File Name: whole-genome random sequencing and assembly of haemophilus influenzae rd .zip
Metrics details. Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease. High-throughput DNA sequencing was used to investigate differences in genome content within this species.
Anaplasma marginale is the main etiologic agent of bovine anaplasmosis, and it is extensively distributed worldwide. We have previously reported the first genome sequence of a Mexican strain of A. We found that the genome average size is 1. The genomic comparison reveals that most of the A.
The genomic information contained in the four draft genomes of A. Bovine anaplasmosis is an infectious, tick-borne disease caused mainly by Anaplasma marginale ; typical signs include anemia, fever, abortion, weight loss, decreased milk production, jaundice, and potentially death. Although a sick bovine may recover when antibiotics are administered, it usually remains as a carrier for life, being a risk of infection for susceptible cattle.
Anaplasma marginale is an obligate intracellular Gram-negative bacterium with a genetic composition that is highly diverse among geographical isolates [ 1 ]. Currently, there are no fully effective vaccines against bovine anaplasmosis; therefore, the economic losses due to the disease are present.
Whole-genome sequencing WGS is an applicable tool for many pathogenic bacterial studies since , when the first bacterial genomes were determined [ 2 , 3 ]. Up to date, there are several genomes reported from A. New data could be useful for focusing in alternative antigens that induce specific and protective responses against bovine anaplasmosis.
In this work, we present draft genomes from four Anaplasma marginale Mexican strains. In addition, a first approach for comparative analyses between them and Brazilian, Australian, and North American strains is shown.
In order to advance in the identification of potential vaccine molecules, pathogenicity, transmission and infection mechanisms, and genetic diversity of Anaplasma marginale , further analyses are necessary. The resulting paired-end reads were de novo assembled using the SPAdes version 3.
The gene sequence datasets of Mexican strains were compared to 13 downloaded gene sequence datasets of A. Alignment sequences per genome were concatenated using a Python script. The jModelTest v2. Phylogenetic tree was inferred based on a maximum likelihood method using the PhyML v3. The phylogenetic tree was visualized and edited using the FigTree v1. The presence of large-scale evolutionary events, such as rearrangement and inversion of genomic segments, was detected by aligning the ordered contigs of the four Mexican strains and the genomes of Florida, Dawn, Gypsy Plains, Jaboticabal and Palmeira strains GenBank accession numbers CP Maries GenBank accession number CP The percentage of GC values for Mexican strains is very similar to that for the reference strain A.
Maries Other genomic characteristics of each strain are shown in Table 1. Maries GenBank accession CP We compared the four Mexican draft genomes of A. In Figure 1 , the comparative genomics is shown. Although most of the genomes are highly conserved, the Dawn and Gypsy Plains strains showed some differences from the Mexican, North American, and Brazilian strains.
We randomly selected fourteen ORFs found in the genomic annotation predicted as membrane proteins, and then, we located them in the genomes; as observed, most of these proteins are conserved in all genomes Figure 2. The genome synteny of 11 A.
In addition, the genome synteny of A. In general, the structure of A. So far, only one draft genome of a Mexican strain of A. The number of Genes and CDS is very similar in the four strains. In fact, in the genome annotation, using the different subsystem classification of RAST server, we identified genes related to cell wall and capsule, virulence, disease and defense, membrane transport, and protein and DNA metabolism, among others.
In the virulence, disease, and defense categories, we found genes associated with the cobalt-zinc-cadmium resistance, fluoroquinolone resistance, cooper homeostasis, and beta lactamase. Mycobacterium operon is present in several species, including Mycobacterium tuberculosis , Streptococcus pneumoniae , Bartonella bovis , and Streptococcus suis , among other animal and plant pathogens [ 23 — 25 ].
In the stress response category, we found genes associated with oxidative stress, cold shock, heat shock, periplasmic stress response, and detoxification. For most of the obligate intracellular bacteria, the presence of peptidoglycan is not necessarily needed to maintain the integrity of the bacterial cell.
An interesting feature of A. In alphaproteobacteria, the role of nitrogen metabolism may be essential for full virulence [ 27 ]. The phylogeny analysis indicates that Mexican strains are more related to Brazilian strains than to North American ones. The genomic comparison of the strains reveals the high percent of identity between A.
The report of four draft genomes of A. Still, more genomic analyses are needed to complete the molecular landscape of this pathogen. We present here, the genomic report and analyses of four Mexican strains of A. So far, only one genome of a Mexican strain has been reported; with this contribution, we compare our results with information of strains from the USA, Brazil, and Australia and provide more information of this pathogen.
This is an open access article distributed under the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Journal overview. Special Issues. Academic Editor: Marco Gerdol. Received 30 Oct Revised 21 Jan Accepted 06 Mar Published 14 Apr Abstract Anaplasma marginale is the main etiologic agent of bovine anaplasmosis, and it is extensively distributed worldwide. Introduction Bovine anaplasmosis is an infectious, tick-borne disease caused mainly by Anaplasma marginale ; typical signs include anemia, fever, abortion, weight loss, decreased milk production, jaundice, and potentially death.
Materials and Methods 2. Genome Synteny Analysis The presence of large-scale evolutionary events, such as rearrangement and inversion of genomic segments, was detected by aligning the ordered contigs of the four Mexican strains and the genomes of Florida, Dawn, Gypsy Plains, Jaboticabal and Palmeira strains GenBank accession numbers CP Results 3. Table 1. Genomic statistics of the four draft genomes of Mexican strains. Strain MEX MEX MEX MEX Cofactors, vitamins, prosthetic groups, pigments Cell wall and capsule 37 37 37 37 Virulence, disease, and defense 17 18 18 17 Potassium metabolism 3 3 3 3 Miscellaneous 4 4 4 4 Phages, prophages, transposable elements, plasmids 1 1 1 1 Membrane transport 13 13 14 13 Iron acquisition and metabolism 3 3 3 3 RNA metabolism 52 50 52 50 Nucleosides and nucleotides 42 46 42 43 Protein metabolism Cell division and cell cycle 24 24 26 24 Regulation and cell signaling 1 1 1 1 DNA metabolism 51 52 46 49 Fatty acids, lipids, and isoprenoids 54 56 54 56 Nitrogen metabolism 5 5 5 5 Dormancy and sporulation 1 1 1 1 Respiration 61 61 60 69 Stress response 26 26 26 26 Amino acids and derivatives 51 51 51 51 Sulfur metabolism 4 4 4 4 Phosphorus metabolism 9 9 9 9 Carbohydrates 41 43 45 Table 2.
Figure 1. The tree shows that Mexican strains of the A. The phylogenetic tree was obtained using the PhyML v3. GenBank accession numbers of the genomes are shown in square brackets.
Bootstrap values are displayed in the nodes. Figure 2. Circular comparative genomic map between five Mexican strains with six strains of A. The innermost ring black represents the A. Rings represent the A.
The outermost ring highlights 10 genes red arrows and numbers that are highly conserved in the genomes. The annotated function on the RAST server of the 10 proteins is shown on the left side. Figure 3. Genome synteny of A.
In general, a highly conserved structure is observed in all genomes, with the exception of Mexican strains that show rearrangements and inversions along the genome sequences. References R.
Amaro-Estrada, and S. Fleischmann, M. Adams, O. White et al. Fraser, J. Gocayne, O. Agnes, K. Brayton, M.
LaFollett, J. Norimine, W. Brown, and G. Brown, D. Zhu, V. Shkap et al. Ducken, W. Alperin et al. Lopez, G. Palmer, K.
Double-barreled DB data have been widely used for the assembly of large genomes. Based on the experience of building the whole-genome working draft of Oryza sativa L. Indica , we present here the prevailing and improved uses of DB data in the assembly procedure and report on novel applications during the following data-mining processes such as acquiring precise insert fragment information of each clone across the genome, and a new kind of low-cost whole-genome microarray. With the increasing number of organisms being sequenced, we believe that DB data will play an important role both in other assembly procedures and in future genomic studies. This is a preview of subscription content, access via your institution.
Whole genome sequencing of bacteria has become daily routine in many fields. Advances in DNA sequencing technologies and continuously dropping costs have resulted in a tremendous increase in the amounts of available sequence data. However, comprehensive in-depth analysis of the resulting data remains an arduous and time-consuming task.
Skip navigation. The Human Genome Project HGP was an international scientific effort to sequence the entire human genome , that is, to produce a map of the base pairs of DNA in the human chromosomes, most of which do not vary among individuals. Scientists hypothesized that mapping and sequencing the human genome would facilitate better theories of human development, the genetic causes and predispositions for a number of diseases, and individualized medicine.
The human genome project is entering its decisive final phase, in which the genome sequence will be determined in large-scale efforts in multiple laboratories worldwide. A number of sequencing groups are in the process of scaling up their throughput; over the next few years they will need to attain a collective capacity approaching half a gigabase per year to complete the 3-Gb genome sequence by the target date of At present, all contributing groups are using a clone-by-clone approach, in which mapped bacterial clones typically 40— kb in size from known chromosomal locations are sequenced to completion. Among other advantages, this permits a variety of alternative sequencing strategies and methods to be explored independently without redundancy of effort. Although it is not too late to consider implementing a different approach, any such approach must have as high a probability of success as the current one and offer significant advantages such as decreased cost.
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