scholarly journals Genome characterization of 'Candidatus Phytoplasma meliae' (isolate ChTYXIII)

2021 ◽  
Author(s):  
Franco Daniel Fernandez ◽  
Luis Rogelio Conci
Keyword(s):  
Draft Genome ◽  
Infected Plant ◽  
Single Copy ◽  
Pathways Analysis ◽  
Yellowing Disease ◽  
Sec System ◽  
Forestry Production ◽  
Genome Information ◽  
Core Genes

Candidatus Phytoplasma meliae (subgroups 16SrXIII-G and XIII-C) has been reported in association to chinaberry yellowing disease in Argentina, Bolivia and Paraguay. In Argentina, this disease constitutes a major phytosanitary problem for chinaberry forestry production. To date, no genome information of this phytoplasma and others from 16SrXIII-group has been published, hindered its characterization at genomic level. Here we analyze the draft genome of Candidatus Phytoplasma meliae strain ChTYXIII obtained from a chinaberry-infected plant using a metagenomics approach. The draft assembly consists of twenty-one contigs with a total length of 751.949 bp. The annotation contains 669 CDSs, 34tRNA and one set of rRNA operons. Metabolic pathways analysis indicated that the ChTYXIII contains the complete core genes for glycolysis and functional sec system for translocation of proteins. The phylogenetic relationships inferred 132 single copy genes (orthologues core) analysis revealed that Ca. P. meliae constitutes a clade closely related to the Ca. australiense and Ca. P. solani. Thirty-one putative effectors were identified, among which a homologue to SAP11 was found and others that have only been described in this pathogen. This work provides relevant genomic information for Ca. P. meliae and constitutes the first genome described for the group 16SrXIII (MPV).

scholarly journals Transcriptome Profiling of Two Ornamental and Medicinal Papaver Herbs

2018 ◽  
Vol 19 (10) ◽  
pp. 3192 ◽  
Author(s):  
Jaehyeon Oh ◽  
Younhee Shin ◽  
In Ha ◽  
Min Lee ◽  
Seok-Geun Lee ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Plant Development ◽  
Functional Characterization ◽  
Transcriptome Profiling ◽  
Single Copy ◽  
Isoquinoline Alkaloid ◽  
Metabolite Profiles ◽  
Secondary Metabolite Biosynthesis ◽  
Core Genes

The Papaver spp. (Papaver rhoeas (Corn poppy) and Papaver nudicaule (Iceland poppy)) genera are ornamental and medicinal plants that are used for the isolation of alkaloid drugs. In this study, we generated 700 Mb of transcriptome sequences with the PacBio platform. They were assembled into 120,926 contigs, and 1185 (82.2%) of the benchmarking universal single-copy orthologs (BUSCO) core genes were completely present in our assembled transcriptome. Furthermore, using 128 Gb of Illumina sequences, the transcript expression was assessed at three stages of Papaver plant development (30, 60, and 90 days), from which we identified 137 differentially expressed transcripts. Furthermore, three co-occurrence heat maps are generated from 51 different plant genomes along with the Papaver transcriptome, i.e., secondary metabolite biosynthesis, isoquinoline alkaloid biosynthesis (BIA) pathway, and cytochrome. Sixty-nine transcripts in the BIA pathway along with 22 different alkaloids (quantified with LC-QTOF-MS/MS) were mapped into the BIA KEGG map (map00950). Finally, we identified 39 full-length cytochrome transcripts and compared them with other genomes. Collectively, this transcriptome data, along with the expression and quantitative metabolite profiles, provides an initial recording of secondary metabolites and their expression related to Papaver plant development. Moreover, these profiles could help to further detail the functional characterization of the various secondary metabolite biosynthesis and Papaver plant development associated problems.

scholarly journals First report of reference guided genome assembly of Black Bengal goat (Capra hircus)

2019 ◽  
Author(s):  
Amam Z. Siddiki ◽  
A. Baten ◽  
M. Billah ◽  
MAU. Alam ◽  
KSM. Shawrob ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
Capra Hircus ◽  
Sequencing Platform ◽  
Gene Annotations ◽  
Skin Quality ◽  
Genome Information ◽  
Black Bengal Goat ◽  
Illumina Sequencing Platform

AbstractObjectivesBlack Bengal goat (Capra hircus), a member of the Bovidae family with the unique traits of high prolificacy, skin quality and low demand for food is the most socioeconomically significant goat breed in Bangladesh. Furthermore, the aptitude of adaptation and disease resistance capacity of it is highly notable which makes its whole genome information an area of research interest.Data descriptionThe genomic DNA of local (Chittagong, Bangladesh) healthy Black Bengal goat (Capra hircus) was extracted and then sequenced. The de novo assembly and structural annotations are being presented here. Sequencing was done using Illumina sequencing platform and the draft genome assembled is about 3.04 Gb. 26458 Genes were annotated using Maker gene annotations tool which predicted BUSCO Gene models. Universal Single Copy Orthologs refer 82.5% completeness of the assembled genome.

scholarly journals Molecular Characterization of the Cucurbit Yellow Stunting Disorder Virus Coat Protein Gene

1999 ◽  
Vol 89 (11) ◽  
pp. 1050-1055 ◽  
Author(s):  
Ioannis C. Livieratos ◽  
Apostolos D. Avgelis ◽  
Robert H. A. Coutts
Keyword(s):  
Coat Protein ◽  
Infected Plant ◽  
Open Reading Frames ◽  
Gene Arrangement ◽  
Cp Gene ◽  
Contiguous Gene ◽  
Lettuce Infectious Yellows Virus ◽  
Yellowing Disease ◽  
Virus Coat

Cucurbit yellow stunting disorder virus (CYSDV) is a partially characterized bipartite closterovirus transmitted by the tobacco whitefly (Bemisia tabaci). CYSDV has emerged as a serious pathogen in southeastern Spain and the Mediterranean Region, causing yellowing disease of cucumber and melon crops. Using a modified reverse-transcription polymerase chain reaction protocol with gel-extracted dsRNA templates, fragments of CYSDV RNA2 were amplified and cloned. Sequence analysis of the cloned fragments revealed open reading frames encoding the heat shock protein 70 homolog, two proteins of unknown function (p58 and p9), and the coat protein (CP) of the virus in a contiguous gene arrangement similar to that of lettuce infectious yellows virus (LIYV) RNA2. The complete CYSDV CP gene is 756 nt long and encodes a protein with a molecular mass of 28.5 kDa. A comparison of the amino acid sequence of the CYSDV CP gene with those of other closteroviruses revealed significant levels of similarity with sweet potato chlorotic stunt virus and LIYV (36 and 27%, respectively), both of which are members of the recently proposed Crinivirus genus of closteroviruses. The complete CYSDV CP gene was cloned into a bacterial expression vector, and the resulting fusion protein was purified and used to produce antiserum. Purified immunoglobulins specifically detected CYSDV in infected plant extracts, both in immunoblot and indirect enzyme-linked immunosorbent assays with a titer exceeding 2,000 times for both assays.

scholarly journals STRONG: metagenomics strain resolution on assembly graphs

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Christopher Quince ◽  
Sergey Nurk ◽  
Sebastien Raguideau ◽  
Robert James ◽  
Orkun S. Soyer ◽  
...  
Keyword(s):  
Time Series ◽  
De Novo ◽  
Single Copy ◽  
Bayesian Algorithm ◽  
Anaerobic Digestor ◽  
Core Genes

AbstractWe introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.

scholarly journals Characterization of the Major Antigenic Protein 2 of Ehrlichia canis and Ehrlichia chaffeensis and Its Application for Serodiagnosis of Ehrlichiosis

2003 ◽  
Vol 10 (4) ◽  
pp. 520-524 ◽  
Author(s):  
Tamece T. Knowles ◽  
A. Rick Alleman ◽  
Heather L. Sorenson ◽  
David C. Marciano ◽  
Edward B. Breitschwerdt ◽  
...  
Keyword(s):  
Blot Analysis ◽  
Single Copy ◽  
Ehrlichia Canis ◽  
Specific Method ◽  
Ehrlichia Chaffeensis ◽  
Antigenic Protein ◽  
Canine Monocytic Ehrlichiosis ◽  
Copy Gene ◽  
Species Specific

ABSTRACT Canine monocytic ehrlichiosis, caused by Ehrlichia canis or Ehrlichia chaffeensis, can result in clinical disease in naturally infected animals. Coinfections with these agents may be common in certain areas of endemicity. Currently, a species-specific method for serological diagnosis of monocytic ehrlichiosis is not available. Previously, we developed two indirect enzyme-linked immunosorbent assays (ELISAs) using the major antigenic protein 2 (MAP2) of E. chaffeensis and E. canis. In this study, we further characterized the conservation of MAP2 among various geographic isolates of each organism and determined if the recombinant MAP2 (rMAP2) of E. chaffeensis would cross-react with E. canis-infected dog sera. Genomic Southern blot analysis using digoxigenin-labeled species-specific probes suggested that map2 is a single-copy gene in both Ehrlichia species. Sequences of the single map2 genes of seven geographically different isolates of E. chaffeensis and five isolates of E. canis are highly conserved among the various isolates of each respective ehrlichial species. ELISA and Western blot analysis confirmed that the E. chaffeensis rMAP2 failed to serologically differentiate between E. canis and E. chaffeensis infections.

Characterization of Tomato leaf curl Palampur virus associated with leaf curl and yellowing disease of watermelon from India

2021 ◽  
Author(s):  
Yamuna Hanamasagar ◽  
Priya Naganur ◽  
K. S. Shankarappa ◽  
V. Venkataravanappa ◽  
C. N. Lakshminarayana Reddy
Keyword(s):  
Tomato Leaf ◽  
Yellowing Disease ◽  
Tomato Leaf Curl ◽  
Leaf Curl

scholarly journals Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 725
Author(s):  
Fernando Clavijo-Coppens ◽  
Nicolas Ginet ◽  
Sophie Cesbron ◽  
Martial Briand ◽  
Marie-Agnès Jacques ◽  
...  
Keyword(s):  
Phage Therapy ◽  
Xylella Fastidiosa ◽  
Infected Plant ◽  
Mediterranean Area ◽  
Genomic Features ◽  
Phylogeny Analysis ◽  
Plant Pest ◽  
European Regulations ◽  
Surrogate Host

Xylella fastidiosa (Xf) is a plant pathogen causing significant losses in agriculture worldwide. Originating from America, this bacterium caused recent epidemics in southern Europe and is thus considered an emerging pathogen. As the European regulations do not authorize antibiotic treatment in plants, alternative treatments are urgently needed to control the spread of the pathogen and eventually to cure infected crops. One such alternative is the use of phage therapy, developed more than 100 years ago to cure human dysentery and nowadays adapted to agriculture. The first step towards phage therapy is the isolation of the appropriate bacteriophages. With this goal, we searched for phages able to infect Xf strains that are endemic in the Mediterranean area. However, as Xf is truly a fastidious organism, we chose the phylogenetically closest and relatively fast-growing organism X. albineans as a surrogate host for the isolation step. Our results showed the isolation from various sources and preliminary characterization of several phages active on different Xf strains, namely, from the fastidiosa (Xff), multiplex (Xfm), and pauca (Xfp) subspecies, as well as on X. albilineans. We sequenced their genomes, described their genomic features, and provided a phylogeny analysis that allowed us to propose new taxonomic elements. Among the 14 genomes sequenced, we could identify two new phage species, belonging to two new genera of the Caudoviricetes order, namely, Usmevirus (Podoviridae family) and Subavirus (Siphoviridae family). Interestingly, no specific phages could be isolated from infected plant samples, whereas one was isolated from vector insects captured in a contaminated area, and several from surface and sewage waters from the Marseille area.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

Molecular characterization of the goat CSN1S101 allele

2003 ◽  
Vol 70 (2) ◽  
pp. 237-240 ◽  
Author(s):  
Gianfranco Cosenza ◽  
Rosa Illario ◽  
Andrea Rando ◽  
Paola di Gregorio ◽  
Piero Masina ◽  
...  
Keyword(s):  
Protein Content ◽  
Molecular Characterization ◽  
Single Copy ◽  
Chromosome 6

Caseins (αs1, β, αs2, e κ) represent about 80% of the whole protein content of ruminant milk. Each of these proteins is encoded by single copy genes (CSN1S1, CSN2, CSN1S2 and CSN3, respectively) clustered on a ∼200-kb segment of chromosome 6 (Ferretti et al. 1990; Gallagher et al. 1994) in the order: CSN1S1, CSN2, CSN1S2 and CSN3 (Mercier & Vilotte, 1993). Furthermore, in cattle and goat CSN1S1 and CSN2 are convergently transcribed (Leroux & Martin, 1996; Rijnkles et al. 1997) and are only 20 and 12 kb apart, respectively.

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