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1.
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
2.
PLoS Genet ; 16(6): e1008866, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32530914

RESUMO

Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.


Assuntos
Escherichia coli/genética , Evolução Molecular , Transferência Genética Horizontal , Variação Genética , Genoma Bacteriano/genética , Animais , Animais Selvagens/microbiologia , Austrália , Galinhas/microbiologia , Farmacorresistência Bacteriana/genética , Escherichia coli/isolamento & purificação , Escherichia coli/patogenicidade , Fezes/microbiologia , Água Doce/microbiologia , Tamanho do Genoma , Humanos , Doenças Inflamatórias Intestinais/microbiologia , Sequências Repetitivas Dispersas/genética , Mucosa Intestinal/microbiologia , Carne/microbiologia , Anotação de Sequência Molecular , Filogenia , Microbiologia do Solo , Fatores de Virulência/genética , Sequenciamento Completo do Genoma
3.
Nat Commun ; 11(1): 2085, 2020 04 29.
Artigo em Inglês | MEDLINE | ID: mdl-32350251

RESUMO

Allopolyploidy generates diversity by increasing the number of copies and sources of chromosomes. Many of the best-known evolutionary radiations, crops, and industrial organisms are ancient or recent allopolyploids. Allopolyploidy promotes differentiation and facilitates adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added. The six-species hybrids initially grow slowly, but they rapidly regain fitness and adapt, even as they retain traits from multiple species. These new synthetic yeast hybrids and the iHyPr method have potential applications for the study of polyploidy, genome stability, chromosome segregation, and bioenergy.


Assuntos
Hibridização Genética , Saccharomyces/genética , Evolução Molecular Direcionada , Tamanho do Genoma , Genoma Fúngico , Instabilidade Genômica , Genótipo , Padrões de Herança/genética , Mitocôndrias/genética , Fenótipo , Característica Quantitativa Herdável
4.
Arch Virol ; 165(7): 1707-1710, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32409876

RESUMO

One large contig with high sequence similarity to Asian prunus virus 2 was identified by high-throughput sequencing from a camellia (Camellia japonica) tree with ringspot symptoms. The complete genome of this new virus was determined to be 8829 nucleotides long, excluding the 3' poly(A) tail. Its genome organization resembles that of known foveaviruses but contains an additional open reading frame in the 3'-terminal region. Phylogenetic analysis also places this virus with members of the genus Foveavirus in the family Betaflexiviridae in the same subgroup. The virus, which is provisionally named "camellia ringspot-associated virus 4″, shares 50-56% nucleotide sequence identity with other foveaviruses and should represent a new species in the genus.


Assuntos
Camellia/virologia , Flexiviridae/isolamento & purificação , Doenças das Plantas/virologia , Flexiviridae/classificação , Flexiviridae/genética , Tamanho do Genoma , Genoma Viral , Fases de Leitura Aberta , Filogenia
5.
PLoS One ; 15(3): e0229468, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32119699

RESUMO

There is renewed interest in the regulation and consequences of cell size adaptations in studies on understanding the ecophysiology of ectotherms. Here we test if induction of triploidy, which increases cell size in zebrafish (Danio rerio), makes for a good model system to study consequences of cell size. Ideally, diploid and triploid zebrafish should differ in cell size, but should otherwise be comparable in order to be suitable as a model. We induced triploidy by cold shock and compared diploid and triploid zebrafish larvae under standard rearing conditions for differences in genome size, cell size and cell number, development, growth and swimming performance and expression of housekeeping genes and hsp70.1. Triploid zebrafish have larger but fewer cells, and the increase in cell size matched the increase in genome size (+ 50%). Under standard conditions, patterns in gene expression, ontogenetic development and larval growth were near identical between triploids and diploids. However, under demanding conditions (i.e. the maximum swimming velocity during an escape response), triploid larvae performed poorer than their diploid counterparts, especially after repeated stimuli to induce swimming. This result is consistent with the idea that larger cells have less capacity to generate energy, which becomes manifest during repeated physical exertion resulting in increased fatigue. Triploidy induction in zebrafish appears a valid method to increase specifically cell size and this provides a model system to test for consequences of cell size adaptation for the energy budget and swimming performance of this ectothermic vertebrate.


Assuntos
Natação/fisiologia , Triploidia , Peixe-Zebra/fisiologia , Animais , Comportamento Animal , Tamanho Celular , Resposta ao Choque Frio , Diploide , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Tamanho do Genoma , Larva/genética , Larva/crescimento & desenvolvimento , Larva/fisiologia , Masculino , Peixe-Zebra/genética , Peixe-Zebra/crescimento & desenvolvimento
6.
Nat Commun ; 11(1): 836, 2020 02 11.
Artigo em Inglês | MEDLINE | ID: mdl-32047145

RESUMO

In the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a simple functional assay whether the cell replicates or not. We used the first (and currently only published) whole-cell model for the bacterium Mycoplasma genitalium. Our computational design-simulate-test cycles discovered novel in silico minimal genomes which, if biologically correct, predict in vivo genomes smaller than JCVI-Syn3.0; a bacterium with, currently, the smallest genome that can be grown in pure culture. In the process, we identified 10 low essential genes and produced evidence for at least two Mycoplasma genitalium in silico minimal genomes. This work brings combined computational and laboratory genome engineering a step closer.


Assuntos
Algoritmos , Simulação por Computador , Genoma Bacteriano , Mycoplasma genitalium/genética , Ontologia Genética , Genes Bacterianos/genética , Genes Essenciais/genética , Engenharia Genética/métodos , Tamanho do Genoma , Biologia Sintética/métodos
7.
mBio ; 11(1)2020 02 25.
Artigo em Inglês | MEDLINE | ID: mdl-32098813

RESUMO

Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.


Assuntos
Besouros/microbiologia , Transferência Genética Horizontal , Genoma Bacteriano/genética , Microbiota/genética , Simbiose/genética , Animais , Bactérias/genética , Produtos Biológicos , Burkholderia/genética , Evolução Molecular , Tamanho do Genoma , Metagenômica , Família Multigênica , Simbiose/fisiologia
8.
Ann Bot ; 125(7): 1057-1064, 2020 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-32064492

RESUMO

BACKGROUND AND AIMS: Unlike other nuclear genes in eukaryotes, rDNA genes (5S and 35S loci) are present in numerous copies per cell and, when stained, can therefore provide basic information about genome organization. In tracheophytes (vascular plants), they are usually located on separate chromosomes, the so-called S-type organization. An analysis of 1791 species of land plants suggested that S-type arrays might be ancestral in land plants, while linked (L-type) organization may be derived. However, no outgroup and only a handful of ferns and bryophytes were included. METHODS: We analysed genome sizes and the distribution of telomere, 5S and 35S rDNA FISH signals in up to 12 monoicous or dioicous species of liverworts from throughout a phylogeny that includes 287 of the 386 currently recognized genera. We also used the phylogeny to plot chromosome numbers and the occurrence of visibly distinct sex chromosomes. KEY RESULTS: Chromosome numbers are newly reported for the monoicous Lejeunea cavifolia and for females of the dioicous Scapania aequiloba. We detected sex-related differences in the number of rDNA signals in the dioicous Plagiochila asplenioides and Frullania dilatata. In the latter, the presence of two UU chromosomes in females and additional 5S-35S rDNA loci result in a haploid genome 0.2082 pg larger than the male genome; sex-specific genome differences in the other dioicous species were small. Four species have S-type rDNA, while five species have mixed L-S rDNA organization, and transitions may have occurred multiple times, as suggested by rDNA loci not being conserved among closely related species of Pellia. All species shared an Arabidopsis-like telomere motif, and its detection allowed verification of the chromosome number of Radula complanata and chromosome rearrangements in Aneura pinguis and P. asplenioides, the latter also showing sex-specific interstitial telomere repeats. CONCLUSIONS: The S and L rDNA arrangements appear to have evolved repeatedly within liverworts, even in the same species. Evidence for differential accumulation of rDNA between the sexes so far is limited.


Assuntos
Hepatófitas , Traqueófitas , DNA Ribossômico , Tamanho do Genoma , Filogenia
9.
Ann Bot ; 125(4): iv-v, 2020 03 29.
Artigo em Inglês | MEDLINE | ID: mdl-32073607

RESUMO

Major differences between moss and vascular plant genome sizes have major implications for stomatal biology whilst an absence of endopolyploidy in Sphagnum is most probably related to the unique development of the capitulum.


Assuntos
Briófitas , Tamanho do Genoma , Genoma de Planta , Filogenia , Plantas
10.
Int J Syst Evol Microbiol ; 70(3): 1800-1804, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31951192

RESUMO

A novel Streptomyces strain (SSL-25T) was isolated from mangrove soil sampled at QinzhouBay, PR China. The isolate was observed to be Gram-stain-positive and to form greyish-white aerial mycelia that differentiated into straight spore chains with smooth-surfaced spores on International Streptomyces Project 2 medium. The cell-wall peptidoglycan was determined to contain ll-diaminopimelicacid. The cell-wall sugars were glucose and mannose. The predominant menaquinones were MK-9 (H6), MK-9 (H8) and MK-9 (H4). The major polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and several unidentified phospholipids. The predominant cellular fatty acids were C16:0, iso-C16:0 and summed feature 3 (C16:1ω7c/C16:1ω6c). The genome size of strain SSL-25T was 8.1 Mbp with a G+C content of 71.5 mol%. Phylogenetic analysis indicated that strain SSL-25T is closely related to Streptomyces tsukubensis NRRL 18488T (99.4 % sequence similarity). However, the digital DNA-DNA hybridization (39.8 %) and average nucleotide identity (91.3 %) values between them showed that it represents a distinct species. Furthermore, the results of morphological, physiological and biochemical tests allowed further phenotypic differentiation of strain SSL-25T from S. tsukubensis NRRL 18488T. Therefore, based on these results, it is concluded that strain SSL-25T represents a novel Streptomyces species, for which the name Streptomyces qinzhouensis sp. nov. is proposed. The type strain is SSL-25T (=CICC 11054T=JCM33585T).


Assuntos
Filogenia , Microbiologia do Solo , Streptomyces/classificação , Técnicas de Tipagem Bacteriana , Parede Celular/química , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Tamanho do Genoma , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo , Streptomyces/isolamento & purificação , Vitamina K 2/análogos & derivados , Vitamina K 2/química
11.
Int J Syst Evol Microbiol ; 70(3): 1868-1875, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31985391

RESUMO

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6-97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA-DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-ß-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus, for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).


Assuntos
Gammaproteobacteria/classificação , Filogenia , Água do Mar/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Gammaproteobacteria/isolamento & purificação , Tamanho do Genoma , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química , Sequenciamento Completo do Genoma
12.
Gene ; 732: 144355, 2020 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-31935501

RESUMO

Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.


Assuntos
Curcuma/classificação , Genoma de Cloroplastos , Sequenciamento Completo do Genoma/métodos , Cloroplastos/genética , Curcuma/citologia , Curcuma/genética , Evolução Molecular , Tamanho do Genoma , Repetições de Microssatélites , Filogenia
13.
Int J Syst Evol Microbiol ; 70(3): 1769-1776, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31976852

RESUMO

To date, there is sparse information for the genus Robertkochia with Robertkochia marina CC-AMO-30DT as the only described member. We report here a new species isolated from mangrove soil collected at Malaysia Tanjung Piai National Park and perform polyphasic characterization to determine its taxonomic position. Strain CL23T is a Gram-negative, yellow-pigmented, strictly aerobic, catalase-positive and oxidase-positive bacterium. The optimal growth conditions were determined to be at pH 7.0, 30-37 °C and in 1-2 % (w/v) NaCl. The major respiratory quinone was menaquinone-6 (MK-6) and the highly abundant polar lipids were four unidentified lipids, a phosphatidylethanolamine and two unidentified aminolipids. The 16S rRNA gene similarity between strain CL23T and R. marina CC-AMO-30DT is 96.67 %. Strain CL23T and R. marina CC-AMO-30DT clustered together and were distinguished from taxa of closely related genera in 16S rRNA gene phylogenetic analysis. Genome sequencing revealed that strain CL23T has a genome size of 4.4 Mbp and a G+C content of 40.72 mol%. Overall genome related indexes including digital DNA-DNA hybridization value and average nucleotide identity are 17.70 % and approximately 70%, below the cutoffs of 70 and 95%, respectively, indicated that strain CL23T is a distinct species from R. marina CC-AMO-30DT. Collectively, based on the phenotypic, chemotaxonomic, phylogenetic and genomic evidences presented here, strain CL23T is proposed to represent a new species with the name Robertkochia solimangrovi sp. nov. (KCTC 72252T=LMG 31418T). An emended description of the genus Robertkochia is also proposed.


Assuntos
Flavobacteriaceae/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Tamanho do Genoma , Malásia , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
14.
J Environ Sci Health B ; 55(5): 447-454, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31941390

RESUMO

The genome of Acidiphilium multivorum strain AIU 301, acidophilic, aerobic Gram-negative bacteria, was investigated for potential metabolic pathways associated with organic acid production and metal uptake. The genome was compared to other acidic mine drainage isolates, Acidiphilium cryptum JF-5 and Acidithiobacillus ferrooxidans ATCC 23270, as well as Acetobacter pasteurianus 386B, which ferments cocoa beans. Plasmids between two Acidiphilium spp. were compared, and only two of the sixteen plasmids were identified as potentially similar. Comparisons of the genome size to the number of protein coding sequences indicated that A. multivorum and A. cryptum follow the line of best fit unlike A. pasteurianus 386B, which suggests that it was improperly annotated in the database. Pathways between these four species were analyzed bioinformatically and are discussed here. A. multivorum AIU 301, shares pathways with A. pasteurianus 386B including aldehyde and alcohol dehydrogenase pathways, which are used in the generation of vinegar. Mercury reductase, arsenate reductase and sulfur utilization proteins were identified and discussed at length. The absence of sulfur utilization proteins from A. multivorum AIU 301 suggests that this species uses previously undefined pathways for sulfur acquisition. Bioinformatic examination revealed novel pathways that may benefit commercial fields including acetic acid production and biomining.


Assuntos
Ácido Acético/metabolismo , Acidiphilium/genética , Genoma Bacteriano , Acidiphilium/metabolismo , Arseniato Redutases/genética , Biologia Computacional , Simulação por Computador , Tamanho do Genoma , Redes e Vias Metabólicas/genética , Metais/metabolismo , Mineração , Oxirredutases/genética , Plasmídeos , Enxofre/metabolismo
15.
Genes Genet Syst ; 94(6): 269-281, 2020 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-31932541

RESUMO

In the current era, as a growing number of genome sequence assemblies have been reported in animals, an in-depth analysis of transposable elements (TEs) is one of the most fundamental and essential studies for evolutionary genomics. Although TEs have, in general, been regarded as non-functional junk/selfish DNA, parasitic elements or harmful mutagens, studies have revealed that TEs have had a substantial and sometimes beneficial impact on host genomes in several ways. First, TEs are themselves diverse and thus provide lineage-specific characteristics to the genomes. Second, because TEs constitute a substantial fraction of animal genomes, they are a major contributing factor to evolutionary changes in genome size and composition. Third, host organisms have co-opted many repetitive sequences as genes, cis-regulatory elements and chromatin domain boundaries, which alter gene regulatory networks and in addition are partly involved in morphological evolution, as has been well documented in mammals. Here, I review the impact of TEs on various aspects of the genome, such as genome size and diversity in animals, as well as the evolution of gene networks and genome architecture in mammals. Given that a number of TE families probably remain to be discovered in many non-model organisms, unknown TEs may have contributed to gene networks in a much wider variety of animals than considered previously.


Assuntos
Elementos de DNA Transponíveis , Evolução Molecular , Genoma , Retroelementos , Animais , Núcleo Celular/genética , Redes Reguladoras de Genes , Tamanho do Genoma , Genoma Humano , Humanos , Mamíferos/genética
16.
Nucleic Acids Res ; 48(5): 2357-2371, 2020 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-31943068

RESUMO

The spatiotemporal expression of genes is controlled by enhancer sequences that bind transcription factors. Identifying the target genes of enhancers remains difficult because enhancers regulate gene expression over long genomic distances. To address this, we used an evolutionary approach to build two genome-wide maps of predicted enhancer-gene associations in the human and zebrafish genomes. Evolutionary conserved sequences were linked to their predicted target genes using PEGASUS, a bioinformatics method that relies on evolutionary conservation of synteny. The analysis of these maps revealed that the number of predicted enhancers linked to a gene correlate with its expression breadth. Comparison of both maps identified hundreds of putative vertebrate ancestral regulatory relationships from which we could determine that predicted enhancer-gene distances scale with genome size despite strong positional conservation. The two maps represent a resource for further studies, including the prioritization of sequence variants in whole genome sequence of patients affected by genetic diseases.


Assuntos
Elementos Facilitadores Genéticos , Regulação da Expressão Gênica no Desenvolvimento , Ligação Genética , Fatores de Transcrição/genética , Animais , Sequência de Bases , Evolução Biológica , Mapeamento Cromossômico , Biologia Computacional/métodos , Sequência Conservada , Embrião não Mamífero , Tamanho do Genoma , Humanos , Sintenia , Fatores de Transcrição/metabolismo , Peixe-Zebra
17.
Int J Mol Sci ; 21(2)2020 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-31940908

RESUMO

Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.


Assuntos
Ascomicetos/crescimento & desenvolvimento , Mapeamento Cromossômico/métodos , Sequenciamento Completo do Genoma/métodos , Ascomicetos/genética , Regulação Fúngica da Expressão Gênica , Tamanho do Genoma , Genoma Fúngico , Genoma Mitocondrial , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Filogenia
18.
J Appl Genet ; 61(1): 25-35, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31919659

RESUMO

In the present study, an efficient in vitro propagation protocol has been developed from clove explants of Allium sativum L., one of the oldest vegetable and medicinal plant used worldwide. Garlic is propagated vegetatively as cross-fertilization is strictly precluded due to sterile flowers. Due to a low rate of multiplication, limited genetic improvement possibility and increased germplasm degradation, plant tissue culture becomes an efficient and preferred tool for quality and rapid propagation of garlic. Here, the clove explants were cultured on Murashige and Skoog basal medium amended with different concentrations of Plant Growth Regulators (PGRs) namely 2,4-dichlorophenoxy acetic acid (2,4-D), 6-benzyl amino purine (BAP), and 1-naphthalene acetic acid (NAA). Within 2 weeks of inoculation, white compact callus was formed, maximum callus induction frequency (85.99%) was on 1.5 mg l-1 2, 4-D added MS medium. Induced callus transformed into an embryogenic callus on 2, 4-D and BAP amended MS medium with highest embryogenic frequency (77.7%) was noted on 0.25 mg l-1 2, 4-D and 1.0 mg l-1 BAP added medium. Embryogenic callus differentiated into progressive stages of somatic embryos starting from globular, scutellar, and finally to coleoptilar stage of the embryo. Histological and scanning electron microscopic study of embryogenic callus was conducted, showing different stages of embryos, their origin and development, re-confirming somatic embryogenesis incidence in A. sativum. Green and mature somatic embryos were germinated and converted into plantlets on 0.5 mg l-1 BAP amended MS medium. The in vitro regenerated plants were cultured separately in IBA and NAA supplemented media for root induction. The MS medium amended with 1.0 mg l-1 IBA proved to be the best PGR treatment in inducing roots. The rooted plants were acclimatized and transferred ex vitro with about 87% survival rate. Cytological and flow cytometric analyses were performed to assess the genetic stability of in vitro regenerated plants. Cytological studies of in vitro regenerated plants showed 2n = 16 chromosome number and did not reveal any numerical variation in chromosomes. Flow cytometry was employed to measure the 2C DNA content of somatic embryo regenerated A. sativum plants and compared with in vivo grown garlic. The histogram peaks of relative 2C DNA content of in vitro regenerated plantlets were similar to the corresponding 2C DNA peak of in vivo grown plants. Flow cytometric 2C DNA content of embryo regenerated and field-grown A. sativum plants were the same, i.e., 33.45 pg and 33.56 pg, respectively, confirming genetic similarity. In conclusion, the present cytological and flow cytometric study suggest that the in vitro culture conditions are quite safe, did not encourage genetic alterations, and regenerants were "true to type."


Assuntos
Alho/crescimento & desenvolvimento , Alho/genética , Tamanho do Genoma , Genoma de Planta , Genômica , Sementes , Alho/citologia , Alho/ultraestrutura , Genômica/métodos , Germinação , Desenvolvimento Vegetal/genética , Regeneração , Sementes/citologia , Sementes/genética , Sementes/crescimento & desenvolvimento , Sementes/ultraestrutura
19.
Genetica ; 148(1): 13-23, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31960179

RESUMO

Long terminal repeats (LTR) retrotransposons have a major role in determining genome size, structure and function, thanks to their ability to transpose. We performed a meta-analysis of LTR-retrotransposon expression in roots of sunflower plantlets treated with different plant hormones, chemicals and NaCl. By using Illumina cDNA libraries, available from public repositories, we measured the number of reads matching the retrotranscriptase domains isolated from a whole genome library of retrotransposons. LTR-retrotransposons resulted in general barely expressed, except for 4 elements, all belonging to the AleII lineage, which showed high transcription levels in roots of both control and treated plants. The expression of retrotransposons in treated plants was slightly higher than in the control. Transcribed elements belonged to specific chromosomal loci and were not abundant in the genome. A few elements resulted differentially expressed depending on the treatment. Results suggest that, although most retrotransposons are not expressed, the transcription of such elements is related to their abundance, to their position in the chromosome and to their lineage.


Assuntos
Helianthus/genética , Retroelementos/genética , Sequências Repetidas Terminais/genética , Evolução Molecular , Regulação da Expressão Gênica de Plantas/genética , Tamanho do Genoma/genética , Genoma de Planta/genética , Estudo de Associação Genômica Ampla/métodos , Filogenia , Raízes de Plantas
20.
Arch Virol ; 165(1): 249-252, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31748875

RESUMO

Tapping panel dryness (TPD) is a complex disorder that causes partial or complete cessation of latex drainage upon tapping of rubber trees (Hevea brasiliensis). In this work, we determined the complete genome sequences of a novel virus identified in a rubber tree with TPD syndrome in China. The genome of the virus consists of 6811 nt and possesses two overlapping open reading frames (ORF1 and ORF2), encoding a polyprotein and a movement protein, respectively. The polyprotein shares 37% amino acid sequence identity with cherry virus A (CVA, ARQ83874.1) over 99% coverage. The genome architecture is similar to that of members of the genus Capillovirus (family Betaflexiviridae). Phylogenetic analysis of the replicase proteins showed that the virus clustered together with members of the genus Capillovirus. The new virus is tentatively called "rubber tree virus 1" (RTV1). RTV1 is the first virus reported to infect rubber trees. This work lays a foundation for research into finding the potential causal agent of TPD in Hevea brasiliensis.


Assuntos
Flexiviridae/genética , Hevea/virologia , Sequenciamento Completo do Genoma/métodos , Sequência de Aminoácidos , Flexiviridae/classificação , Tamanho do Genoma , Genoma Viral , Fases de Leitura Aberta , Filogenia
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