5,660 results match your criteria genomic synteny


Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton.

Mol Biol Evol 2021 May 11. Epub 2021 May 11.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.

Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging three-fold in genome size, namely Gossypium rotundifolium (K2), G. arboreum (A2), and G. Read More

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Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae.

J Zhejiang Univ Sci B 2021 May;22(5):366-382

Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation in plants and animals by targeting messenger RNAs (mRNAs) for cleavage or repressing translation of specific mRNAs. The first miRNA identified in plants, miRNA156 (miR156), targets the SQUAMOSA promoter-binding protein-like (SPL) transcription factors, which play critical roles in plant phase transition, flower and plant architecture, and fruit development. We identified multiple copies of and in the rice, , sorghum, maize, and foxtail millet genomes. Read More

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Pests, diseases, and aridity have shaped the genome of Corymbia citriodora.

Commun Biol 2021 May 10;4(1):537. Epub 2021 May 10.

University of Queensland/QAAFI, Brisbane, QLD, Australia.

Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts (Eucalyptus, Corymbia and Angophora; ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora, anchored into eleven chromosomes. Read More

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Genome wide identification, classification and functional characterization of heat shock transcription factor in cultivated and ancestral cotton (Gossypium).

Int J Biol Macromol 2021 May 6. Epub 2021 May 6.

Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China. Electronic address:

Heat shock transcription factors (HSF) have been demonstrated to play a significant transcriptional regulatory role in plants and considered as an integral part of signal transduction pathways against environmental stresses. 42, 39, 67, and 79 nonredundant HSF genes were identified from G. arboreum (A2), G. Read More

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A method for achieving complete microbial genomes and improving bins from metagenomics data.

PLoS Comput Biol 2021 May 7;17(5):e1008972. Epub 2021 May 7.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America.

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. Read More

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Genomic appraisal of Klebsiella PGPB isolated from soil to enhance the growth of barley.

Genes Genomics 2021 May 7. Epub 2021 May 7.

Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India.

Background: PGPR has substituted chemical fertilizers to enhance the nutrient profile of the soil. Although gene encoding for PGP activity is present in PGPB their activity changes in response to conditions.

Objective: To study comparative genomics for three Klebsiella strains and their PGPR activity in response to in vitro and soil condition. Read More

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Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study.

Methods Mol Biol 2021 ;2242:91-112

Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland.

High availability of fast, cheap, and high-throughput next generation sequencing techniques resulted in acquisition of numerous de novo sequenced and assembled bacterial genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization of several handy open source comparative genomic tools. Read More

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January 2021

The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high-density linkage maps in comparative mapping and synteny analysis.

Plant Genome 2021 May 7:e20090. Epub 2021 May 7.

Instituto de Tecnologia Química e Biológica António Xavier, Univ. Nova de Lisboa, Oeiras, 2780-157, Portugal.

Powdery mildews are major diseases for a range of crops. The loss of function of specific Mildew Locus O (MLO) genes has long been associated with pre-haustorial plant resistance to powdery mildew and has proven to be durable in several species. Erysiphe pisi is the major causal agent of powdery mildew in pea (Pisum sativum L. Read More

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Effects of hatching enzymes on egg envelope digestion in the male-brooding seahorse.

Mol Reprod Dev 2021 May 7. Epub 2021 May 7.

CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.

In the present study, we aimed to evaluate the effects of hatching enzymes on the egg envelope digestion during the hatching period in the male brooding seahorse. The complementary DNAs encoding two hatching-enzyme genes, high choriolytic enzyme (HCE) and low choriolytic enzyme (LCE), were cloned and functionally characterized from the lined seahorse (Hippocampus erectus). The genomic-synteny analysis confirmed that teleosts shared LCE gene synteny. Read More

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Evidence of Recombination Suppression Blocks on the Y Chromosome of Date Palm ().

Front Plant Sci 2021 20;12:634901. Epub 2021 Apr 20.

Genomics Laboratory, Weill Cornell Medicine in Qatar, Doha, Qatar.

The genus includes the fruit producing date palm tree among 14 species that are all dioecious. Females produce the fruit that are high in sugar content and used in multiple countries ranging from North Africa to South Asia, especially from the , , and species. While females produce the fruit, understanding of the genetic basis of sex control only began recently. Read More

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Comprehensive molecular dissection of TIFY Transcription factors reveal their dynamic responses to biotic and abiotic stress in wheat (Triticum aestivum L.).

Sci Rep 2021 May 6;11(1):9739. Epub 2021 May 6.

Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India.

The plant specific TIFY (previously known as ZIM) transcription factor (TF) family plays crucial roles in cross talk between Jasmonic Acid and other phytohormones like gibberellins, salicylic acid, abscisic acid, auxin, and ethylene signaling pathways. Wheat yield is severely affected by rust diseases and many abiotic stresses, where different phytohormone signaling pathways are involved. TIFYs have been studied in many plants yet reports describing their molecular structure and function in wheat are lacking. Read More

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A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum.

Mol Plant Pathol 2021 May 5. Epub 2021 May 5.

Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics and Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany.

Amphidiploid fungal Verticillium longisporum strains Vl43 and Vl32 colonize the plant host Brassica napus but differ in their ability to cause disease symptoms. These strains represent two V. longisporum lineages derived from different hybridization events of haploid parental Verticillium strains. Read More

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Genome wide identification, phylogeny, and synteny analysis of family in common carp ().

Biotechnol Rep (Amst) 2021 Jun 16;30:e00607. Epub 2021 Mar 16.

Division of Fish Genetics and Biotechnology, Fauclty of Fisheries Rangil, Ganderbal, SKUAST-Kashmir, India.

Common carp () is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcription factors found in a broad range of animal taxa and extensively known for its contribution in multiple developmental processes including contribution in sex determination across phyla. In our current study, we initially accomplished a genome-wide analysis to report the SOX gene family in common carp fish based on available genomic sequences of zebrafish retrieved from gene repository databases, we focused on the global identification of the Sox gene family in Common carp among wide range of vertebrates and teleosts based on bioinformatics tools and techniques and explore the evolutionary relationships. Read More

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Assembly and characterization of the genome of chard (Beta vulgaris ssp. vulgaris var. cicla).

J Biotechnol 2021 Apr 28;333:67-76. Epub 2021 Apr 28.

Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria. Electronic address:

Chard (Beta vulgaris ssp. vulgaris var. cicla) is a member of one of four different cultigroups of beets. Read More

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Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time.

Sci Rep 2021 Apr 29;11(1):9256. Epub 2021 Apr 29.

Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.

Enterotoxigenic Escherichia coli (ETEC) is an enteric pathogen responsible for the majority of diarrheal cases worldwide. ETEC infections are estimated to cause 80,000 deaths annually, with the highest rates of burden, ca 75 million cases per year, amongst children under 5 years of age in resource-poor countries. It is also the leading cause of diarrhoea in travellers. Read More

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Noncanonical DNA polymerization by aminoadenine-based siphoviruses.

Science 2021 04;372(6541):520-524

Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France.

Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous to the Klenow fragment of bacterial DNA polymerase I that includes 3'-exonuclease but lacks 5'-exonuclease, were found to preferentially select for aminoadenine instead of adenine in deoxynucleoside triphosphate incorporation templated by thymine. Read More

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Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes.

Microorganisms 2021 Apr 27;9(5). Epub 2021 Apr 27.

Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile.

Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. Read More

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Catalase (CAT) Gene Family in Rapeseed ( L.): Genome-Wide Analysis, Identification, and Expression Pattern in Response to Multiple Hormones and Abiotic Stress Conditions.

Int J Mol Sci 2021 Apr 20;22(8). Epub 2021 Apr 20.

College of Agriculture, Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, Yangtze University, Jingzhou 434025, China.

Catalase (CAT) is an antioxidant enzyme expressed by the gene family and exists in almost all aerobic organisms. Environmental stresses induce the generation of reactive oxygen species (ROS) that eventually hinder plant growth and development. The CAT enzyme translates the hydrogen peroxide (HO) to water (HO) and reduce the ROS levels to shelter the cells' death. Read More

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Genome-Wide Identification and Characterization of TALE Superfamily Genes in Soybean ( L.).

Int J Mol Sci 2021 Apr 16;22(8). Epub 2021 Apr 16.

Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.

The three-amino-acid-loop-extension (TALE) superfamily genes broadly existed in plants, which played important roles in plant growth, development and abiotic stress responses. In this study, we identified 68 TALE (GmTALE) superfamily members. Phylogenetic analysis divided the GmTALE superfamily into the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Read More

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Delineating the Insertion Landscape of the Model Legume cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly.

Int J Mol Sci 2021 Apr 21;22(9). Epub 2021 Apr 21.

Noble Research Institute, LLC., Ardmore, OK 73401, USA.

Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. is a well-established model legume, and extensive studies in fundamental molecular, physiological, and developmental biology have been undertaken to translate into trait improvements in economically important legume crops worldwide. However, reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. Read More

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Genome-Wide Screening of AP2 Transcription Factors Involving in Fruit Color and Aroma Regulation of Cultivated Strawberry.

Genes (Basel) 2021 Apr 5;12(4). Epub 2021 Apr 5.

College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.

Duch, which among the youngest fruit crops, comprises many popular cultivars that are famous for their favored color and aroma. The regulation roles of AP2/ERF (APETALA2/ethylene-responsive element-binding factor) transcription factors in fruit flavor and color regulation have been studied in several fruit crops. The AP2 family of strawberry, which was ignored in recent AP2/ERF identification studies, was explored in this study. Read More

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High Rates of Genome Rearrangements and Pathogenicity of spp.

Front Microbiol 2021 12;12:628622. Epub 2021 Apr 12.

Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia.

are pathogens originating within the lineage but frequently classified as a separate genus. genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of and strains to assess the contribution of genomic rearrangements to evolution. Read More

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A pseudomolecule assembly of the Rocky Mountain elk genome.

PLoS One 2021 28;16(4):e0249899. Epub 2021 Apr 28.

Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America.

Rocky Mountain elk (Cervus canadensis) populations have significant economic implications to the cattle industry, as they are a major reservoir for Brucella abortus in the Greater Yellowstone area. Vaccination attempts against intracellular bacterial diseases in elk populations have not been successful due to a negligible adaptive cellular immune response. A lack of genomic resources has impeded attempts to better understand why vaccination does not induce protective immunity. Read More

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Reevaluation of the and genomes reveals misassembly, karyotype differences, and chromosomal rearrangements.

Genome Res 2021 May 27;31(5):823-833. Epub 2021 Apr 27.

Laboratory of Host Pathogen Interactions-Molecular Biology Unit, Institut Pasteur de Montevideo, 11400 Montevideo, Uruguay.

primarily infects cattle, causing abortions, with an estimated impact of a billion dollars on the worldwide economy annually. However, the study of its biology has been unheeded by the established paradigm that it is virtually identical to its close relative, the widely studied human pathogen By revisiting the genome sequence, assembly, and annotation using third-generation sequencing technologies, here we show that the genome was originally incorrectly assembled under the presumption of synteny with We show that major chromosomal rearrangements have occurred between these species. Importantly, we show that chromosomes originally named Chr VIIb and VIII are indeed fused, reducing the karyotype of both and to 13 chromosomes. Read More

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Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia.

Gigascience 2021 Apr;10(4)

International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.

Background: The hard-shelled mussel (Mytilus coruscus) is widely distributed in the temperate seas of East Asia and is an important commercial bivalve in China. Chromosome-level genome information of this species will contribute not only to the development of hard-shelled mussel genetic breeding but also to studies on larval ecology, climate change biology, marine biology, aquaculture, biofouling, and antifouling.

Findings: We applied a combination of Illumina sequencing, Oxford Nanopore Technologies sequencing, and high-throughput chromosome conformation capture technologies to construct a chromosome-level genome of the hard-shelled mussel, with a total length of 1. Read More

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Complete mitochondrial genome of and comparison with related species in Halymeniales (Rhodophyta).

Mitochondrial DNA B Resour 2021 Apr 8;6(4):1365-1366. Epub 2021 Apr 8.

Department of Biology & Research Institute of Basic Sciences, Jeju National University, Jeju, Republic of Korea.

is a species of Halymeniales, the fifth species-rich order within Rhodophyta. Using next-generation sequencing techniques, we recovered the complete mitochondrial genome of , i.e. Read More

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The Degenerate Tale of Ascidian Tails.

Integr Comp Biol 2021 Apr 20. Epub 2021 Apr 20.

Biology Department, University of Washington, Seattle, Washington, 98195, USA.

Ascidians are invertebrate chordates, with swimming chordate tadpole larvae that have distinct heads and tails. The head contains the small brain, sensory organs, including the ocellus (light) and otolith (gravity) and the presumptive endoderm, while the tail has a notochord surrounded by muscle cells and a dorsal nerve cord. One of the chordate features is a post-anal tail. Read More

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Homoeolog inference methods requiring bidirectional best hits or synteny miss many pairs.

Genome Biol Evol 2021 Apr 19. Epub 2021 Apr 19.

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Homoeologs are pairs of genes or chromosomes in the same species that originated by speciation and were brought back together in the same genome by allopolyploidization. Bioinformatic methods for accurate homoeology inference are crucial for studying the evolutionary consequences of polyploidization, and homoeology is typically inferred on the basis of bidirectional best hit (BBH) and/or positional conservation (synteny). However, these methods neglect the fact that genes can duplicate and move, both prior to and after the allopolyploidization event. Read More

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The Insights of Genomic Synteny and Codon Usage Preference on Genera Demarcation of Family.

Front Microbiol 2021 31;12:657887. Epub 2021 Mar 31.

Laboratory Animal Center, Southwest Medical University, Luzhou, China.

The members of the family are large, double-stranded DNA viruses that infect various hosts, including both vertebrates and invertebrates. Although great progress has been made in genomic and phylogenetic analyses, the adequacy of the existing criteria for classification within the family remains unknown. In this study, we redetermined 23 core genes by re-annotation, core-pan analysis and local BLASTN search. Read More

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Genome-wide identification and comparative analysis of the WRKY gene family in aquatic plants and their response to abiotic stresses in giant duckweed (Spirodela polyrhiza).

Genomics 2021 Apr 20;113(4):1761-1777. Epub 2021 Apr 20.

The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

WRKY is one of the largest transcription factor families across higher plant species and is involved in important biological processes and plant responses to various biotic/abiotic stresses. However, only a few investigations on WRKYs have been conducted in aquatic plants. This study first systematically analyzed the gene structure, protein properties, and phylogenetic relationship of 693 WRKYs in nine aquatic and two wetland plants at the genome-wide level. Read More

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