scholarly journals Advances in the sequencing of the genome of the adenophorean nematode Trichinella spiralis

Parasitology ◽  
2008 ◽  
Vol 135 (8) ◽  
pp. 869-880 ◽  
Author(s):  
M. Mitreva ◽  
D. P. Jasmer
Keyword(s):  
Genome Sequence ◽  
Evolutionary Biology ◽  
Trichinella Spiralis ◽  
Control Strategies ◽  
Cell Interaction ◽  
Parasitic Nematodes ◽  
Molecular Characteristics ◽  
Dnase Ii ◽  
Interspecific Comparisons ◽  
Insight Into

SUMMARYThe adenophorean nematodes are evolutionarily distant from other species in the phylum Nematoda. Interspecific comparisons of predicted proteins have supported such an ancient divergence. Accordingly, Trichinella spiralis represents a basal nematode representative for genome sequencing focused on gaining a deeper insight into the evolutionary biology of nematodes. In addition, molecular characteristics that are conserved across the phylum could be of great value for control strategies with broad application. In this review, we describe and summarize progress that has been made on the sequencing and analysis of the T. spiralis genome. The genome sequence was used in preliminary analyses for the investigation of specific questions relating to the biology of T. spiralis and, more generally, to parasitic nematodes. For instance, we evaluated an unusually large DNase II-like protein family, predicted proteins of prospective interest in the parasite-host muscle cell interaction, anthelmintic targets and prospective intestinal genes, the encoded proteins (potentially) linked to immunological control against other nematodes. The results are discussed in relation to characteristics that are broadly conserved among evolutionary distant nematodes. The results lead to expectations that this genome sequence will contribute to advances in research on T. spiralis and other parasitic nematodes.

scholarly journals Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker Bacterium Lonsdalea populi

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 246
Author(s):  
Xiaomeng Chen ◽  
Rui Li ◽  
Yonglin Wang ◽  
Aining Li
Keyword(s):  
Genome Sequence ◽  
Extracellular Enzymes ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Hybrid Poplars ◽  
A Genome ◽  
Conserved Genes ◽  
Genomic Characterization ◽  
Molecular Bases ◽  
Insight Into

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cold Adaptation ◽  
Gc Content ◽  
Glycogen Metabolism ◽  
Extreme Environment ◽  
Circular Chromosome ◽  
Cold Regions ◽  
Insight Into

Abstract Background The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Results Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. Conclusions We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

scholarly journals Marine Organisms for the Sustainable Management of Plant Parasitic Nematodes

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 369
Author(s):  
Pasqua Veronico ◽  
Maria Teresa Melillo
Keyword(s):  
Crop Production ◽  
Control Strategies ◽  
Marine Organisms ◽  
New Drugs ◽  
Effective Control ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Wide Range ◽  
Plant Growth Stimulants ◽  
Plant Parasitic

Plant parasitic nematodes are annually responsible for the loss of 10%–25% of worldwide crop production, most of which is attributable to root-knot nematodes (RKNs) that infest a wide range of agricultural crops throughout the world. Current nematode control tools are not enough to ensure the effective management of these parasites, mainly due to the severe restrictions imposed on the use of chemical pesticides. Therefore, it is important to discover new potential nematicidal sources that are suitable for the development of additional safe and effective control strategies. In the last few decades, there has been an explosion of information about the use of seaweeds as plant growth stimulants and potential nematicides. Novel bioactive compounds have been isolated from marine cyanobacteria and sponges in an effort to find their application outside marine ecosystems and in the discovery of new drugs. Their potential as antihelmintics could also be exploited to find applicability against plant parasitic nematodes. The present review focuses on the activity of marine organisms on RKNs and their potential application as safe nematicidal agents.

scholarly journals First Insight into Groundwater Copepods of the Polish Lowland

Water ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 2086
Author(s):  
Maciej Karpowicz ◽  
Sabina Smolska ◽  
Magdalena Świsłocka ◽  
Joanna Moroz
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Rna ◽  
Dna Markers ◽  
Coi Gene ◽  
Molecular Characteristics ◽  
Morphological Description ◽  
Single Plate ◽  
North Eastern ◽  
Insight Into

Our results are the first insight into groundwater copepods of the Polish Lowland. The sampling was conducted in 28 wells in north-eastern Poland, and Copepoda were present in 16 wells. We have identified six Copepoda species and one Cladocera. We have classified four species as stygophiles—Eucyclops serrulatus, Diacyclops bisetosus, Diacyclops crassicaudis, and Cyclops furcifer. These species were frequently found in studied wells of different regions of north-eastern Poland, often in high numbers, and females with egg sacs were observed. We present a detailed morphological description of these species, together with molecular characteristics based on mitochondrial DNA markers (COI gene) for E. serrulatus, D. bisetosus, and D. crassicaudis, and 12S ribosomal RNA for C. furcifer. We also present the development of abnormal structures in one specimen of D. crassicaudis, where the upper part of furcal rami was fused to form a single plate.

scholarly journals Biological and Molecular Characteristics of a Novel Partitivirus Infecting the Edible Fungus Lentinula edodes

Plant Disease ◽  
2017 ◽  
Vol 101 (5) ◽  
pp. 726-733 ◽  
Author(s):  
Mengpei Guo ◽  
Yinbing Bian ◽  
Jinjie Wang ◽  
Gangzheng Wang ◽  
Xiaolong Ma ◽  
...  
Keyword(s):  
Lentinula Edodes ◽  
Control Strategies ◽  
Phylogenetic Analyses ◽  
Pcr Analysis ◽  
Molecular Characteristics ◽  
Rt Pcr ◽  
Edible Fungus ◽  
Qpcr Analysis ◽  
Disease Diagnostics ◽  
Wild Strains

A new partitivirus named Lentinula edodes partitivirus 1 (LePV1) was isolated from a diseased L. edodes strain with severe degeneration of the mycelium and imperfect browning in bag cultures. The nucleotide sequences of LePV1 dsRNA-1 and dsRNA-2 were determined; they were 2,382 bp and 2,245 bp in length, and each contained a single ORF encoding RNA-dependent RNA polymerase (RdRp) and coat protein (CP), respectively. The purified virus preparation contained isometric particles 34 nm in diameter encapsidating these dsRNAs. Phylogenetic analyses showed LePV1 to be a new member of Betapartitivirus, with the RdRp sequence most closely related to Grapevine partitivirus. RT-PCR analysis showed that 27 of the 56 Chinese L. edodes core collection strains carry LePV1, with the virus being more common in wild strains than cultivated strains. In addition, qPCR analysis suggested that coinfection with L. edodes mycovirus HKB (LeV-HKB) could increase replication of the RdRp gene of LePV1. This study may be essential for the development of more accurate disease diagnostics and the formulation of control strategies for viral diseases in L. edodes.

scholarly journals Mycobacterium tuberculosis adhesins: potential biomarkers as anti-tuberculosis therapeutic and diagnostic targets

Microbiology ◽  
2014 ◽  
Vol 160 (9) ◽  
pp. 1821-1831 ◽  
Author(s):  
Viveshree S. Govender ◽  
Saiyur Ramsugit ◽  
Manormoney Pillay
Keyword(s):  
Immune Response ◽  
Mycobacterium Tuberculosis ◽  
Control Strategies ◽  
Host Cells ◽  
Tuberculosis Control ◽  
Surface Molecules ◽  
Host Pathogen Interaction ◽  
Bacterial Aggregation ◽  
Insight Into

Adhesion to host cells is a precursor to host colonization and evasion of the host immune response. Conversely, it triggers the induction of the immune response, a process vital to the host’s defence against infection. Adhesins are microbial cell surface molecules or structures that mediate the attachment of the microbe to host cells and thus the host–pathogen interaction. They also play a crucial role in bacterial aggregation and biofilm formation. In this review, we discuss the role of adhesins in the pathogenesis of the aetiological agent of tuberculosis, Mycobacterium tuberculosis. We also provide insight into the structure and characteristics of some of the characterized and putative M. tuberculosis adhesins. Finally, we examine the potential of adhesins as targets for the development of tuberculosis control strategies.

scholarly journals The Gossypium stocksii genome as a novel resource for cotton improvement

2021 ◽  
Author(s):  
Corrinne E Grover ◽  
Daojun Yuan ◽  
Mark A Arick ◽  
Emma R Miller ◽  
Guanjing Hu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Pest Resistance ◽  
Cotton Leaf ◽  
High Quality ◽  
Cotton Leaf Curl Virus ◽  
Cotton Species ◽  
Wild Cotton ◽  
Leaf Curl Virus ◽  
Insight Into

Abstract Cotton is an important textile crop whose gains in production over the last century have been challenged by various diseases. Because many modern cultivars are susceptible to several pests and pathogens, breeding efforts have included attempts to introgress wild, naturally resistant germplasm into elite lines. Gossypium stocksii is a wild cotton species native to Africa, which is part of a clade of vastly understudied species. Most of what is known about this species comes from pest resistance surveys and/or breeding efforts, which suggests that G. stocksii could be a valuable reservoir of natural pest resistance. Here we present a high-quality de novo genome sequence for G. stocksii. We compare the G. stocksii genome with resequencing data from a closely related, understudied species (G. somalense) to generate insight into the relatedness of these cotton species. Finally, we discuss the utility of the G. stocksii genome for understanding pest resistance in cotton, particularly resistance to cotton leaf curl virus.

scholarly journals Draft Genome Sequence of the Putative Marine Pathogen Aquimarina sp. Strain I32.4

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Hilary J. Ranson ◽  
Jason LaPorte ◽  
Edward Spinard ◽  
Andrei Y. Chistoserdov ◽  
Marta Gomez-Chiarri ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Genome Sequence ◽  
Draft Genome ◽  
Homarus Americanus ◽  
Draft Genome Sequence ◽  
American Lobster ◽  
Content Type ◽  
Shell Disease ◽  
Insight Into

ABSTRACT Aquimarina sp. strain I32.4 (formerly Aquimarina sp. ‘ homaria ’) is a putative pathogen involved in epizootic shell disease in the American lobster ( Homarus americanus ). We report here the draft genome sequence for Aquimarina sp. strain I32.4 and describe virulence factors that may provide insight into its mechanism of pathogenicity.

scholarly journals Draft Genome Sequence of “ Candidatus Phytoplasma oryzae” Strain Mbita1, the Causative Agent of Napier Grass Stunt Disease in Kenya

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Anne Fischer ◽  
Ivette Santana-Cruz ◽  
Lillian Wambua ◽  
Cassandra Olds ◽  
Charles Midega ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Agricultural Production ◽  
Plant Pathogens ◽  
Genomic Organization ◽  
Draft Genome ◽  
Napier Grass ◽  
Eastern Africa ◽  
Draft Genome Sequence ◽  
Economic Losses ◽  
Insight Into

Phytoplasmas are bacterial plant pathogens with devastating impact on agricultural production worldwide. In eastern Africa, Napier grass stunt disease causes serious economic losses in the smallholder dairy industry. This draft genome sequence of “ Candidatus Phytoplasma oryzae” strain Mbita1 provides insight into its genomic organization and the molecular basis of pathogenicity.

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