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1.
Nat Commun ; 12(1): 2204, 2021 04 13.
Artículo en Inglés | MEDLINE | ID: mdl-33850139

RESUMEN

Intra-tumor heterogeneity renders the identification of somatic single-nucleotide variants (SNVs) a challenging problem. In particular, low-frequency SNVs are hard to distinguish from sequencing artifacts. While the increasing availability of multi-sample tumor DNA sequencing data holds the potential for more accurate variant calling, there is a lack of high-sensitivity multi-sample SNV callers that utilize these data. Here we report Moss, a method to identify low-frequency SNVs that recur in multiple sequencing samples from the same tumor. Moss provides any existing single-sample SNV caller the ability to support multiple samples with little additional time overhead. We demonstrate that Moss improves recall while maintaining high precision in a simulated dataset. On multi-sample hepatocellular carcinoma, acute myeloid leukemia and colorectal cancer datasets, Moss identifies new low-frequency variants that meet manual review criteria and are consistent with the tumor's mutational signature profile. In addition, Moss detects the presence of variants in more samples of the same tumor than reported by the single-sample caller. Moss' improved sensitivity in SNV calling will enable more detailed downstream analyses in cancer genomics.


Asunto(s)
ADN de Neoplasias/genética , Neoplasias Hepáticas/genética , Nucleótidos , Algoritmos , Carcinoma Hepatocelular , Neoplasias Colorrectales/genética , Frecuencia de los Genes , Genómica/métodos , Humanos , Leucemia Mieloide Aguda/genética , Mutación , Polimorfismo de Nucleótido Simple
2.
Int J Mol Sci ; 22(6)2021 Mar 19.
Artículo en Inglés | MEDLINE | ID: mdl-33808829

RESUMEN

To date, soil salinity becomes a huge obstacle for food production worldwide since salt stress is one of the major factors limiting agricultural productivity. It is estimated that a significant loss of crops (20-50%) would be due to drought and salinity. To embark upon this harsh situation, numerous strategies such as plant breeding, plant genetic engineering, and a large variety of agricultural practices including the applications of plant growth-promoting rhizobacteria (PGPR) and seed biopriming technique have been developed to improve plant defense system against salt stress, resulting in higher crop yields to meet human's increasing food demand in the future. In the present review, we update and discuss the advantageous roles of beneficial PGPR as green bioinoculants in mitigating the burden of high saline conditions on morphological parameters and on physio-biochemical attributes of plant crops via diverse mechanisms. In addition, the applications of PGPR as a useful tool in seed biopriming technique are also updated and discussed since this approach exhibits promising potentials in improving seed vigor, rapid seed germination, and seedling growth uniformity. Furthermore, the controversial findings regarding the fluctuation of antioxidants and osmolytes in PGPR-treated plants are also pointed out and discussed.


Asunto(s)
Desarrollo de la Planta , Fenómenos Fisiológicos de las Plantas , Rhizobiaceae/fisiología , Salinidad , Estrés Salino , Tolerancia a la Sal , Productos Agrícolas , Variación Genética , Genómica/métodos , Fotosíntesis , Proteómica/métodos , Plantones/fisiología , Simbiosis
3.
Gene ; 786: 145624, 2021 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-33798681

RESUMEN

The genus Synalpheus is a cosmopolitan clade of marine shrimps found in most tropical regions. Species in this genus exhibit a range of social organizations, including pair-forming, communal breeding, and eusociality, the latter only known to have evolved within this genus in the marine realm. This study examines the complete mitochondrial genomes of seven species of Synalpheus and explores differences between eusocial and non-eusocial species considering that eusociality has been shown before to affect the strength of purifying selection in mitochondrial protein coding genes. The AT-rich mitochondrial genomes of Synalpheus range from 15,421 bp to 15,782 bp in length and comprise, invariably, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 648 bp to 994 bp long intergenic space is assumed to be the D-loop. Mitochondrial gene synteny is identical among the studied shrimps. No major differences occur between eusocial and non-eusocial species in nucleotide composition and codon usage profiles of PCGs and in the secondary structure of tRNA genes. Maximum likelihood phylogenetic analysis of the complete concatenated PCG complement of 90 species supports the monophyly of the genus Synalpheus and its family Alpheidae. Moreover, the monophyletic status of the caridean families Alvinocaridae, Atyidae, Thoridae, Lysmatidae, Palaemonidae, and Pandalidae within caridean shrimps are fully or highly supported by the analysis. We therefore conclude that mitochondrial genomes contain sufficient phylogenetic information to resolve relationships at high taxonomic levels within the Caridea. Our analysis of mitochondrial genomes in the genus Synalpheus contributes to the understanding of the coevolution between genomic architecture and sociality in caridean shrimps and other marine organisms.


Asunto(s)
Decápodos/clasificación , Genómica/métodos , Mitocondrias/genética , Animales , Uso de Codones , Decápodos/genética , Tamaño del Genoma , Genoma Mitocondrial , Filogenia , ARN de Transferencia/genética , Selección Genética
4.
Nat Commun ; 12(1): 2033, 2021 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-33795679

RESUMEN

Genetic correlation analysis has quickly gained popularity in the past few years and provided insights into the genetic etiology of numerous complex diseases. However, existing approaches oversimplify the shared genetic architecture between different phenotypes and cannot effectively identify precise genetic regions contributing to the genetic correlation. In this work, we introduce LOGODetect, a powerful and efficient statistical method to identify small genome segments harboring local genetic correlation signals. LOGODetect automatically identifies genetic regions showing consistent associations with multiple phenotypes through a scan statistic approach. It uses summary association statistics from genome-wide association studies (GWAS) as input and is robust to sample overlap between studies. Applied to seven phenotypically distinct but genetically correlated neuropsychiatric traits, we identify 227 non-overlapping genome regions associated with multiple traits, including multiple hub regions showing concordant effects on five or more traits. Our method addresses critical limitations in existing analytic strategies and may have wide applications in post-GWAS analysis.


Asunto(s)
Algoritmos , Biología Computacional/métodos , Predisposición Genética a la Enfermedad/genética , Estudio de Asociación del Genoma Completo/métodos , Polimorfismo de Nucleótido Simple , Genómica/métodos , Genotipo , Humanos , Desequilibrio de Ligamiento , Fenotipo , Reproducibilidad de los Resultados
5.
Medicine (Baltimore) ; 100(14): e24969, 2021 Apr 09.
Artículo en Inglés | MEDLINE | ID: mdl-33832071

RESUMEN

ABSTRACT: Pancreatic cancer has a very high mortality with a 5-year survival of <5%. The purpose of this study was to classify specific molecular subtypes associated with prognosis of pancreatic cancer using The Cancer Genome Atlas (TCGA) multiplatform genomic data.Multiplatform genomic data (N = 178), including gene expression, copy number alteration, and somatic mutation data, were obtained from cancer browser (https://genome-cancer.ucsc.edu, cohort: TCGA Pancreatic Cancer). Clinical data including survival results were analyzed. We also used validation cohort (GSE50827) to confirm the robustness of these molecular subtypes in pancreatic cancer.When we performed unsupervised clustering using TCGA gene expression data, we found three distinct molecular subtypes associated with different survival results. Copy number alteration and somatic mutation data showed different genomic patterns for these three subtypes. Ingenuity pathway analysis revealed that each subtype showed differentially altered pathways. Using each subtype-specific genes (200 were selected), we could predict molecular subtype in another cohort, confirming the robustness of these molecular subtypes of pancreatic cancer. Cox regression analysis revealed that molecular subtype is the only significant prognostic factor for pancreatic cancer (P = .042, 95% confidence interval 0.523-0.98).Genomic analysis of pancreatic cancer revealed 3 distinct molecular subtypes associated with different survival results. Using these subtype-specific genes and prediction model, we could predict molecular subtype associated with prognosis of pancreatic cancer.


Asunto(s)
Genómica/métodos , Neoplasias Pancreáticas/genética , Anciano , Biomarcadores de Tumor/genética , Variaciones en el Número de Copia de ADN , Bases de Datos Factuales , Femenino , Perfilación de la Expresión Génica/métodos , Humanos , Masculino , Persona de Mediana Edad , Neoplasias Pancreáticas/clasificación , Neoplasias Pancreáticas/mortalidad , Estudios Retrospectivos , Transducción de Señal
6.
Proc Natl Acad Sci U S A ; 118(14)2021 04 06.
Artículo en Inglés | MEDLINE | ID: mdl-33737447

RESUMEN

When addressing a genomic question, having a reliable and adequate reference genome is of utmost importance. This drives the necessity to refine and customize reference genomes (RGs). Our laboratory has recently developed a strategy, the Perfect Match Genomic Landscape (PMGL), to detect variation between genomes [K. Palacios-Flores et al. Genetics 208, 1631-1641 (2018)]. The PMGL is precise and sensitive and, in contrast to most currently used algorithms, is nonstatistical in nature. Here we demonstrate the power of PMGL to refine and customize RGs. As a proof-of-concept, we refined different versions of the Saccharomyces cerevisiae RG. We applied the automatic PMGL pipeline to refine the genomes of microorganisms belonging to the three domains of life: the archaea Methanococcus maripaludis and Pyrococcus furiosus; the bacteria Escherichia coli, Staphylococcus aureus, and Bacillus subtilis; and the eukarya Schizosaccharomyces pombe, Aspergillus oryzae, and several strains of Saccharomyces paradoxus. We analyzed the reference genome of the virus SARS-CoV-2 and previously published viral genomes from patients' samples with COVID-19. We performed a mutation-accumulation experiment in E. coli and show that the PMGL strategy can detect specific mutations generated at any desired step of the whole procedure. We propose that PMGL can be used as a final step for the refinement and customization of any haploid genome, independently of the strategies and algorithms used in its assembly.


Asunto(s)
Variación Genética , Genoma Microbiano , Genómica/métodos , /genética , Algoritmos , Acumulación de Mutaciones , Prueba de Estudio Conceptual , Saccharomyces cerevisiae/genética
7.
Mol Omics ; 17(2): 317-337, 2021 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-33683246

RESUMEN

Comprehensive clinical pictures, comorbid conditions, and long-term complications of COVID-19 are still unknown. Recently, using a multi-omics-based strategy, we predicted potential drugs for COVID-19 with ∼70% accuracy. Herein, using a novel multi-omics-based bioinformatic approach and three ways of analysis, we identified the symptoms, comorbid conditions, and short-, mid-, and possible long-term complications of COVID-19 with >90% precision including 27 parent, 170 child, and 403 specific conditions. Among the specific conditions, 36 viral, 53 short-term, 62 short-mid-long-term, 194 mid-long-term, and 57 congenital conditions are identified. At a threshold "count of occurrence" of 4, we found that 83-100% (average 92.67%) of enriched conditions are associated with COVID-19. Except for dry cough and loss of taste, all the other COVID-19-associated mild and severe symptoms are enriched. CVDs, and pulmonary, metabolic, musculoskeletal, neuropsychiatric, kidney, liver, and immune system disorders are top comorbid conditions. Specific diseases like myocardial infarction, hypertension, COPD, lung injury, diabetes, cirrhosis, mood disorders, dementia, macular degeneration, chronic kidney disease, lupus, arthritis, etc. along with several other NCDs were found to be top candidates. Interestingly, many cancers and congenital disorders associated with COVID-19 severity are also identified. Arthritis, gliomas, diabetes, psychiatric disorders, and CVDs having a bidirectional relationship with COVID-19 are also identified as top conditions. Based on our accuracy (>90%), the long-term presence of SARS-CoV-2 RNA in human, and our "genetic remittance" assumption, we hypothesize that all the identified top-ranked conditions could be potential long-term consequences in COVID-19 survivors, warranting long-term observational studies.


Asunto(s)
/complicaciones , Genómica/métodos , /genética , Comorbilidad , Humanos , Índice de Severidad de la Enfermedad
9.
Epidemiol Infect ; 149: e78, 2021 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-33722321

RESUMEN

The molecular epidemiology of the virus and mapping helps understand the epidemics' evolution and apply quick control measures. This study provides genomic evidence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introductions into Sri Lanka and virus evolution during circulation. Whole-genome sequences of four SARS-CoV-2 strains obtained from coronavirus disease 2019 (COVID-19) positive patients reported in Sri Lanka during March 2020 were compared with sequences from Europe, Asia, Africa, Australia and North America. The phylogenetic analysis revealed that the sequence of the sample of the first local patient collected on 10 March, who contacted tourists from Italy, was clustered with SARS-CoV-2 strains collected from Italy, Germany, France and Mexico. Subsequently, the sequence of the isolate obtained on 19 March also clustered in the same group with the samples collected in March and April from Belgium, France, India and South Africa. The other two strains of SARS-CoV-2 were segregated from the main cluster, and the sample collected from 16 March clustered with England and the sample collected on 30 March showed the highest genetic divergence to the isolate of Wuhan, China. Here we report the first molecular epidemiological study conducted on circulating SARS-CoV-2 in Sri Lanka. The finding provides the robustness of molecular epidemiological tools and their application in tracing possible exposure in disease transmission during the pandemic.


Asunto(s)
/genética , /aislamiento & purificación , Aminoácidos/análisis , Brotes de Enfermedades/prevención & control , Genómica/métodos , Humanos , Sri Lanka
10.
Methods Mol Biol ; 2278: 31-44, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33649946

RESUMEN

Genome assembly and annotation are two of the key actions that must be undertaken in order to explore the genomic repertoire of (bifido)bacteria. The gathered information can be employed to genomically characterize a given microorganism, and can also be used to perform comparative genome analysis by including other sequenced (bifido)bacterial strains. Here, we highlight various bioinformatic programs able to manage next generation sequencing data starting from the assembly of a genome to the comparative analyses between strains.


Asunto(s)
Bifidobacterium/genética , Genoma Bacteriano , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Anotación de Secuencia Molecular/métodos , Filogenia , Análisis de Secuencia de ADN/métodos , Secuenciación Completa del Genoma/métodos
11.
J Biosci ; 462021.
Artículo en Inglés | MEDLINE | ID: mdl-33709963

RESUMEN

SARS-CoV-2 is a member of the Coronavirus family which recently originated from the Wuhan province of China and spread very rapidly through the world infecting more than 4 million people. In the past, other Coronaviruses have also been found to cause human infection, but not as widespread as COVID-19. Since Coronavirus sequences constantly change due to mutation and recombination, it is important to understand the pattern of changes and likely path the virus can take in the future. In this study, we have used the Shewhart control chart to identify and analyze hypervariable (hotspots) and hypovariable (coldspots) regions of the virus. Our analysis shows that SARS-CoV-2 has changed in a few regions of the genome. Analysis of SARS-CoV-1 and MERS sequences suggests that over time, mutations start accumulating in different regions and most likely SARS-CoV-2 may also follow a similar path. The results suggest a possible emergence of modified viruses over some time.


Asunto(s)
Variación Genética , Genoma Viral , /genética , China , Genómica/métodos , Genómica/estadística & datos numéricos , Humanos , Coronavirus del Síndrome Respiratorio de Oriente Medio/genética , Polimorfismo de Nucleótido Simple , Virus del SRAS/genética , Proteínas Virales/genética
12.
Leukemia ; 35(4): 956-967, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33664464

RESUMEN

T-cell lymphomas (TCL) are a group of biologically and clinically heterogenous neoplasms derived from mature T lymphocytes. Recent findings in biology have advanced the classification of these neoplasms; however, clinical investigations based on biologic features have yet to be designed. Two biomarker-driven treatments for TCL are promising: brentuximab vedotin (BV) in combination with chemotherapy or as monotherapy is the standard treatment for newly diagnosed CD30-positive TCL and relapsed/refractory anaplastic large cell lymphoma (ALCL), while ALK inhibitors have induced responses in ALK+ ALCLs. Common genetic alterations in TCL, such as aberrations in PI3K/mTOR, JAK/STAT, and epigenetic regulators are also targetable by pathway inhibitors and HDAC/DNMT inhibitors; however, responses to these treatments as monotherapy are neither satisfactory nor durable, even in patients pre-stratified by several biomarkers. Additional work is needed to extend biology/biomarker-driven treatment in these neoplasms. As T-cell lymphomagenesis is multistep and multifactorial, trials are ongoing to evaluate combination treatments. The focus of this article is to summarize the status and the current role of targeted-based therapy in nodal TCL.


Asunto(s)
Ganglios Linfáticos/patología , Linfoma de Células T/diagnóstico , Linfoma de Células T/tratamiento farmacológico , Terapia Molecular Dirigida , Biomarcadores de Tumor , Manejo de la Enfermedad , Susceptibilidad a Enfermedades , Aprobación de Drogas , Predisposición Genética a la Enfermedad , Genómica/métodos , Humanos , Inmunofenotipificación , Ganglios Linfáticos/metabolismo , Linfoma de Células T/etiología , Linfoma de Células T/metabolismo , Terapia Molecular Dirigida/efectos adversos , Terapia Molecular Dirigida/métodos , Fenotipo , Transducción de Señal/efectos de los fármacos
13.
JCI Insight ; 6(6)2021 03 22.
Artículo en Inglés | MEDLINE | ID: mdl-33749660

RESUMEN

The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2 - the virus that causes COVID-19 - in the region. We analyzed 620 samples collected from the Johns Hopkins Health System during March 11-31, 2020, comprising 28.6% of the total cases in Maryland and Washington, DC. From these samples, we generated 114 complete viral genomes. Analysis of these genomes alongside a subsampling of over 1000 previously published sequences showed that the diversity in this region rivaled global SARS-CoV-2 genetic diversity at that time and that the sequences belong to all of the major globally circulating lineages, suggesting multiple introductions into the region. We also analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and found that clinically severe cases had viral genomes belonging to all major viral lineages. We conclude that efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and the interconnectedness of the region as a whole.


Asunto(s)
/virología , Genoma Viral , Pandemias , Filogenia , /genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Baltimore , Secuencia de Bases , /transmisión , Niño , Brotes de Enfermedades , Transmisión de Enfermedad Infecciosa , District of Columbia , Femenino , Genómica/métodos , Salud Global , Humanos , Masculino , Persona de Mediana Edad , Adulto Joven
14.
Nat Commun ; 12(1): 1963, 2021 03 30.
Artículo en Inglés | MEDLINE | ID: mdl-33785756

RESUMEN

The order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, we develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi-C experiments on the model organism Caulobacter crescentus. The predictive power of our model is validated by independent experiments. We find that on large genomic scales, organizational features are predominantly present along the long cell axis: chromosomal loci exhibit striking long-ranged two-point axial correlations, indicating emergent order. This organization is associated with large genomic clusters we term Super Domains (SuDs), whose existence we support with super-resolution microscopy. On smaller genomic scales, our model reveals chromosome extensions that correlate with transcriptional and loop extrusion activity. Finally, we quantify the information contained in chromosome organization that may guide cellular processes. Our approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.


Asunto(s)
Caulobacter crescentus/genética , Cromosomas Bacterianos/genética , Modelos Moleculares , Conformación Molecular , Algoritmos , Sitios de Unión , Caulobacter crescentus/citología , Caulobacter crescentus/metabolismo , Segregación Cromosómica/genética , Cromosomas Bacterianos/metabolismo , Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano/genética , Genómica/métodos , Modelos Genéticos
15.
Anticancer Res ; 41(3): 1341-1348, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33788725

RESUMEN

BACKGROUND/AIM: Cancer profiling tests using formalin-fixed paraffin-embedded (FFPE) specimens with various conditions have become an essential tool for cancer treatment. The robustness of these tests needs to be addressed. MATERIALS AND METHODS: A cancer profiling test, NCC oncopanel, was tested with FFPE specimens from various tissues with different storage conditions and fixation lengths. Next generation sequencing was performed with Miseq and the data were assembled using the human reference genome hg19. RESULTS: Duration of storage and fixation affected the mapping statistics. Prolonged storage increased outward read paring and longer fixation rates caused increased singletons and unmapped reads. CONCLUSION: Our results indicate that a cancer profiling test with target capturing method, NCC oncopanel, shows robustness for FFPE cancer specimens with various storage conditions.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Neoplasias/genética , Adhesión en Parafina/métodos , Manejo de Especímenes/métodos , Fijación del Tejido/métodos , Fijadores/química , Formaldehído/química , Genómica/métodos , Humanos , Mutación , Neoplasias/patología
16.
Methods Mol Biol ; 2292: 95-104, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33651354

RESUMEN

Application of next generation sequencing techniques in the field of liquid biopsy, in particular urine, requires specific bioinformatics methods in order to deal with its peculiarity. Many aspects of cancer can be explored starting from nucleic acids, especially from cell-free DNA and circulating tumor DNA in order to characterize cancer. It is possible to detect small mutations, as single nucleotide variants, small insertions and deletions, copy-number alterations, and epigenetic profiles. Due to the low fraction of circulating tumor DNA over the whole cell-free DNA, some methods have been exploited. One of them is the application of unique barcodes to each DNA fragment in order to lower the limit of detection of cancer-related variants. Some bioinformatics workflows and tools are the same of a classic analysis of tumor tissue, but there are some steps in which specific algorithms have to be introduced.


Asunto(s)
Ácidos Nucleicos Libres de Células/orina , Neoplasias/orina , Animales , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/orina , Ácidos Nucleicos Libres de Células/genética , Variaciones en el Número de Copia de ADN , Metilación de ADN , Epigénesis Genética , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Biopsia Líquida/métodos , Neoplasias/genética
17.
Nat Commun ; 12(1): 1661, 2021 03 12.
Artículo en Inglés | MEDLINE | ID: mdl-33712601

RESUMEN

CRISPR-Cas9 viability screens are increasingly performed at a genome-wide scale across large panels of cell lines to identify new therapeutic targets for precision cancer therapy. Integrating the datasets resulting from these studies is necessary to adequately represent the heterogeneity of human cancers and to assemble a comprehensive map of cancer genetic vulnerabilities. Here, we integrated the two largest public independent CRISPR-Cas9 screens performed to date (at the Broad and Sanger institutes) by assessing, comparing, and selecting methods for correcting biases due to heterogeneous single-guide RNA efficiency, gene-independent responses to CRISPR-Cas9 targeting originated from copy number alterations, and experimental batch effects. Our integrated datasets recapitulate findings from the individual datasets, provide greater statistical power to cancer- and subtype-specific analyses, unveil additional biomarkers of gene dependency, and improve the detection of common essential genes. We provide the largest integrated resources of CRISPR-Cas9 screens to date and the basis for harmonizing existing and future functional genetics datasets.


Asunto(s)
Neoplasias/genética , Biomarcadores de Tumor , Sistemas CRISPR-Cas , Línea Celular Tumoral , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Variaciones en el Número de Copia de ADN , Genes Esenciales/genética , Genómica/métodos , Humanos , ARN Guia/genética
18.
Nat Commun ; 12(1): 1783, 2021 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-33741994

RESUMEN

Resolving the relationships between the major lineages in the animal tree of life is necessary to understand the origin and evolution of key animal traits. Sponges, characterized by their simple body plan, were traditionally considered the sister group of all other animal lineages, implying a gradual increase in animal complexity from unicellularity to complex multicellularity. However, the availability of genomic data has sparked tremendous controversy as some phylogenomic studies support comb jellies taking this position, requiring secondary loss or independent origins of complex traits. Here we show that incorporating site-heterogeneous mixture models and recoding into partitioned phylogenomics alleviates systematic errors that hamper commonly-applied phylogenetic models. Testing on real datasets, we show a great improvement in model-fit that attenuates branching artefacts induced by systematic error. We reanalyse key datasets and show that partitioned phylogenomics does not support comb jellies as sister to other animals at either the supermatrix or partition-specific level.


Asunto(s)
Ctenóforos/genética , Genoma/genética , Genómica/métodos , Filogenia , Poríferos/genética , Animales , Evolución Biológica , Ctenóforos/clasificación , Modelos Genéticos , Poríferos/clasificación , Especificidad de la Especie
20.
J Biosci ; 462021.
Artículo en Inglés | MEDLINE | ID: mdl-33737495

RESUMEN

Since its emergence as a pneumonia-like outbreak in the Chinese city of Wuhan in late 2019, the novel coronavirus disease COVID-19 has spread widely to become a global pandemic. The first case of COVID-19 in India was reported on 30 January 2020 and since then it has affected more than ten million people and resulted in around 150,000 deaths in the country. Over time, the viral genome has accumulated mutations as it passes through its human hosts, a common evolutionary mechanism found in all microorganisms. This has implications for disease surveillance and management, vaccines and therapeutics, and the emergence of reinfections. Sequencing the viral genome can help monitor these changes and provides an extraordinary opportunity to understand the genetic epidemiology and evolution of the virus as well as tracking its spread in a population. Here we review the past year in the context of the phylogenetic analysis of variants isolated over the course of the pandemic in India and highlight the importance of continued sequencing-based surveillance in the country.


Asunto(s)
/epidemiología , /genética , Brasil , /inmunología , Dinamarca , Genoma Viral , Genómica/métodos , Humanos , Evasión Inmune , India/epidemiología , Mutación , Filogenia , Prevalencia , Sudáfrica , España , Reino Unido
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