A bacteriophage infecting Mesorhizobium species has a prolate capsid and shows similarities to a family of Caulobacter crescentus phages

Mesorhizobium phage vB_MloS_Cp1R7A-A1 was isolated from soil planted with chickpea in Saskatchewan. It is dissimilar in sequence and morphology to previously described rhizobiophages. It is a B3 morphotype virus with a distinct prolate capsid and belongs to the tailed phage family Siphoviridae. Its genome has a GC content of 60.3% and 238 predicted genes. Putative functions were predicted for 57 genes, which include 27 tRNA genes with anticodons corresponding to 18 amino acids. This represents the highest number of tRNA genes reported yet in a rhizobiophage. The gene arrangement shows a partially modular organization. Most of the structural genes are found in one module, whereas tRNA genes are in another. Genes for replication, recombination, and nucleotide metabolism form the third module. The arrangement of the replication module resembles the replication module of Enterobacteria phage T5, raising the possibility that it uses a recombination-based replication mechanism, but there is also a suggestion that a T7-like replication mechanism could be used. Phage termini appear to be long direct repeats of just over 12 kb in length. Phylogenetic analysis revealed that Cp1R7A-A1 is more closely related to PhiCbK-like Caulobacter phages and other B3 morphotype phages than to other rhizobiophages sequenced thus far.

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The Complete Chloroplast Genome of Tamarix Ramosissima and Comparative Analysis of Tamaricaceae Species

10.21203/rs.3.rs-60520/v1 ◽

2020 ◽

Author(s):

Le Wang ◽

Li Wang ◽

Zhihong Guo

Keyword(s):

Species Delimitation ◽

De Novo ◽

Gc Content ◽

Single Copy ◽

Tamarix Ramosissima ◽

Rrna Genes ◽

Gene Arrangement ◽

Species Discrimination ◽

Trna Genes ◽

Cp Genome

Abstract Background: Tamarix ramosissima is a deciduous shrub resided in arid and semi-arid regions. Although of ecological and medicinal values, some Tamarix species are considered invasive as they have dominated the riparian zones of dryland in some parts of the world. Chloroplast (cp) DNA is highly conserved in structure and gene arrangement, making cp genomic data valuable resources for species delimitation and phylogenetics. The cp genome of T. ramosissima was de novo assembled with the aim of providing reference and data resource for further cp-derived marker development and species delimitation of Tamarix.Results: Here, the complete chloroplast (CP) genome of T. ramosissima was sequenced and analyzed, showing a size of 156150 bp and a GC content of 36.5%. The plastome displayed a typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions of 26554 bp, separated by a large single copy (LSC) region of 84795 bp, and a small single copy (SSC) region of 18247 bp. The cp genome encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 32 repeat sequences and 64 simple sequence repeats (SSR) were identified in the plastome, and an obvious A/T bias was observed in the majority of the SSRs detected. By comparing the T. ramosissima cp genome with those of four other Tamaricaceae species, a number of divergence hotspots were identified among these plastomes. Together with the SSRs and long repeats identified, these divergence hotspots could be developed as potential molecular markers facilitating species discrimination and evolutionary studies. Using plastome sequences, we re-investigated the phylogenetic relationship among 19 species, and T. ramosissima was found to be a sister of Tamarix chinensis.Conclusions: Taken together, our study provides valuable genomic resources to deepen the understanding of the plant photosynthetic mechanism and phylogenomics.

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Isolation and characterization of Hena1 – a novel Erwinia amylovora bacteriophage

FEMS Microbiology Letters ◽

10.1093/femsle/fnaa070 ◽

2020 ◽

Vol 367 (9) ◽

Author(s):

Natalya V Besarab ◽

Artur E Akhremchuk ◽

Maryna A Zlatohurska ◽

Liudmyla V Romaniuk ◽

Leonid N Valentovich ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Fire Blight ◽

Antimicrobial Agents ◽

Erwinia Amylovora ◽

Gc Content ◽

Control Measures ◽

Effective Control ◽

Lytic Phage ◽

Trna Genes ◽

Isolation And Characterization

ABSTRACT Fire blight, caused by plant pathogenic bacterium Erwinia amylovora, is one of the most important diseases of Rosaceae plants. Due to the lack of effective control measures, fire blight infections pose a recurrent threat on agricultural production worldwide. Recently, bacterial viruses, or bacteriophages, have been proposed as environmentally friendly natural antimicrobial agents for fire blight control. Here, we isolated a novel bacteriophage Hena1 with activity against E. amylovora. Further analysis revealed that Hena1 is a narrow-host-range lytic phage belonging to Myoviridae family. Its genome consists of a linear 148,842 bp dsDNA (48.42% GC content) encoding 240 ORFs and 23 tRNA genes. Based on virion structure and genomic composition, Hena1 was classified as a new species of bacteriophage subfamily Vequintavirinae. The comprehensive analysis of Hena1 genome may provide further insights into evolution of bacteriophages infecting plant pathogenic bacteria.

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Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection

Biomedicines ◽

10.3390/biomedicines9040342 ◽

2021 ◽

Vol 9 (4) ◽

pp. 342

Author(s):

Ahmed R. Sofy ◽

Noha K. El-Dougdoug ◽

Ehab E. Refaey ◽

Rehab A. Dawoud ◽

Ahmed A. Hmed

Keyword(s):

Klebsiella Pneumoniae ◽

Burst Size ◽

Phylogenetic Analyses ◽

Foodborne Pathogen ◽

Gc Content ◽

Full Genome Sequence ◽

Multiple Drug ◽

Lytic Phage ◽

Trna Genes ◽

Bacteriophage Therapy

Klebsiella pneumoniae is a hazardous opportunistic pathogen that is involved in many serious human diseases and is considered to be an important foodborne pathogen found in many food types. Multidrug resistance (MDR) K. pneumoniae strains have recently spread and increased, making bacteriophage therapy an effective alternative to multiple drug-resistant pathogens. As a consequence, this research was conducted to describe the genome and basic biological characteristics of a novel phage capable of lysing MDR K. pneumoniae isolated from food samples in Egypt. The host range revealed that KPP-5 phage had potent lytic activity and was able to infect all selected MDR K. pneumoniae strains from different sources. Electron microscopy images showed that KPP-5 lytic phage was a podovirus morphology. The one-step growth curve exhibited that KPP-5 phage had a relatively short latent period of 25 min, and the burst size was about 236 PFU/infected cells. In addition, KPP-5 phage showed high stability at different temperatures and pH levels. KPP-5 phage has a linear dsDNA genome with a length of 38,245 bp with a GC content of 50.8% and 40 predicted open reading frames (ORFs). Comparative genomics and phylogenetic analyses showed that KPP-5 is most closely associated with the Teetrevirus genus in the Autographviridae family. No tRNA genes have been identified in the KPP-5 phage genome. In addition, phage-borne virulence genes or drug resistance genes were not present, suggesting that KPP-5 could be used safely as a phage biocontrol agent.

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Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Molecules ◽

10.3390/molecules23092137 ◽

2018 ◽

Vol 23 (9) ◽

pp. 2137 ◽

Cited By ~ 6

Author(s):

Xiang-Xiao Meng ◽

Yan-Fang Xian ◽

Li Xiang ◽

Dong Zhang ◽

Yu-Hua Shi ◽

...

Keyword(s):

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Future Studies ◽

Chloroplast Genomes ◽

Close Relationship ◽

Cp Genome ◽

Sanguisorba Officinalis

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

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Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Plants ◽

10.3390/plants9010061 ◽

2020 ◽

Vol 9 (1) ◽

pp. 61 ◽

Cited By ~ 5

Author(s):

Huyen-Trang Vu ◽

Ngan Tran ◽

Thanh-Diem Nguyen ◽

Quoc-Luan Vu ◽

My-Huyen Bui ◽

...

Keyword(s):

Chloroplast Genome ◽

Inverted Repeat ◽

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Complete Chloroplast Genome ◽

Critically Endangered Species ◽

Plastid Genomes ◽

Chloroplast Genomes

Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

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Sequencing, characterization and phylogenomics of the complete mitochondrial genome of Dactylogyrus lamellatus (Monogenea: Dactylogyridae)

Journal of Helminthology ◽

10.1017/s0022149x17000578 ◽

2017 ◽

Vol 92 (4) ◽

pp. 455-466 ◽

Cited By ~ 15

Author(s):

D. Zhang ◽

H. Zou ◽

S.G. Wu ◽

M. Li ◽

I. Jakovlić ◽

...

Keyword(s):

Complete Mitochondrial Genome ◽

Sister Group ◽

Ctenopharyngodon Idella ◽

Rrna Genes ◽

Gene Arrangement ◽

Trna Genes ◽

Coding Region ◽

Worldwide Distribution ◽

Phylogenetic Resolution ◽

Complete Mitogenome

AbstractDespite the worldwide distribution and pathogenicity of monogenean parasites belonging to the largest helminth genus, Dactylogyrus, there are no complete Dactylogyrinae (subfamily) mitogenomes published to date. In order to fill this knowledge gap, we have sequenced and characterized the complete mitogenome of Dactylogyrus lamellatus, a common parasite on the gills of grass carp (Ctenopharyngodon idella). The circular mitogenome is 15,187 bp in size, containing the standard 22 tRNA genes, 2 rRNA genes, 12 protein-encoding genes and a long non-coding region (NCR). There are two highly repetitive regions in the NCR. We have used concatenated nucleotide sequences of all 36 genes to perform the phylogenetic analysis using Bayesian inference and maximum likelihood approaches. As expected, the two dactylogyrids, D. lamellatus (Dactylogyrinae) and Tetrancistrum nebulosi (Ancyrocephalinae), were closely related to each other. These two formed a sister group with Capsalidae, and this cluster finally formed a further sister group with Gyrodactylidae. Phylogenetic affinity between Dactylogyrinae and Ancyrocephalinae was further confirmed by the similarity in their gene arrangement. The sequencing of the first Dactylogyrinae, along with a more suitable selection of outgroups, has enabled us to infer a much better phylogenetic resolution than recent mitogenomic studies. However, as many lineages of the class Monogenea remain underrepresented or not represented at all, a much larger number of mitogenome sequences will have to be available in order to infer the evolutionary relationships among the monogeneans fully, and with certainty.

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Complete genome sequence of Chryseobacterium sp. ZHDP1 with protease activity

10.21203/rs.3.rs-581195/v1 ◽

2021 ◽

Author(s):

Huanshuai Zhao ◽

Jianxin Wang ◽

Jiamao Huang ◽

Yuncheng Ma ◽

Yunfei Chen ◽

...

Keyword(s):

Complete Genome ◽

Protease Activity ◽

Fermentation Broth ◽

Gc Content ◽

Rrna Genes ◽

Trna Genes ◽

Rrna Gene ◽

The Novel ◽

Maximum Similarity ◽

Insight Into

Abstract This study reported a complete genome of Chryseobacterium sp. ZHDP1 isolated from the soils of a seafood market. The ZHDP1 genome with a size of 4,917,748 bp and a GC content of 35.95% possessed 4,478 coding genes, 5 rRNA genes, 26 sRNA genes, and 89 tRNA genes. The 16S rRNA gene sequence of ZHDP1 had a maximum similarity of 99.07% with that of C. gambrini 5-1St1a. The maximum values of average nucleotide identity and DNA-DNA hybridization of ZHDP1 genome were 91.39 and 47.8, respectively, which were lower than the thresholds for a new genome. Different protease genes were annotated in the genome of ZHDP1, and the protease activity was also detected in the fermentation broth of ZHDP1. Furthermore, the activity of protease in the fermentation broth was optimized through temperature, pH, and metal irons, and the results showed that 60°C and pH 7.0 were the optimum conditions and Fe3+ could positively increase the protease activity of ZHDP1. This study provides the first insight into the novel genomic information of Chryseobacterium sp. ZHDP1 and its protein-degrading ability, thereby broadening our knowledge of the industrial potentials in genus Chryseobacterium strains.

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The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes

ZooKeys ◽

10.3897/zookeys.925.47820 ◽

2020 ◽

Vol 925 ◽

pp. 73-88

Author(s):

Chaoyi Hu ◽

Shuaibin Wang ◽

Bisheng Huang ◽

Hegang Liu ◽

Lei Xu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Gc Content ◽

Sister Group ◽

Rrna Genes ◽

Sister Group Relationship ◽

Trna Genes ◽

Protein Coding ◽

Generation Sequencing ◽

Simple Sequence

Scolopendra mutilans L. Koch, 1878 is an important Chinese animal with thousands of years of medicinal history. However, the genomic information of this species is limited, which hinders its further application. Here, the complete mitochondrial genome (mitogenome) of S. mutilans was sequenced and assembled by next-generation sequencing. The genome is 15,011 bp in length, consisting of 13 protein-coding genes (PCGs), 14 tRNA genes, and two rRNA genes. Most PCGs start with the ATN initiation codon, and all PCGs have the conventional stop codons TAA and TAG. The S. mutilans mitogenome revealed nine simple sequence repeats (SSRs), and an obviously lower GC content compared with other seven centipede mitogenomes previously sequenced. After analysis of homologous regions between the eight centipede mitogenomes, the S. mutilans mitogenome further showed clear genomic rearrangements. The phylogenetic analysis of eight centipedes using 13 conserved PCG genes was finally performed. The phylogenetic reconstructions showed Scutigeromorpha as a separate group, and Scolopendromorpha in a sister-group relationship with Lithobiomorpha and Geophilomorpha. Collectively, the S. mutilans mitogenome provided new genomic resources, which will improve its medicinal research and applications in the future.

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The complete mitochondrial genome of Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

PeerJ ◽

10.7717/peerj.8762 ◽

2020 ◽

Vol 8 ◽

pp. e8762

Author(s):

Yue Shen ◽

Yu-Zhou Du

Keyword(s):

Mitochondrial Genome ◽

Northern Hemisphere ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Trna Genes ◽

Protein Coding ◽

The Family ◽

Maximum Likelihood Methods ◽

Rna Genes

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

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Draft Genome Sequence of Bacillus pacificus KVCMST-8A-12, Isolated from a Marine Sediment Sample from the Kanyakumari Coast, India

Microbiology Resource Announcements ◽

10.1128/mra.01011-21 ◽

2021 ◽

Vol 10 (50) ◽

Author(s):

Asha Santhi ◽

Venkatesh Subramanian ◽

Krishnaveni Muthan

Keyword(s):

Genome Sequence ◽

Draft Genome ◽

Gc Content ◽

Draft Genome Sequence ◽

Whole Genome Sequence ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Content Type ◽

Marine Sediment Sample

A DNase-producing Bacillus pacificus strain was isolated, and the whole-genome sequence is reported in this paper. The draft genome sequence of Bacillus pacificus KVCMST-8A-12 constitutes 2.4 Gbp of raw reads, with a GC content of 35.24%. In total, 5,661 protein-coding genes, 64 tRNA genes, and 4 rRNA genes were predicted.

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