scholarly journals Shrimp draft genome contains independent clusters of ancient and current endogenous viral elements (EVE) of the parvovirus IHHNV

2021 ◽  
Author(s):  
Suparat Taengchaiyaphum ◽  
Prapatsorn Wongkhaluang ◽  
Timothy William Flegel ◽  
Kallaya Sritunyalucksana
Keyword(s):  
Linkage Group ◽  
Draft Genome ◽  
Penaeus Monodon ◽  
Gene Clusters ◽  
Rnai Pathway ◽  
High Homology ◽  
Persistent Infections ◽  
Link Type ◽  
Viral Type ◽  
Endogenous Viral Elements

Shrimp have the ability to accommodate viruses in long term, persistent infections without signs of disease. Endogenous viral elements (EVE) play a role in this process probably via production of negative-sense Piwi-interacting RNA (piRNA)-like fragments. These bind with Piwi proteins to dampen viral replication via the RNA interference (RNAi) pathway. We searched a draft genome of the giant tiger shrimp (Penaeus monodon)(GenBank record JABERT000000000) for the presence of EVE related to a shrimp parvovirus originally named infectious hypodermal and hematopoietic necrosis virus (IHHNV). The shrimp draft genome contained 3 piRNA-like gene clusters containing scrambled IHHNV EVE. Two clusters were located distant from one another in linkage group 35 (LG35). Both LG35 clusters contained multiple DNA fragments with high homology (99%) to GenBank records DQ228358 and EU675312 that were both called non-infectious IHHNV Type A (IHHNV-A) when originally discovered. However, our results and those from a recent Australian P. monodon genome assembly indicate that the relevant GenBank records for IHHNV-A are sequence-assembly artifacts derived from scrambled and fragmental IHHNV-EVE. Although the EVE in the two LG35 clusters showed high homology only to IHHNV-A, the clusters were separate and distinct with respect to the arrangement (i.e., order and reading direction) and proportional content of the IHHNV-A GenBank records. We conjecture that these 2 clusters may constitute independent allele-like clusters on a pair of homologous chromosomes. The third EVE cluster was found in linkage group 7 (LG7). It contained EVE with high homology (99%) only to GenBank record AF218266 with the potential to protect shrimp against infectious IHHNV. Our results suggested the possibility of viral-type specificity in EVE clusters. Specificity is important whole EVE clusters for one viral type would be transmitted to offspring as collective hereditary units. This would be advantageous if one or more of the EVE within the cluster were protective against disease caused by the cognate virus. It would also facilitate gene editing for removal of non-protective EVE clusters or for transfer of protective EVE clusters to genetically improve existing shrimp breeding stocks that might lack them.

scholarly journals Shrimp parvovirus circular DNA fragments arise from both endogenous viral elements (EVE) and the infecting virus

2021 ◽  
Author(s):  
Suparat Taengchaiyaphum ◽  
Phasini Buathongkam ◽  
Suchitraporn Sukthaworn ◽  
Prapatsorn Wongkhaluang ◽  
Kallaya Sritunyalucksana ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Rnai Pathway ◽  
Breeding Programs ◽  
Sequence Identity ◽  
Link Type ◽  
Viral Copy ◽  
Copy Dna ◽  
Endogenous Viral Elements ◽  
Next Generation Sequencing Ngs ◽  
Interfering Rna

Some insects use endogenous reverse transcriptase (RT) to make variable linear and circular viral copy DNA (vcDNA) fragments from viral RNA. The vcDNA produces small interfering RNA (siRNA) variants that inhibit viral replication via the RNA interference (RNAi) pathway. The vcDNA is also autonomously inserted into the host genome as endogenous viral elements (EVE) that can also result in RNAi. We hypothesized that similar mechanisms occurred in shrimp. We used the insect methods to extract circular viral copy DNA (cvcDNA) from the giant tiger shrimp (Penaeus monodon) infected with a virus originally named infectious hypodermal and hematopoietic necrosis virus (IHHNV). Simultaneous injection of the extracted cvcDNA plus IHHNV into whiteleg shrimp (Penaeus vannamei) resulted in a significant reduction in IHHNV replication when compared to shrimp injected with IHHNV only. Next generation sequencing (NGS) revealed that the extract contained a mixture of two general IHHNV-cvcDNA types. One showed 98 to 99% sequence identity to GenBank record AF218266 from an extant type of infectious IHHNV. The other type showed 98% sequence identity to GenBank record DQ228358, an EVE formerly called non-infectious IHHNV. The startling discovery that EVE could also give rise to cvcDNA revealed that cvcDNA provided an easy means to identify and characterize EVE in shrimp and perhaps other organisms. These studies open the way for identification, characterization and use of protective cvcDNA as a potential shrimp vaccine and as a tool to identify, characterize and select naturally protective EVE to improve shrimp tolerance to homologous viruses in breeding programs.

scholarly journals Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a fragmented IHHNV EVE sequence

2021 ◽  
Author(s):  
Roger Huerlimann ◽  
Jeff A Cowley ◽  
Nicholas M Wade ◽  
Yinan Wang ◽  
Naga Kasinadhuni ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Penaeus Monodon ◽  
Penaeid Shrimp ◽  
Protein Coding ◽  
Black Tiger Shrimp ◽  
Draft Genome Assembly ◽  
Repeat Content ◽  
Tiger Shrimp ◽  
Endogenous Viral Elements

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements (EVEs) have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such EVEs and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of EVEs. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for one generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific EVEs identified an element comprised of a 9,045 bp stretch of repeated, inverted and jumbled genome fragments of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) bounded by a repeated 591/590 bp host sequence. As only near complete linear ~4 kb IHHNV genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear EVE types. The existence of conjoined inverted IHHNV genome fragments also provides a means by which hairpin dsRNAs could be expressed and processed by the shrimp RNA interference (RNAi) machinery.

scholarly journals Glycomyces terrestris sp. nov., isolated from extremely arid soil from Yuanmou Earth Forest

2020 ◽  
Author(s):  
Qinyuan Li ◽  
Guiding Li ◽  
Lei Lang ◽  
Defeng An ◽  
Chenglin Jiang ◽  
...  
Keyword(s):  
Type Species ◽  
Draft Genome ◽  
Gene Clusters ◽  
Major Fatty Acid ◽  
Closely Related Species ◽  
Content Type ◽  
Arid Soil ◽  
Link Type ◽  
Pr China ◽  
Fatty Acid Compositions

A Gram-stain-positive, mycelium-forming actinobacterium, YIM 121974T was isolated from an extreme arid soil sample collected at Yuanmou Earth Forest, Yunnan Province, PR China. Classification using a polyphasic approach suggested that strain YIM 121974T belonged to the genus Glycomyces and was closely related to Glycomyces dulcitolivorans SJ-25T (98.3 %), Glycomyces scopariae YIM 56256T (98 %), Glycomyces mayteni YIM 61331T (97.9 %), Glycomyces albidus NEAU-7082T (97.9 %), Glycomyces sambucus CGMCC 4.3147T (97.7 %), Glycomyces artemisiae IXS4T (97.6 %) and Glycomyces parisis CPCC 204357T (97.5 %), but could be distinguished from its closest relatives by a combination of phenotypic and phylogenetic features. Average nucleotide identity values of YIM 121974T to its closest phylogenetic neighbours were 70.7–88.9 %, which are lower than the threshold of 95 %. The digital DNA–DNA hybridization values between YIM 121974T and these relative species were 18.0–36.3 %, which are also well below the cut-off value (>70 %) for species delineation. The DNA G+C content of strain YIM 121974T was 72.3 mol% (draft genome sequence). The predominant menaquinone was MK-11. The phospholipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphoglycolipid and glycolipid. The major fatty acid compositions were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The draft genome of isolate YIM 121974T was found to contain 11 secondary metabolite biosynthesis gene clusters by using the antiSMASH server. Based on the above observations, strain YIM 121974T could be distinguished from closely related species belonging to the genus Glycomyces . Thus, strain YIM 121974T represents a novel species of the genus Glycomyces , for which the name Glycomyces terrestris sp. nov. is proposed. The type strain is YIM 121974T (=KCTC 39870T=DSM 106742T).

scholarly journals Shrimp Parvovirus Circular DNA Fragments Arise From Both Endogenous Viral Elements and the Infecting Virus

2021 ◽  
Vol 12 ◽  
Author(s):  
Suparat Taengchaiyaphum ◽  
Phasini Buathongkam ◽  
Suchitraporn Sukthaworn ◽  
Prapatsorn Wongkhaluang ◽  
Kallaya Sritunyalucksana ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Rnai Pathway ◽  
Breeding Programs ◽  
Sequence Identity ◽  
Viral Copy ◽  
Copy Dna ◽  
Endogenous Viral Elements ◽  
Next Generation Sequencing Ngs ◽  
Interfering Rna ◽  
Generation Sequencing

Some insects use endogenous reverse transcriptase (RT) to make variable viral copy DNA (vcDNA) fragments from viral RNA in linear (lvcDNA) and circular (cvcDNA) forms. The latter form is easy to extract selectively. The vcDNA produces small interfering RNA (siRNA) variants that inhibit viral replication via the RNA interference (RNAi) pathway. The vcDNA is also autonomously inserted into the host genome as endogenous viral elements (EVE) that can also result in RNAi. We hypothesized that similar mechanisms occurred in shrimp. We used the insect methods to extract circular viral copy DNA (cvcDNA) from the giant tiger shrimp (Penaeus monodon) infected with a virus originally named infectious hypodermal and hematopoietic necrosis virus (IHHNV). Simultaneous injection of the extracted cvcDNA plus IHHNV into whiteleg shrimp (Penaeus vannamei) resulted in a significant reduction in IHHNV replication when compared to shrimp injected with IHHNV only. Next generation sequencing (NGS) revealed that the extract contained a mixture of two general IHHNV-cvcDNA types. One showed 98 to 99% sequence identity to GenBank record AF218266 from an extant type of infectious IHHNV. The other type showed 98% sequence identity to GenBank record DQ228358, an EVE formerly called non-infectious IHHNV. The startling discovery that EVE could also give rise to cvcDNA revealed that cvcDNA provided an easy means to identify and characterize EVE in shrimp and perhaps other organisms. These studies open the way for identification, characterization and use of protective cvcDNA as a potential shrimp vaccine and as a tool to identify, characterize and select naturally protective EVE to improve shrimp tolerance to homologous viruses in breeding programs.

Pontibacter aquaedesilientis sp. nov., isolated from Jeongbang Waterfall, Jeju Island

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Geeta Chhetri ◽  
Taegun Seo
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Stream Water ◽  
Draft Genome ◽  
Gene Clusters ◽  
Jeju Island ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type

A red-pigmented, aerobic, motile by gliding, pleomorphic to long-rods and divided by budding bacterium, Gram-stain negative bacterium, designated JH31T, was isolated from stream water of Jeongbang Waterfall, famous feature of Jeju Island, Republic of Korea. The cells grew at 9–40 °C (optimum, 28–30 °C), at pH 5.0–10.0 (pH 6.5–7.5) and with 0–6% NaCl (0% NaCl). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JH31T forms a lineage within the family Hymenobacteriaceae and clusters with its closest related species Pontibacter virorsus KCTC 42941T (98.1%), Pontibacter salisaro KACC 16885T (98.0%), Pontibacter amylolyticus JCM 19653T (97.2%), Pontibacter ramchanderi KACC 17384T (97.2%) and Pontibacter lucknowensis DM9T (96.4%). Strain JH31T produced carotenoid-type pigments but no flexirubin-type pigments. The genome was 4117105 bp long with 18 contigs and 3509 protein-coding genes. The DNA G+C content was 49.7 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain JH31T and its closely related reference strains were less than 19 and 72%, respectively. The draft genome of strain JH31T contained vital gene clusters involved in resistance against various metals, antibiotics, toxic compounds and radiation. The respiratory quinone of strain JH31T was menaquinone 7 and the predominant cellular fatty acids were iso-C15:0, and summed feature 4 (comprising iso-C17:1 I and/or anteiso B). The major polar lipids were phosphatidylethanolamine, three unidentified glycolipids, one unidentified phospholipid, one unidentified phosphoglycolipid and one unidentified aminoglycolipid. The phylogenetic, physiochemical and biochemical data showed that strain JH31T should represent a novel species in the genus Pontibacter , for which the name Pontibacter aquaedesilientis sp. nov. is proposed. The type strain for this novel species is JH31T (KACC 21705T=NBRC 114480T).

scholarly journals Draft Genome Sequences of Fungus Aspergillus calidoustus

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Fabian Horn ◽  
Jörg Linde ◽  
Derek J. Mattern ◽  
Grit Walther ◽  
Reinhard Guthke ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genome Sequence ◽  
Functional Annotation ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Genome Sequences

Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504) . The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Dominic A. Stoll ◽  
Nicolas Danylec ◽  
Christina Grimmler ◽  
Sabine E. Kulling ◽  
Melanie Huch
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Average Amino Acid Identity ◽  
Biochemical Analyses

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria . However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

scholarly journals Draft Genome Sequence of Streptomyces sp. TP-A0874, a Catechoserine Producer

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Hisayuki Komaki ◽  
Akira Hosoyama ◽  
Natsuko Ichikawa ◽  
Yasuhiro Igarashi
Keyword(s):  
Genome Sequence ◽  
Cell Invasion ◽  
Draft Genome ◽  
Gene Clusters ◽  
Bioinformatic Analysis ◽  
Biosynthetic Gene Cluster ◽  
Tumor Cell Invasion ◽  
Draft Genome Sequence ◽  
Biosynthetic Gene ◽  
Streptomyces Sp

We report the draft genome sequence of Streptomyces sp. TP-A0874 isolated from compost. This strain produces catechoserine, a new catecholate-type inhibitor of tumor cell invasion. The genome harbors at least six gene clusters for polyketide and nonribosomal peptide biosyntheses. The biosynthetic gene cluster for catechoserines was identified by bioinformatic analysis.

scholarly journals Isolation and Identification of Actinomycetes Strains from Switzerland and their Biotechnological Potential

2020 ◽  
Vol 74 (5) ◽  
pp. 382-390 ◽  
Author(s):  
Fabienne Arn ◽  
David Frasson ◽  
Ivana Kroslakova ◽  
Fabio Rezzonico ◽  
Joël F. Pothier ◽  
...  
Keyword(s):  
Draft Genome ◽  
Genome Mining ◽  
Bioactive Compound ◽  
Gene Clusters ◽  
Natural Compounds ◽  
Rrna Gene ◽  
Cultivation Conditions ◽  
Screening Assay ◽  
Isolation And Identification ◽  
Bioinformatics Analyses

Actinomycetes strains isolated from different habitats in Switzerland were investigated for production of antibacterial and antitumoral compounds. Based on partial 16S rRNA gene sequences, the isolated strains were identified to genus level. Streptomyces as the largest genus of Actinobacteriawas isolated the most frequently. A screening assay using the OmniLog instrument was established to facilitate the detection of active compounds from actinomycetes. Extracts prepared from the cultivated strains able to inhibit Staphylococcus aureusand Escherichia coliwere further analysed by HPLC and MALDI-TOF MS to identify the produced antibiotics. In this study, the bioactive compound echinomycin was identified from two isolated Streptomycesstrains. Natural compounds similar to TPU-0037-C, azalomycin F4a 2-ethylpentyl ester, a derivative of bafilomycin A1, milbemycin-α8 and dihydropicromycin were detected from different isolated Streptomyces strains. Milbemycin-α8 showed cytotoxic activity against HT-29 colon cancer cells. The rare actinomycete,Micromonospora sp. Stup16_C148 produced a compound that matches with the antibiotic bottromycin A2. The draft genome sequence from Actinokineospora strain B136.1 was determined using Illumina and nanopore-based technologies. The isolated strain was not able to produce antibacterial compounds under standard cultivation conditions. The antiSMASH bioinformatics analyses of the genome from strain B136.1 identified biosynthetic gene clusters with identity values between 4% to 90% to known gene clusters encoding antibiotics. The combinations of cultivation conditions, screening assays, analytical methods and genome mining are important tools to characterize strains of actinomycetes for the identification of their potential to produce natural compounds with antimicrobial activity.

scholarly journals Rufibacter latericius sp. nov., isolated from Baiyang Lake

2020 ◽  
Vol 70 (11) ◽  
pp. 5943-5949 ◽  
Author(s):  
Yun-zhen Yang ◽  
Ji-feng Chen ◽  
Wan-ru Huang ◽  
Ran-ran Zhang ◽  
Shuangjiang Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Pr China

A novel Gram-stain-negative, strictly aerobic, rod-shaped, brick red-pigmented bacterium, designated R-22-1 c-1T, was isolated from water from Baiyang Lake, Hebei Province, PR China. The strain was able to grow at 20–30 °C (optimum, 30 °C) and pH 6–7 (optimum, pH 6) in Reasoner’s 2A medium. 16S rRNA gene sequence and phylogenetic analyses of R-22-1 c-1T revealed closest relationships to Rufibacter immobilis MCC P1T (97.8 %), Rufibacter sediminis H-1T (97.9 %) and Rufibacter glacialis MDT1-10-3T (97.0 %), with other species of the genus Rufibacter showing less than 97.0 % sequence similarity. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids. The major cellular fatty acids were iso-C15 : 0, C15 : 1  ω6c, C17 : 1  ω6c, anteiso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B). The respiratory quinone was MK-7. The draft genome of R-22-1 c-1T was 5.6 Mbp in size, with a G+C content of 50.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain R-22-1 c-1T and related type strains were R. immobilis MCC P1T (77.2 and 21.8 %), R. sediminis H-1T (81.6 and 21.4 %) and R. tibetensis 1351T (78.5 and 22.9 %). Based on these phylogenetic, chemotaxonomic and genotypic results, strain R-22-1 c-1T represents a novel species in the genus Rufibacter , for which the name Rufibacter latericius sp. nov. is proposed. The type strain is R-22-1 c-1T (=CGMCC 1.13570T=KCTC 62781T).

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