The genome of Bacillus amyloliquefaciens strain BH072, isolated from a honey sample and showing strong antimicrobial activity against plant pathogens, is 4.07 Mb and harbors 3,785 coding sequences (CDS). Several gene clusters for nonribosomal synthesis of antimicrobial peptides and a complete gene cluster for biosynthesis of mersacidin were detected. Copyright © 2015 Zhao et al.
The genome of Paenibacillus polymyxa Sb3-1, a strain that shows antagonistic activities against pathogenic fungi and bacteria, consists of one 5.6-Mb circular chromosome and two plasmids of 223 kb and 8 kb. The genome reveals several genes that potentially contribute to its antagonistic and plant growth promotion activity. Copyright © 2015 Rybakova et al.
We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain HI1 using Roche 454 and PacBio single-molecule real-time hybrid-sequencing analysis. This strain is of biological importance since it has the capacity to induce the settlement and metamorphosis of the serpulid polychaete Hydroides elegans and the coral Pocillopora damicornis. Copyright © 2015 Asahina and Hadfield.
Kosakonia radicincitans strain YD4 is a rhizospheric isolate from yerba mate (Ilex paraguariensis St. Hill.) with plant growth-promoting effects on this crop. Genes involved in different plant growth-promoting activities are present in this genome, suggesting its potential as a bioinoculant for yerba mate. Copyright © 2015 Bergottini et al.
Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome sequences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16-epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.
By phylogenetic analysis, Mycobacterium kansasii is closely related to Mycobacterium tuberculosis. Yet, although both organisms cause pulmonary disease, M. tuberculosis is a global health menace, whereas M. kansasii is an opportunistic pathogen. To illuminate the differences between these organisms, we have sequenced the genome of M. kansasii ATCC 12478 and its plasmid (pMK12478) and conducted side-by-side in vitro and in vivo investigations of these two organisms. The M. kansasii genome is 6,432,277 bp, more than 2 Mb longer than that of M. tuberculosis H37Rv, and the plasmid contains 144,951 bp. Pairwise comparisons reveal conserved and discordant genes and genomic regions. A notable example of genomic conservation is the virulence locus ESX-1, which is intact and functional in the low-virulence M. kansasii, potentially mediating phagosomal disruption. Differences between these organisms include a decreased predicted metabolic capacity, an increased proportion of toxin-antitoxin genes, and the acquisition of M. tuberculosis-specific genes in the pathogen since their common ancestor. Consistent with their distinct epidemiologic profiles, following infection of C57BL/6 mice, M. kansasii counts increased by less than 10-fold over 6 weeks, whereas M. tuberculosis counts increased by over 10,000-fold in just 3 weeks. Together, these data suggest that M. kansasii can serve as an image of the environmental ancestor of M. tuberculosis before its emergence as a professional pathogen, and can be used as a model organism to study the switch from an environmental opportunistic pathogen to a professional host-restricted pathogen. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Dickeya solani is an important bacterial pathogen of potato cultivars in Europe. Here, we present the draft genome of D. solani strain IFB0099 isolated from potato in Poland that shows a high level of pectinolytic activity and a high virulence. This genome sequence is 5,094,121 bp and contains 4,365 protein-coding sequences. Copyright © 2015 Golanowska et al.
Polycyclovorans algicola strain TG408 is a recently discovered bacterium associated with marine eukaryotic phytoplankton and exhibits the ability to utilize polycyclic aromatic hydrocarbons (PAHs) almost exclusively as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 3,653,213 bp, with 3,477 genes and an average G+C content of 63.8%. Copyright © 2015 Gutierrez et al.
Mycoplasma flocculare is a commensal or low-virulence pathogen of swine. The complete 778,866-bp genome sequence of M. flocculare strain Ms42(T) has been determined, enabling further comparison to genomes of the closely related pathogen Mycoplasma hyopneumoniae. The absence of the p97 and glpD genes may contribute to the attenuated virulence of M. flocculare. Copyright © 2015 Calcutt et al.
Here, we report two genomes, one complete and one draft, from isolates of serotype A2 Mannheimia haemolytica recovered from pneumonic bovine lung. Copyright © 2015 Hauglund et al.
Here, we report the completed genome sequence of a carbapenem-resistant extraintestinal pathogenic Escherichia coli sequence type 131 (ST131) isolate, MNCRE44. The isolate was obtained in 2012 in Minnesota, USA, from a sputum sample from a hospitalized patient with multiple comorbidities, and it belongs to the H30R sublineage. Copyright © 2015 Johnson et al.
We announce here the complete genome sequence of the Pseudomonas aeruginosa mucoid strain FRD1, isolated from the sputum of a cystic fibrosis patient. The complete genome of P. aeruginosa FRD1 is 6,712,339 bp. This genome will allow comparative genomics to be used to identify genes associated with virulence, especially those involved in chronic pulmonary infections. Copyright © 2015 Silo-Suh et al.
The last decade of decreasing DNA sequencing costs and proliferating sequencing services in core labs and companies has brought the de-novo genome sequencing and assembly of insect species within reach for many entomologists. However, sequence production alone is not enough to generate a high quality reference genome, and in many cases, poor planning can lead to extremely fragmented genome assemblies preventing high quality gene annotation and other desired analyses. Insect genomes can be problematic to assemble, due to combinations of high polymorphism, inability to breed for genome homozygocity, and small physical sizes limiting the quantity of DNA able to be isolated from a single individual. Recent advances in sequencing technology and assembly strategies are enabling a revolution for insect genome reference sequencing and assembly. Here we review historical and new genome sequencing and assembly strategies, with a particular focus on their application to arthropod genomes. We highlight both the need to design sequencing strategies for the requirements of the assembly software, and new long-read technologies that are enabling a return to traditional assembly approaches. Finally, we compare and contrast very cost effective short read draft genome strategies with the long read approaches that although entailing additional cost, bring a higher likelihood of success and the possibility of archival assembly qualities approaching that of finished genomes.
Rhodococcus erythropolis is a worldwide-distributed actinobacterium that exhibits a remarkable metabolic versatility illustrated by its ability to degrade complex compounds, such as quorum-sensing signals N-acylhomoserine lactones (NAHLs), phenols, sterols and fuel derivatives. Because of its catabolic properties, R. erythropolis strains are proposed as anti-biofouling agents against NAHL-dependent biofilms, biocontrol agents against NAHL-emitting plant pathogens, and bioremediation agents in contaminated waters and soils. Here, we used the PacBio technology to resolve the complete genome sequence of the biocontrol strain R. erythropolis R138. Its genome consisted in a circular chromosome (6,236,862 bp), a linear plasmid pLRE138 (477,915 bp) and a circular plasmid pCRE138 (91,729 bp). In addition, draft genomes of five R. erythropolis strains were determined by Illumina technology and compared with the other five R. erythropolis genomes that are available in public databases: 5,825 common CDSs were present in all of the eleven analyzed genomes and represented up to 87 % of those identified in R. erythropolis R138. This study highlighted the high proportion of core-genome genes in R. erythropolis, but a high variability of the plasmid content. Key-metabolic pathways which are involved in the degradation of complex molecules, such as NAHLs and phenol, catechol and sterol derivatives are coded by the R. erythropolis core-genome.
Seaweeds are essential for marine ecosystems and have immense economic value. Here we present a comprehensive analysis of the draft genome of Saccharina japonica, one of the most economically important seaweeds. The 537-Mb assembled genomic sequence covered 98.5% of the estimated genome, and 18,733 protein-coding genes are predicted and annotated. Gene families related to cell wall synthesis, halogen concentration, development and defence systems were expanded. Functional diversification of the mannuronan C-5-epimerase and haloperoxidase gene families provides insight into the evolutionary adaptation of polysaccharide biosynthesis and iodine antioxidation. Additional sequencing of seven cultivars and nine wild individuals reveal that the genetic diversity within wild populations is greater than among cultivars. All of the cultivars are descendants of a wild S. japonica accession showing limited admixture with S. longissima. This study represents an important advance toward improving yields and economic traits in Saccharina and provides an invaluable resource for plant genome studies.
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