Comparative genomic analysis of Mycoplasma anatis strains
Qi Zhou,Kaijie Mai,Dehong Yang,Junfa Liu,Zhuanqiang Yan,Cuifen Luo,Yangtong Tan,Sheng Cao,Qingfeng Zhou,Li Chen,Feng Chen +10 more
TL;DR: Wang et al. as discussed by the authors reported the structure and function of the pan-genome of Mycoplasma anatis, which may provide a valuable genetic basis for many aspects of future research on the pathogens of waterfowl.
read more
Abstract: The Gram-negative intracellular bacterium Mycoplasma anatis is a pathogen of respiratory infectious diseases in ducks and has caused significant economic losses in the poultry industry. This study, as the first report of the structure and function of the pan-genome of Mycoplasma anatis, may provide a valuable genetic basis for many aspects of future research on the pathogens of waterfowl. We sequenced the whole genomes of 15 Mycoplasma anatis isolated from ducks in China. Draft genome sequencing was carried out and whole-genome sequencing was performed by the sequencers of the PacBio Sequel and an IonTorrent Personal Genome Machine (PGM). Then the common genic elements of protein-coding genes, tRNAs, and rRNAs of Mycoplasma anatis genomes were predicted by using the pipeline Prokka v1.13.7. To investigate homologous protein clusters across Mycoplasma anatis genomes, we adopted Roary v3.13.0 to cluster orthologous genes (OGs) based on the following criteria. We obtained one complete genome and 14 genome sketches. Microbial mobile genetic element analysis revealed the distribution of insertion sequences (IS30, IS3, and IS1634), prophage regions, and CRISPR arrays in the genome of Mycoplasma anatis. Comparative genomic analysis decoded the genetic components and functional classification of the pan-genome of Mycoplasma anatis that comprised 646 core genes, 231 dispensable genes and among them 110 was strain-specific. Virulence-related gene profiles of Mycoplasma anatis were systematically identified, and the products of these genes included bacterial ABC transporter systems, iron transport proteins, toxins, and secretion systems. A complete virulence-related gene profile of Mycoplasma anatis has been identified, most of the genes are highly conserved in all strains. Sequencing results are relevant to the molecular mechanisms of drug resistance, adaptive evolution of pathogens, population structure, and vaccine development.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Characterization of atypical Mycoplasma anserisalpingitidis strains.
Áron B. Kovács,Enikő Wehmann,Dénes Grózner,Krisztina Bali,Edina Nemesházi,Veronika Hrivnák,Chris J. Morrow,Krisztián Bányai,Zsuzsa Kreizinger,Miklós Gyuranecz +9 more
TL;DR: In this article , the authors compared the whole genomes of five atypical M. anserisalpingitidis strains originating from China, Vietnam and Hungary, with the rest of the collection.
1
Epidemiological and genomic characteristics of global mcr-positive Escherichia coli isolates
TL;DR: In this article , the global genomic epidemiology of E. coli isolates carrying mobilized colistin resistance (mcr) genes, providing information to assist in infection and prevention.
References
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Trimmomatic: a flexible trimmer for Illumina sequence data
TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
57.9K
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich,Sergey Nurk,Dmitry Antipov,Alexey Gurevich,Mikhail Dvorkin,Alexander S. Kulikov,Valery M. Lesin,Sergey I. Nikolenko,Son Pham,Andrey D. Prjibelski,Alexey V. Pyshkin,Alexander Sirotkin,Nikolay Vyahhi,Glenn Tesler,Max A. Alekseyev,Pavel A. Pevzner +15 more
TL;DR: SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies.
IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies
TL;DR: It is shown that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented and found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space.
21.8K
Prokka: Rapid Prokaryotic Genome Annotation
TL;DR: Prokka is introduced, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer, and produces standards-compliant output files for further analysis or viewing in genome browsers.