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1.
BMC Genomics ; 22(1): 707, 2021 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-34592920

RESUMO

BACKGROUND: The order Oedogoniales within the single family Oedogoniaceae comprised of three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales. RESULTS: The five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats. CONCLUSIONS: Our results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.


Assuntos
Genoma de Cloroplastos , Teorema de Bayes , Evolução Molecular , Tamanho do Genoma , Filogenia , Sequenciamento Completo do Genoma
2.
Commun Biol ; 4(1): 851, 2021 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-34239036

RESUMO

Water scarcity and salinity are major challenges facing agriculture today, which can be addressed by engineering plants to grow in the boundless seawater. Understanding the mangrove plants at the molecular level will be necessary for developing such highly salt-tolerant agricultural crops. With this objective, we sequenced the genome of a salt-secreting and extraordinarily salt-tolerant mangrove species, Avicennia marina, that grows optimally in 75% seawater and tolerates >250% seawater. Our reference-grade ~457 Mb genome contains 31 scaffolds corresponding to its chromosomes. We identified 31,477 protein-coding genes and a salinome consisting of 3246 salinity-responsive genes and homologs of 614 experimentally validated salinity tolerance genes. The salinome provides a strong foundation to understand the molecular mechanisms of salinity tolerance in plants and breeding crops suitable for seawater farming.


Assuntos
Avicennia/genética , Genoma de Planta/genética , Tolerância ao Sal/genética , Sais/metabolismo , Agricultura/métodos , Avicennia/metabolismo , DNA de Plantas/química , DNA de Plantas/genética , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas , Tamanho do Genoma/genética , Genômica/métodos , RNA-Seq/métodos , Salinidade , Água do Mar , Análise de Sequência de DNA/métodos
3.
Int J Mol Sci ; 22(13)2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34209998

RESUMO

Acne vulgaris, which is mostly associated with the colonization of Cutibacterium acnes (C. acnes), is a common skin inflammatory disease in teenagers. However, over the past few years, the disease has extended beyond childhood to chronically infect approximately 40% of adults. While antibiotics have been used for several decades to treat acne lesions, antibiotic resistance is a growing crisis; thus, finding a new therapeutic target is urgently needed. Studies have shown that phage therapy may be one alternative for treating multi-drug-resistant bacterial infections. In the present study, we successfully isolated a C. acnes phage named TCUCAP1 from the skin of healthy volunteers. Morphological analysis revealed that TCUCAP1 belongs to the family Siphoviridae with an icosahedral head and a non-contractile tail. Genome analysis found that TCUCAP1 is composed of 29,547 bp with a G+C content of 53.83% and 56 predicted open reading frames (ORFs). The ORFs were associated with phage structure, packing, host lysis, DNA metabolism, and additional functions. Phage treatments applied to mice with multi-drug-resistant (MDR) C.-acnes-induced skin inflammation resulted in a significant decrease in inflammatory lesions. In addition, our attempt to formulate the phage into hydroxyethyl cellulose (HEC) cream may provide new antibacterial preparations for human infections. Our results demonstrate that TCUCAP1 displays several features that make it an ideal candidate for the control of C. acnes infections.


Assuntos
Acne Vulgar/terapia , Terapia por Fagos/métodos , Propionibacterium acnes/virologia , Siphoviridae/classificação , Sequenciamento Completo do Genoma/métodos , Acne Vulgar/microbiologia , Animais , Composição de Bases , Celulose/química , Modelos Animais de Doenças , Composição de Medicamentos , Farmacorresistência Bacteriana Múltipla , Tamanho do Genoma , Genoma Viral , Voluntários Saudáveis , Humanos , Injeções Intradérmicas , Camundongos , Fases de Leitura Aberta , Filogenia , Propionibacterium acnes/fisiologia , Siphoviridae/genética , Siphoviridae/isolamento & purificação , Pele/virologia
4.
Trends Plant Sci ; 26(10): 1039-1049, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34219022

RESUMO

Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO2-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.


Assuntos
Magnoliopsida , Tamanho do Genoma , Magnoliopsida/genética , Nitrogênio , Fósforo , Fotossíntese/genética
5.
Ann Bot ; 128(5): 639-651, 2021 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-34318876

RESUMO

BACKGROUND AND AIMS: Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. METHODS: We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples. KEY RESULTS: We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. CONCLUSIONS: We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.


Assuntos
Euphrasia , Evolução Biológica , Variação Genética , Tamanho do Genoma , Genoma de Planta/genética , Hibridização Genética , Ploidias
6.
Genes (Basel) ; 12(6)2021 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-34208200

RESUMO

Polyploidy has played an important evolutionary role in the genus Festuca (Poaceae), and several ploidy levels (ranging from 2n = 2x = 14 to 2n = 12x = 84) have been detected to date. This study aimed to estimate the genome size and ploidy level of two subspecies belonging to the F. yvesii polyploid complex by flow cytometry and chromosome counting. The phenotypic variation of the cytotypes was also explored, based on herbarium material. The genome size of F. yvesii subsp. lagascae has been estimated for the first time. Nuclear 2C DNA content of F. yvesii subsp. summilusitana ranged from 21.44 to 31.91 pg, while that of F. yvesii subsp. lagascae was from 13.60 to 22.31 pg. We report the highest ploidy level detected for Festuca (2n = 14x = 98) and previously unknown cytotypes. A positive correlation between holoploid genome size and chromosome number counts shown herein was confirmed. The morphometric approach showed a slight trend towards an increase in the size of some organs consistent with the variation in the ploidy level. Differences in characters were usually significant only among the most extreme cytotypes of each subspecies, but, even in this case, the high overlapping ranges prevent their distinction.


Assuntos
Festuca/genética , Tamanho do Genoma , Polimorfismo Genético , Poliploidia , Cromossomos de Plantas/genética
7.
Artigo em Inglês | MEDLINE | ID: mdl-34292147

RESUMO

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic, yellow-pigmented bacterium was isolated from chicken feather waste collected from an abattoir in Bloemfontein, South Africa. A polyphasic taxonomy study was used to describe and name the bacterial isolate, strain 1_F178T. The 16S rRNA gene sequence analysis and sequence comparison data indicated that strain 1_F178T was a member of the genus Chryseobacterium and was closely related to Chryseobacterium jejuense (99.1%) and Chryseobacterium nakagawai (98.7%). Overall genome similarity metrics (average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity) revealed greatest similarity to the C. jejuense and C. nakagawai type strains but were below the threshold for species delineation. Genome sequencing revealed a genome size of 6.18 Mbp and a G+C content of 35.6 mol%. The major respiratory quinone and most abundant polar lipid of strain 1_F178T were menaquinone-6 and phosphatidylethanolamine, respectively. Strain 1_F178T had a typical fatty acid composition for Chryseobacterium species. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic data, strain 1_F178T constitutes a novel species of Chryseobacterium, for which the name Chryseobacterium pennae sp. nov. is proposed. The type strain is 1_F178T (=LMG 30779T=KCTC 62759T).


Assuntos
Chryseobacterium/classificação , Plumas/microbiologia , Filogenia , Aves Domésticas/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Chryseobacterium/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Tamanho do Genoma , Hibridização de Ácido Nucleico , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , África do Sul , Vitamina K 2/análogos & derivados , Vitamina K 2/química
8.
Philos Trans R Soc Lond B Biol Sci ; 376(1832): 20200426, 2021 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-34247497

RESUMO

Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.


Assuntos
Evolução Biológica , Tamanho do Genoma , Cromossomos Sexuais/genética , Processos de Determinação Sexual , Diferenciação Sexual/genética , Vertebrados/genética , Animais , Evolução Molecular , Feminino , Masculino , Ovário/crescimento & desenvolvimento , Testículo/crescimento & desenvolvimento
9.
Arch Virol ; 166(8): 2333-2335, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34075444

RESUMO

The complete genome sequence of a novel iflavirus isolated from the gregarious and koinobiont endoparasitoid Tetrastichus brontispae, tentatively named "Tetrastichus brontispae RNA virus 3" (TbRV-3), was determined by total RNA and Sanger sequencing. The complete genome is 9998 nucleotides in length, 8934 nt of which encodes a putative polyprotein of 2978 amino acids. TbRV-3 was found to have a similar genome organization and to contain conserved domains and motifs found in other iflaviruses, with some variations. Phylogenetic analysis based on deduced amino acid sequences of the RdRp domain showed that TbRV-3 clustered with Dinocampus coccinellae paralysis virus (DcPV). However, the percent amino acid sequence identity of the putative capsid proteins of TbRV-3 and DcPV determined using BLASTp was below the species demarcation threshold (90%), suggesting that TbRV-3 is a new iflavirus. This is the first virus of the family Iflaviridae to be isolated from a wasp of the family Eulophidae.


Assuntos
Vírus de Insetos/classificação , Vespas/virologia , Sequenciamento Completo do Genoma/métodos , Sequência de Aminoácidos , Animais , Tamanho do Genoma , Genoma Viral , Vírus de Insetos/genética , Vírus de Insetos/isolamento & purificação , Fases de Leitura Aberta , Filogenia , Análise de Sequência de RNA
10.
Arch Virol ; 166(8): 2343-2346, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34097143

RESUMO

Viola mottle virus (VMoV) was discovered in Viola odorata showing symptoms of reduced growth, leaf mottling, and whitish stripes on flowers in northern Italy in 1977. This virus has been provisionally classified as a member of the genus Potexvirus based on its morphological, serological, and biological characteristics. However, since genetic information of VMoV has never been reported, the taxonomic status of this virus is unclear. Here, we report the first complete genome sequence of VMoV to clarify its taxonomic position. Its genomic RNA is 6,052 nucleotides long, excluding the 3'-terminal poly(A) tail, and has five open reading frames (ORFs) typical of potexviruses. Among potexviruses, VMoV showed the most similarity to tulip virus X (TVX) with 81.1-81.2% nucleotide and 90.4-90.7% amino acid sequence identity in ORF1 and 82.9-83.5% nucleotide and 93.2-95.2% amino acid sequence identity in ORF5. These values are much higher than the species demarcation threshold for the genus. Phylogenetic analysis also indicated that VMoV is nested within the clade of TVX isolates. These data demonstrate that VMoV and TVX are members of the same species.


Assuntos
Doenças das Plantas/virologia , Potexvirus/classificação , Viola/virologia , Sequenciamento Completo do Genoma/métodos , Tamanho do Genoma , Genoma Viral , Itália , Fases de Leitura Aberta , Filogenia , Potexvirus/genética , Potexvirus/isolamento & purificação
11.
Arch Virol ; 166(8): 2119-2130, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34100162

RESUMO

Phages are viruses of bacteria and are the smallest and most common biological entities in the environment. They can reproduce immediately after infection or integrate as a prophage into their host genome. SPß is a prophage of the Gram-positive model organism Bacillus subtilis 168, and it has been known for more than 50 years. It is sensitive to dsDNA damage and is induced through exposure to mitomycin C or UV radiation. When induced from the prophage, SPß requires 90 min to produce and release about 30 virions. Genomes of sequenced related strains range between 128 and 140 kb, and particle-packed dsDNA exhibits terminal redundancy. Formed particles are of the Siphoviridae morphotype. Related isolates are known to infect other B. subtilis clade members. When infecting a new host, SPß presumably follows a two-step strategy, adsorbing primarily to teichoic acid and secondarily to a yet unknown factor. Once in the host, SPß-related phages pass through complex lysis-lysogeny decisions and either enter a lytic cycle or integrate as a dormant prophage. As prophages, SPß-related phages integrate at the host chromosome's replication terminus, and frequently into the spsM or kamA gene. As a prophage, it imparts additional properties to its host via phage-encoded proteins. The most notable of these functional proteins is sublancin 168, which is used as a molecular weapon by the host and ensures prophage maintenance. In this review, we summarise the existing knowledge about the biology of the phage regarding its life cycle and discuss its potential as a research object.


Assuntos
Fagos Bacilares/crescimento & desenvolvimento , Bacillus subtilis/virologia , Siphoviridae/crescimento & desenvolvimento , Fagos Bacilares/genética , Tamanho do Genoma , Genoma Viral , Estágios do Ciclo de Vida , Lisogenia , Siphoviridae/classificação , Siphoviridae/genética , Sequenciamento Completo do Genoma
12.
Genes (Basel) ; 12(5)2021 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-34068148

RESUMO

Breeding programs in ornamentals can be facilitated by integrating knowledge of phylogenetic relatedness of potential parents along with other genomic information. Using AFLP, genetic distances were determined for 59 Geranium genotypes, comprising 55 commercial cultivars of the three subgenera of a total collection of 61 Geranium genotypes. A subgroup of 45 genotypes, including intragroup and intergroup hybrids, were selected and further characterized for genome sizes and chromosome numbers. The variation in genome size ranged from 1.51 ± 0.01 pg/2C to 12.94 ± 0.07 pg/2C. The chromosome numbers ranged from 26 to 108-110 with some hybrids showing an aberrant number of chromosomes based on their parents' constitution. All chromosome numbers of Geranium are an even number, which presumes that unreduced gametes occur in some cross combinations. Overall, parental difference in genome size and chromosome number were not limiting for cross compatibility. Good crossing compatibility was correlated to a Jaccard similarity coefficient as parameter for parental relatedness of about 0.5. Additionally, parent combinations with high differences in the DNA/chromosome value could not result in a successful cross. We expect that our results will enable breeding programs to overcome crossing barriers and support further breeding initiatives.


Assuntos
Cromossomos de Plantas/genética , Tamanho do Genoma , Geranium/genética , Melhoramento Vegetal/métodos , Polimorfismo Genético , Hibridização Genética
13.
Gene ; 793: 145751, 2021 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-34062257

RESUMO

Prunus zhengheensis is a novel species originated in Fujian province, China. However, there is no further information available on its classification and molecular biology study. In this study, we first report the complete chloroplast (cp) genome sequence of P. zhengheensis. The cp genome of P. zhengheensis is 158,106 bp and GC content is 36.73%, is a circular structure composed of LSC (large single copy), SSC (small single copy), and IR (inverted repeat) regions, with the size of the three regions being 86,321 bp, 18,999 bp and 26,393 bp, respectively. The cp genome of P. zhengheensis contains 130 genes, and 242 SSRs are identified in the cp genome. The comparative analysis of cp genomes in eight Prunus plants demonstrates the subtle divergences occur in the protein-coding gene rps18, rps12, psbF, rpl33, matK, and rbcL, and that the KA/KS nucleotide substitution ratio of the ndhF of P. zhengheensis and P. armeniaca is 1.79636. The phylogenetic results indicate that the P. zhengheensis is closely related to P. mume, compared to other species of Prunus. Our research results provide the important genomic information for molecular phylogeny of P. zhengheensis.


Assuntos
Cloroplastos/genética , Genes de Plantas , Genoma de Cloroplastos , Filogenia , Prunus/genética , Composição de Bases , China , Ontologia Genética , Tamanho do Genoma , Repetições de Microssatélites , Anotação de Sequência Molecular , Folhas de Planta/genética , Prunus/classificação , Sequenciamento Completo do Genoma
14.
Gene ; 793: 145748, 2021 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-34077775

RESUMO

The rice root-knot nematode Meloidogyne graminicola is a major biotic stress for the rice crop under upland, rain-fed lowland and irrigated cultivation conditions. Here, we present an improved draft genome assembly of M. graminicola IARI strain using the long-read sequencing approach (PacBio Sequel platform). The assembled genome size was 36.86 Mb with 514 contigs and N50 value of 105 kb. BUSCO estimated the genome to be 88.6% complete. Meloidogyne graminicola genome contained 17.83% repeat elements and showed 14,062 protein-coding gene models, 4,974 conserved orthologous genes, 561 putative secreted proteins, 49 RNAi pathway genes, 1,853 proteins involved in pathogen-host interactions, 1,575 carbohydrate-active enzymes, and 32,138 microsatellites. Five of the carbohydrate-active enzymes were found only in M. graminicola genome and were not present in any other analysed root-knot nematode genome. Together with the previous two genome assemblies, this improved genome assembly would facilitate comparative and functional genomics for M. graminicola.


Assuntos
Genes de Helmintos , Genoma Helmíntico , Proteínas de Helminto/genética , Oryza/parasitologia , Tylenchoidea/genética , Animais , Ontologia Genética , Tamanho do Genoma , Proteínas de Helminto/classificação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Repetições de Microssatélites , Anotação de Sequência Molecular , Fases de Leitura Aberta , Filogenia , Doenças das Plantas/parasitologia , Tylenchoidea/classificação
15.
Nat Commun ; 12(1): 3604, 2021 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-34127667

RESUMO

A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach.


Assuntos
Frutas/genética , Genoma de Planta , Metagenômica , Prunus persica/genética , Frutas/metabolismo , Regulação da Expressão Gênica de Plantas , Genes de Plantas/genética , Loci Gênicos , Variação Genética , Tamanho do Genoma , Genômica , Desequilíbrio de Ligação , Filogenia , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único , Prunus persica/classificação , Prunus persica/metabolismo , Análise de Sequência de DNA , Açúcares
16.
Malar J ; 20(1): 270, 2021 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-34126997

RESUMO

BACKGROUND: Malaria, caused by Plasmodium parasites, is a major global public health problem. To assist an understanding of malaria pathogenesis, including drug resistance, there is a need for the timely detection of underlying genetic mutations and their spread. With the increasing use of whole-genome sequencing (WGS) of Plasmodium DNA, the potential of deep learning models to detect loci under recent positive selection, historically signals of drug resistance, was evaluated. METHODS: A deep learning-based approach (called "DeepSweep") was developed, which can be trained on haplotypic images from genetic regions with known sweeps, to identify loci under positive selection. DeepSweep software is available from https://github.com/WDee/Deepsweep . RESULTS: Using simulated genomic data, DeepSweep could detect recent sweeps with high predictive accuracy (areas under ROC curve > 0.95). DeepSweep was applied to Plasmodium falciparum (n = 1125; genome size 23 Mbp) and Plasmodium vivax (n = 368; genome size 29 Mbp) WGS data, and the genes identified overlapped with two established extended haplotype homozygosity methods (within-population iHS, across-population Rsb) (~ 60-75% overlap of hits at P < 0.0001). DeepSweep hits included regions proximal to known drug resistance loci for both P. falciparum (e.g. pfcrt, pfdhps and pfmdr1) and P. vivax (e.g. pvmrp1). CONCLUSION: The deep learning approach can detect positive selection signatures in malaria parasite WGS data. Further, as the approach is generalizable, it may be trained to detect other types of selection. With the ability to rapidly generate WGS data at low cost, machine learning approaches (e.g. DeepSweep) have the potential to assist parasite genome-based surveillance and inform malaria control decision-making.


Assuntos
Aprendizado Profundo/estatística & dados numéricos , Tamanho do Genoma , Genoma de Protozoário , Plasmodium falciparum/genética , Plasmodium vivax/genética , Seleção Genética , Análise de Sequência de DNA
18.
Mol Ecol Resour ; 21(6): 2145-2165, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-33938156

RESUMO

The hyperdiverse order Coleoptera comprises a staggering ~25% of known species on Earth. Despite recent breakthroughs in next generation sequencing, there remains a limited representation of beetle diversity in assembled genomes. Most notably, the ground beetle family Carabidae, comprising more than 40,000 described species, has not been studied in a comparative genomics framework using whole genome data. Here we generate a high-quality genome assembly for Nebria riversi, to examine sources of novelty in the genome evolution of beetles, as well as genetic changes associated with specialization to high-elevation alpine habitats. In particular, this genome resource provides a foundation for expanding comparative molecular research into mechanisms of insect cold adaptation. Comparison to other beetles shows a strong signature of genome compaction, with N. riversi possessing a relatively small genome (~147 Mb) compared to other beetles, with associated reductions in repeat element content and intron length. Small genome size is not, however, associated with fewer protein-coding genes, and an analysis of gene family diversity shows significant expansions of genes associated with cellular membranes and membrane transport, as well as protein phosphorylation and muscle filament structure. Finally, our genomic analyses show that these high-elevation beetles have endosymbiotic Spiroplasma, with several metabolic pathways (e.g., propanoate biosynthesis) that might complement N. riversi, although its role as a beneficial symbiont or as a reproductive parasite remains equivocal.


Assuntos
Adaptação Fisiológica , Temperatura Baixa , Besouros , Evolução Molecular , Genoma de Inseto , Animais , Besouros/genética , Tamanho do Genoma , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia
19.
Nat Plants ; 7(6): 766-773, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34017083

RESUMO

Sorghum is a drought-tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importance. Cultivated sorghum and its inter-fertile wild relatives constitute the primary gene pool for sorghum. Understanding and characterizing the diversity within this valuable resource is fundamental for its effective utilization in crop improvement. Here, we report analysis of a sorghum pan-genome to explore genetic diversity within the sorghum primary gene pool. We assembled 13 genomes representing cultivated sorghum and its wild relatives, and integrated them with 3 other published genomes to generate a pan-genome of 44,079 gene families with 222.6 Mb of new sequence identified. The pan-genome displays substantial gene-content variation, with 64% of gene families showing presence/absence variation among genomes. Comparisons between core genes and dispensable genes suggest that dispensable genes are important for sorghum adaptation. Extensive genetic variation was uncovered within the pan-genome, and the distribution of these variations was influenced by variation of recombination rate and transposable element content across the genome. We identified presence/absence variants that were under selection during sorghum domestication and improvement, and demonstrated that such variation had important phenotypic outcomes that could contribute to crop improvement. The constructed sorghum pan-genome represents an important resource for sorghum improvement and gene discovery.


Assuntos
Produtos Agrícolas/genética , Variação Genética , Genoma de Planta , Proteínas de Plantas/genética , Sorghum/genética , Domesticação , Tamanho do Genoma , Família Multigênica , Filogenia , Pigmentação/genética , Polimorfismo de Nucleotídeo Único , Sementes/genética
20.
Viruses ; 13(5)2021 04 30.
Artigo em Inglês | MEDLINE | ID: mdl-33946221

RESUMO

We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Overall, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Phylogenetic analysis indicated that within KSB, two FLs from plasma donors O and P comprised two clusters, together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis of the KSB of HIV-1 revealed 91 signature nucleotide residues (1.1%). In total, 48 and 43 signature nucleotides originated from clusters O and P, respectively. Six positions contained 100% specific nucleotide(s) in clusters O and P. In-depth FL analysis for over 30 years indicated that the KSB FL significantly increased over time before combination antiretroviral therapy (cART) and decreased with cART. This increase occurred due to the significant increase in env and nef genes, originating in the variable regions of both genes. The increase in sequence length of HIV-1 over time suggests an evolutionary direction.


Assuntos
Evolução Molecular , Tamanho do Genoma , Genoma Viral , Genótipo , Infecções por HIV/virologia , HIV-1/genética , Estudos de Coortes , Biologia Computacional/métodos , Seguimentos , Infecções por HIV/complicações , Infecções por HIV/epidemiologia , HIV-1/classificação , Hemofilia A/complicações , Hemofilia A/epidemiologia , Humanos , Epidemiologia Molecular , Filogenia , RNA Viral , Análise de Sequência de DNA
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