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Auto Tag: De novo assembly

July 7, 2019

Identification of a GC-rich leptin gene in chicken.

Abstract Leptin (LEP) plays a key role in the regulation of energy balance in mammals, with less well-defined roles in lower vertebrates. The existence of LEP orthologs in birds has been controversial and only recently have several avian LEP genes been reported. Still, LEP has been assumed to be missing from the chicken (Gallus gallus) genome. Here, we identify the chicken LEP (cLEP), which shares only 25% amino acid sequence identity with its human ortholog. However, it has considerably higher homology with avian LEPs, and phylogenetic analysis shows it as clustering with avian LEP sequences. The cLEP and the other known avian LEP sequences all have high GC content. We argue that this property is behind the technical difficulties impeding the identification of these avian genes. The identification of cLEP can be expected to help elucidate leptin signaling pathways in wild and domestic chickens.

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July 7, 2019

Development of Streptomyces sp. FR-008 as an emerging chassis

Microbial-derived natural products are important in both the pharmaceutical industry and academic research. As the metabolic potential of original producer especially Streptomyces is often limited by slow growth rate, complicated cultivation profile, and unfeasible genetic manipulation, so exploring a Streptomyces as a super industrial chassis is valuable and urgent. Streptomyces sp. FR-008 is a fast-growing microorganism and can also produce a considerable amount of macrolide candicidin via modular polyketide synthase. In this study, we evaluated Streptomyces sp. FR-008 as a potential industrial-production chassis. First, PacBio sequencing and transcriptome analyses indicated that the Streptomyces sp. FR-008 genome size is 7.26 Mb, which represents one of the smallest of currently sequenced Streptomyces genomes. In addition, we simplified the conjugation procedure without heat-shock and pre-germination treatments but with high conjugation efficiency, suggesting it is inherently capable of accepting heterologous DNA. In addition, a series of promoters selected from literatures was assessed based on GusA activity in Streptomyces sp. FR-008. Compared with the common used promoter ermE*-p, the strength of these promoters comprise a library with a constitutive range of 60–860%, thus providing the useful regulatory elements for future genetic engineering purpose. In order to minimum the genome, we also target deleted three endogenous polyketide synthase (PKS) gene clusters to generate a mutant LQ3. LQ3 is thus an “updated” version of Streptomyces sp. FR-008, producing fewer secondary metabolites profiles than Streptomyces sp. FR-008. We believe this work could facilitate further development of Streptomyces sp. FR-008 for use in biotechnological applications.

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July 7, 2019

Emergence of epidemic Neisseria meningitidis serogroup C in Niger, 2015: an analysis of national surveillance data.

To combat Neisseria meningitidis serogroup A epidemics in the meningitis belt of sub-Saharan Africa, a meningococcal serogroup A conjugate vaccine (MACV) has been progressively rolled out since 2010. We report the first meningitis epidemic in Niger since the nationwide introduction of MACV.We compiled and analysed nationwide case-based meningitis surveillance data in Niger. Cases were confirmed by culture or direct real-time PCR, or both, of cerebrospinal fluid specimens, and whole-genome sequencing was used to characterise isolates. Information on vaccination campaigns was collected by the Niger Ministry of Health and WHO.From Jan 1 to June 30, 2015, 9367 suspected meningitis cases and 549 deaths were reported in Niger. Among 4301 cerebrospinal fluid specimens tested, 1603 (37·3%) were positive for a bacterial pathogen, including 1147 (71·5%) that were positive for N meningitidis serogroup C (NmC). Whole-genome sequencing of 77 NmC isolates revealed the strain to be ST-10217. Although vaccination campaigns were limited in scope because of a global vaccine shortage, 1·4 million people were vaccinated from March to June, 2015.This epidemic represents the largest global NmC outbreak so far and shows the continued threat of N meningitidis in sub-Saharan Africa. The risk of further regional expansion of this novel clone highlights the need for continued strengthening of case-based surveillance. The availability of an affordable, multivalent conjugate vaccine may be important in future epidemic response.MenAfriNet consortium, a partnership between the US Centers for Disease Control and Prevention, WHO, and Agence de Médecine Preventive, through a grant from the Bill & Melinda Gates Foundation. Copyright © 2016 World Health Organization. Published by Elsevier Ltd/Inc/BV. All rights reserved. Published by Elsevier Ltd.. All rights reserved.

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July 7, 2019

Complete genome sequence of Lactobacillus plantarum LZ227, a potential probiotic strain producing B-group vitamins.

B-group vitamins play an important role in human metabolism, whose deficiencies are associated with a variety of disorders and diseases. Certain microorganisms such as Lactic acid bacteria (LAB) have been shown to have capacities for B-group vitamin production and thus could potentially replace chemically synthesized vitamins for food fortification. A potential probiotic strain named Lactobacillus plantarum LZ227, which was isolated from raw cow milk in this study, exhibits the ability to produce B-group vitamins. Complete genome sequencing of LZ227 was performed to gain insights into the genetic elements involved in B-group vitamin production. The genome of LZ227 contains a circular 3,131,750-bp chromosome, three circular plasmids and two predicted linear plasmids. LZ227 also contains gene clusters for biosynthesis of both riboflavin and folate. This genome sequence provides a basis for further elucidation of its molecular genetics and probiotic functions, and will facilitate its applications as starter cultures in food industry. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Hyper-eccentric structural genes in the mitochondrial genome of the algal parasite Hemistasia phaeocysticola.

Diplonemid mitochondria are considered to have very eccentric structural genes. Coding regions of individual diplonemid mitochondrial genes are fragmented into small pieces and found on different circular DNAs. Short RNAs transcribed from each DNA molecule mature through a unique RNA maturation process involving assembly and three types of RNA editing (i.e., U insertion and A-to-I & C-to-U substitutions), although the molecular mechanism(s) of RNA maturation and the evolutionary history of these eccentric structural genes still remain to be understood. Since the gene fragmentation pattern is generally conserved among the diplonemid species studied to date, it was considered that their structural complexity has plateaued and further gene fragmentation could not occur. Here, we show the mitochondrial gene structure of Hemistasia phaeocysticola, which was recently identified as a member of a novel lineage in diplonemids, by comparison of the mitochondrial DNA sequences with cDNA sequences synthesized from mature mRNA. The genes of H. phaeocysticola are fragmented much more finely than those of other diplonemids studied to date. Furthermore, in addition to all known types of RNA editing, it is suggested that a novel processing step (i.e., secondary RNA insertion) is involved in the RNA maturation in the mitochondria of H. phaeocysticola Our findings demonstrate the tremendous plasticity of mitochondrial gene structures.© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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July 7, 2019

Complete genome sequence of Plesiomonas shigelloides type strain NCTC10360.

Plesiomonas shigelloides is a Gram-negative rod within the Enterobacteriaceae family. It is a gastrointestinal pathogen of increasing notoriety, often associated with diarrheal disease. P. shigelloides is waterborne, and infection is often linked to the consumption of seafood. Here, we describe the first complete genome for P. shigelloides type strain NCTC10360.© Crown copyright 2016.

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July 7, 2019

Complete genome sequence of the proteorhodopsin-containing marine flavobacterium Dokdonia donghaensis DSW-1T, isolated from seawater off Dokdo in the East Sea (Sea of Korea).

Dokdonia spp. have been used for investigating the lifestyles of proteorhodopsin-containing photoheterotrophs and for understanding marine photobiology. Here, we report the complete genome sequence of Dokdonia donghaensis DSW-1(T) using the PacBio sequencing platform. It should provide a valuable resource for comparative genomic studies of marine life harboring microbial rhodopsins among others. Copyright © 2016 Kim et al.

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July 7, 2019

Complete genome sequence of the intracellular bacterial symbiont TC1 in the anaerobic ciliate Trimyema compressum.

A free-living ciliate, Trimyema compressum, found in anoxic freshwater environments harbors methanogenic archaea and a bacterial symbiont named TC1 in its cytoplasm. Here, we report the complete genome sequence of the TC1 symbiont, consisting of a 1.59-Mb chromosome and a 35.8-kb plasmid, which was determined using the PacBio RSII sequencer. Copyright © 2016 Shinzato et al.

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July 7, 2019

Draft genome sequence of Escherichia coli S51, a chicken isolate harboring a chromosomally encoded mcr-1 gene.

We present the draft genome of Escherichia coli S51, a colistin-resistant extended-spectrum ß-lactamase-producing strain isolated in 2015 from raw chicken meat imported from Germany. Assembly and annotation of this draft genome resulted in a 4,994,918-bp chromosome and revealed a chromosomally encoded mcr-1 gene responsible for the colistin resistance of the strain. Copyright © 2016 Zurfluh et al.

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July 7, 2019

Lysosomal Cathepsin A plays a significant role in the processing of endogenous bioactive peptides.

Lysosomal serine carboxypeptidase Cathepsin A (CTSA) is a multifunctional enzyme with distinct protective and catalytic function. CTSA present in the lysosomal multienzyme complex to facilitate the correct lysosomal routing, stability and activation of with beta-galactosidase and alpha-neuraminidase. Beside CTSA has role in inactivation of bioactive peptides including bradykinin, substances P, oxytocin, angiotensin I and endothelin-I by cleavage of 1 or 2 amino acid(s) from C-terminal ends. In this study, we aimed to elucidate the regulatory role of CTSA on bioactive peptides in knock-in mice model of CTSA(S190A) . We investigated the level of bradykinin, substances P, oxytocin, angiotensin I and endothelin-I in the kidney, liver, lung, brain and serum from CTSA(S190A) mouse model at 3- and 6-months of age. Our results suggest CTSA selectively contributes to processing of bioactive peptides in different tissues from CTSA(S190A) mice compared to age matched WT mice.

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July 7, 2019

Genome sequence of Arenibacter algicola strain TG409, a hydrocarbon-degrading bacterium associated with marine eukaryotic phytoplankton.

Arenibacter algicola strain TG409 was isolated from Skeletonema costatum and exhibits the ability to utilize polycyclic aromatic hydrocarbons as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 5,550,230 bp with 4,722 genes and an average G+C content of 39.7%. Copyright © 2016 Gutierrez et al.

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July 7, 2019

Complete genome sequence of a cylindrospermopsin-producing cyanobacterium, Cylindrospermopsis raciborskii CS505, containing a circular chromosome and a single extrachromosomal element.

Cylindrospermopsis raciborskii is a freshwater cyanobacterium producing bloom events and toxicity in drinking water source reservoirs. We present the first genome sequence for C. raciborskii CS505 (Australia), containing one 4.1-Mbp chromosome and one 110-Kbp plasmid having G+C contents of 40.3% (3933 genes) and 39.3% (111 genes), respectively. Copyright © 2016 Fuentes-Valdés et al.

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