scholarly journals High-quality complete genome resource of plant pathogenic bacterium Dickeya solani strain IPO 2019 isolated from Hyacinthus orientalis

2021 ◽  
Author(s):  
Robert Czajkowski ◽  
Lukasz Rabalski ◽  
Przemyslaw Bartnik ◽  
Sylwia Jafra
Keyword(s):  
Gc Content ◽  
Pathogenic Bacterium ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Plant Pathogenic Bacterium ◽  
High Quality ◽  
Ecological Fitness ◽  
Hyacinthus Orientalis ◽  
Dickeya Solani

Dickeya solani is an emerging plant pathogenic bacterium, causing disease symptoms in a variety of agriculturally relevant crop species worldwide. To date a number of D. solani genomes have been sequenced and characterized, the great majority of these genomes have however come from D. solani strains isolated from potato (Solanum tuberosum L.) and not from other plant hosts. Herewith, we present the first complete, high-quality genome of D. solani strain IPO 2019 (LMG 25990) isolated from ornamental plant Hyacinthus orientalis. The genome of D. solani strain IPO 2019 consists of one chromosome of 4,919,542 bp., with a GC content of 56.2% and no plasmids. The genome contains 4502 annotated features, 22 rRNA genes, 73 tRNA genes and 1 CRISPRS. We believe that the information of this high-quality, complete, closed genome of D. solani strain isolated from host plant different than potato (i.e. hyacinth) will provide resources for comparative genomic studies as well as for analyses targeting adaptation and ecological fitness mechanisms present in Dickeya solani species.

scholarly journals High-quality complete genome resource of plant pathogenic bacterium Dickeya solani strain IPO 2019 isolated from Hyacinthus orientalis

2021 ◽  
Author(s):  
Robert Czajkowski ◽  
Lukasz Rabalski ◽  
Przemysław Bartnik ◽  
Sylwia Jafra
Keyword(s):  
Gc Content ◽  
Pathogenic Bacterium ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Plant Pathogenic Bacterium ◽  
High Quality ◽  
Ecological Fitness ◽  
Hyacinthus Orientalis ◽  
Dickeya Solani

AbstractDickeya solani is an emerging plant pathogenic bacterium, causing disease symptoms in a variety of agriculturally relevant crop species worldwide. To date a number of D. solani genomes have been sequenced and characterized, the great majority of these genomes have however come from D. solani strains isolated from potato (Solanum tuberosum L.) and not from other plant hosts. Herewith, we present the first complete, high-quality genome of D. solani strain IPO 2019 (LMG 25990) isolated from ornamental plant Hyacinthus orientalis. The genome of D. solani strain IPO 2019 consists of one chromosome of 4,919,542 bp., with a GC content of 56.2% and no plasmids. The genome contains 4502 annotated features, 22 rRNA genes, 73 tRNA genes and 1 CRISPRS. We believe that the information of this high-quality, complete, closed genome of D. solani strain isolated from host plant different than potato (i.e. hyacinth) will provide resources for comparative genomic studies as well as for analyses targeting adaptation and ecological fitness mechanisms present in Dickeya solani species.

scholarly journals High-quality complete genome resource of plant pathogenic bacterium Pectobacterium atrosepticum strain Green1 isolated from potato (Solanum tuberosum L.) in Greenland

2021 ◽  
Author(s):  
Robert Czajkowski ◽  
Lukasz Rabalski ◽  
Maciej Kosinski ◽  
Eigil de Neergaard ◽  
Susanne Harding
Keyword(s):  
Solanum Tuberosum ◽  
Solanum Tuberosum L ◽  
Pathogenic Bacterium ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Plant Pathogenic Bacterium ◽  
High Quality ◽  
Ecological Fitness ◽  
Pectobacterium Atrosepticum

Pectobacterium atrosepticum is a narrow host range pectinolytic plant pathogenic bacterium causing blackleg of potato (Solanum tuberosum L.) worldwide. Till present, several P. atrosepticum genomes have been sequenced and characterized in detail; all of these genomes have come, however, from P. atrosepticum strains isolates from plants grown in temperate zones, not from hosts cultivated under different climatic conditions. Herewith, we present the first complete, high-quality genome of the P. atrosepticum strain Green1 isolated from potato plants grown under subarctic climate in Greenland. The genome of P. atrosepticum strain Green1 consists of one chromosome of 4,959,719 bp., with a GC content of 51% and no plasmids. The genome contains 4531 annotated features, including 4179 protein-coding genes (CDSs), 22 rRNA genes, 70 tRNA genes, 8 ncRNA genes, 2 CRISPRs and 126 pseudogenes. We believe that the information of this first, high-quality, complete, closed genome of P. atrosepticum strain isolated from host plant grown in subarctic agricultural region will provide resources for comparative genomic studies and for analyses targeting climatic adaptation and ecological fitness mechanisms present in P. atrosepticum.

scholarly journals High-quality complete genome resource of plant pathogenic bacterium Pectobacterium atrosepticum strain Green1 isolated from potato (Solanum tuberosum L.) in Greenland

2021 ◽  
Author(s):  
Robert Czajkowski ◽  
Lukasz Rabalski ◽  
Maciej Kosinski ◽  
Eigil de Neergaard ◽  
Susanne Harding
Keyword(s):  
Solanum Tuberosum ◽  
Solanum Tuberosum L ◽  
Pathogenic Bacterium ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Plant Pathogenic Bacterium ◽  
High Quality ◽  
Ecological Fitness ◽  
Pectobacterium Atrosepticum

Pectobacterium atrosepticum is a narrow host range pectinolytic plant pathogenic bacterium causing blackleg of potato (Solanum tuberosum L.) worldwide. Till present, several P. atrosepticum genomes have been sequenced and characterized in detail; all of these genomes have come, however, from P. atrosepticum strains isolates from plants grown in temperate zones, not from hosts cultivated under different climatic conditions. Herewith, we present the first complete, high-quality genome of the P. atrosepticum strain Green1 isolated from potato plants grown under subarctic climate in Greenland. The genome of P. atrosepticum strain Green1 consists of one chromosome of 4,959,719 bp., with a GC content of 51% and no plasmids. The genome contains 4531 annotated features, including 4179 protein-coding genes (CDSs), 22 rRNA genes, 70 tRNA genes, 8 ncRNA genes, 2 CRISPRs and 126 pseudogenes. We believe that the information of this first, high-quality, complete, closed genome of P. atrosepticum strain isolated from host plant grown in subarctic agricultural region will provide resources for comparative genomic studies and for analyses targeting climatic adaptation and ecological fitness mechanisms present in P. atrosepticum.

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

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2137 ◽  
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.

scholarly journals Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 61 ◽  
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.

Effects of stressful physico-chemical factors on the fitness of the plant pathogenic bacterium Dickeya solani

2019 ◽  
Vol 156 (2) ◽  
pp. 519-535 ◽  
Author(s):  
Tomasz Przepiora ◽  
Donata Figaj ◽  
Marta Radzinska ◽  
Malgorzata Apanowicz ◽  
Malgorzata Sieradzka ◽  
...  
Keyword(s):  
Pathogenic Bacterium ◽  
Plant Pathogenic Bacterium ◽  
Physico Chemical ◽  
Chemical Factors ◽  
Dickeya Solani

scholarly journals High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew

2020 ◽  
Vol 33 (5) ◽  
pp. 718-720
Author(s):  
Karthi Natesan ◽  
Ji Yeon Park ◽  
Cheol-Woo Kim ◽  
Dong Suk Park ◽  
Young-Seok Kwon ◽  
...  
Keyword(s):  
Downy Mildew ◽  
De Novo ◽  
Gc Content ◽  
Comparative Genomic ◽  
High Quality ◽  
Sequencing Platform ◽  
Peronospora Destructor ◽  
Genomic Studies ◽  
Genome Assemblies ◽  
High Quality Genome

Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.

scholarly journals Characterization and Analysis of the Mitochondrial Genome of Common Bean (Phaseolus vulgaris) by Comparative Genomic Approaches

2020 ◽  
Vol 21 (11) ◽  
pp. 3778
Author(s):  
Changwei Bi ◽  
Na Lu ◽  
Yiqing Xu ◽  
Chunpeng He ◽  
Zuhong Lu
Keyword(s):  
Phaseolus Vulgaris ◽  
Mitochondrial Genome ◽  
Common Bean ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Leguminous Plants ◽  
The Common

The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmFC gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmFC, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.

scholarly journals Complete genome sequence of Chryseobacterium sp. ZHDP1 with protease activity

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.

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

ZooKeys ◽  
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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