents. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases, which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA-templated siRNA synthesis and siRNA-directed pUG RNA biogenesis underlie double-stranded-RNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA-siRNA silencing loop enables parents to inoculate progeny against the expression of unwanted or parasitic genetic elements.


Assuntos
Caenorhabditis elegans/genética , Caenorhabditis elegans/parasitologia , Epigênese Genética/genética , Genoma/genética , Hereditariedade , Poli G/genética , Poli U/genética , RNA Mensageiro/genética , Animais , Caenorhabditis elegans/citologia , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/metabolismo , Células Germinativas/citologia , Células Germinativas/metabolismo , Masculino , Nucleotidiltransferases/metabolismo , Interferência de RNA , RNA Replicase/metabolismo , RNA Interferente Pequeno/genética , Moldes Genéticos
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