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Draft genome of Brugia pahangi: high similarity between B. pahangi and B. malayi.

Lau YL, Lee WC, Xia J, Zhang G, Razali R, Anwar A, Fong MY - Parasit Vectors (2015)

Bottom Line: Nevertheless, 166 genes were considered to be unique to B. pahangi, which may be responsible for the distinct properties of B. pahangi as compared to other filarial nematodes.The reporting of B. pahangi draft genome contributes to genomic archive.Albeit with high similarity to B. malayi genome, the B. pahangi-unique genes found in this study may serve as new focus to study differences in virulence, vector selection and host adaptability among different Brugia spp.

View Article: PubMed Central - PubMed

Affiliation: Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. lauyeeling@um.edu.my.

ABSTRACT

Background: Efforts to completely eradicate lymphatic filariasis from human population may be challenged by the emergence of Brugia pahangi as another zoonotic lymphatic filarial nematode. In this report, a genomic study was conducted to understand this species at molecular level.

Methods: After blood meal on a B. pahangi-harbouring cat, the Aedes togoi mosquitoes were maintained to harvest infective third stage larvae, which were then injected into male Mongolian gerbils. Subsequently, adult B. pahangi were obtained from the infected gerbil for genomic DNA extraction. Sequencing and subsequently, construction of genomic libraries were performed. This was followed by genomic analyses and gene annotation analysis. By using archived protein sequences of B. malayi and a few other nematodes, clustering of gene orthologs and phylogenetics were conducted.

Results: A total of 9687 coding genes were predicted. The genome of B. pahangi shared high similarity to that B. malayi genome, particularly genes annotated to fundamental processes. Nevertheless, 166 genes were considered to be unique to B. pahangi, which may be responsible for the distinct properties of B. pahangi as compared to other filarial nematodes. In addition, 803 genes were deduced to be derived from Wolbachia, an endosymbiont bacterium, with 44 of these genes intercalate into the nematode genome.

Conclusions: The reporting of B. pahangi draft genome contributes to genomic archive. Albeit with high similarity to B. malayi genome, the B. pahangi-unique genes found in this study may serve as new focus to study differences in virulence, vector selection and host adaptability among different Brugia spp.

No MeSH data available.


Related in: MedlinePlus

a Plot showing content and sequencing depth. The GC content for B. pahangi is high at the average depth of in between 10 to 180 with GC content value in range of 0.2 to 0.4. b Graph showing GC content distributions within genomes of different species under study. We used 500 bp bins (with 250 bp overlap) sliding along the genome. The highest percent of bins for B. pahangi is in between 5 to 6 % with GC content of 0.3. c Graph showing sequence depth distribution. The filtered reads were aligned onto the assembly genome sequence using SOAP. The percentage of bases is increasing from the starting point up till sequencing depth of 20-29 with optimal percentage of bases of 6 %, and decreases from this point until the sequencing depth of 60-69. From that point, the percentage of bases is stable until sequencing point 80-89 (before falling dramatically). d Plots showing comparison of GC content between different genomes
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Fig1: a Plot showing content and sequencing depth. The GC content for B. pahangi is high at the average depth of in between 10 to 180 with GC content value in range of 0.2 to 0.4. b Graph showing GC content distributions within genomes of different species under study. We used 500 bp bins (with 250 bp overlap) sliding along the genome. The highest percent of bins for B. pahangi is in between 5 to 6 % with GC content of 0.3. c Graph showing sequence depth distribution. The filtered reads were aligned onto the assembly genome sequence using SOAP. The percentage of bases is increasing from the starting point up till sequencing depth of 20-29 with optimal percentage of bases of 6 %, and decreases from this point until the sequencing depth of 60-69. From that point, the percentage of bases is stable until sequencing point 80-89 (before falling dramatically). d Plots showing comparison of GC content between different genomes

Mentions: We sequenced the B. pahangi genome at 168-fold coverage (Additional file 1: Tables S1 and S2) and produced a final draft assembly of 85.4 Mb and 1.4 Mb of bacterial (Wolbachia) chromosomal genome sequences (N50 = 155.8 kb; 29,435 scaffolds) (Table 1). The mean GC-content of the B. pahangi genome was 28.5 % (Fig. 1). A Core Eukaryotic Genes Mapping Approach (CEGMA) score of 94.32 % was detected. The generated draft genome was estimated to contain a repeat content of 5.9 % (~4.9 Mb of DNA), which includes 0.924 % DNA transposons, 0.466 % LINE, 0.009 % SINE, 0.774 % LTR, 0.917 % unclassified dispersed elements and 0.008 % other elements (Additional file 1: Table S3). A total of 476,584 LTR, 369,943 LINE, and 7123 SINE were identified across the whole draft genome (Additional file 1: Table S3). In addition, a total of 9687 protein-encoding genes were predicted. The average sizes of exons and introns were found to be 153 bp and 345 bp respectively, with an average of 5.9 exons per gene (Additional file 1: Table S4).Table 1


Draft genome of Brugia pahangi: high similarity between B. pahangi and B. malayi.

Lau YL, Lee WC, Xia J, Zhang G, Razali R, Anwar A, Fong MY - Parasit Vectors (2015)

a Plot showing content and sequencing depth. The GC content for B. pahangi is high at the average depth of in between 10 to 180 with GC content value in range of 0.2 to 0.4. b Graph showing GC content distributions within genomes of different species under study. We used 500 bp bins (with 250 bp overlap) sliding along the genome. The highest percent of bins for B. pahangi is in between 5 to 6 % with GC content of 0.3. c Graph showing sequence depth distribution. The filtered reads were aligned onto the assembly genome sequence using SOAP. The percentage of bases is increasing from the starting point up till sequencing depth of 20-29 with optimal percentage of bases of 6 %, and decreases from this point until the sequencing depth of 60-69. From that point, the percentage of bases is stable until sequencing point 80-89 (before falling dramatically). d Plots showing comparison of GC content between different genomes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4562187&req=5

Fig1: a Plot showing content and sequencing depth. The GC content for B. pahangi is high at the average depth of in between 10 to 180 with GC content value in range of 0.2 to 0.4. b Graph showing GC content distributions within genomes of different species under study. We used 500 bp bins (with 250 bp overlap) sliding along the genome. The highest percent of bins for B. pahangi is in between 5 to 6 % with GC content of 0.3. c Graph showing sequence depth distribution. The filtered reads were aligned onto the assembly genome sequence using SOAP. The percentage of bases is increasing from the starting point up till sequencing depth of 20-29 with optimal percentage of bases of 6 %, and decreases from this point until the sequencing depth of 60-69. From that point, the percentage of bases is stable until sequencing point 80-89 (before falling dramatically). d Plots showing comparison of GC content between different genomes
Mentions: We sequenced the B. pahangi genome at 168-fold coverage (Additional file 1: Tables S1 and S2) and produced a final draft assembly of 85.4 Mb and 1.4 Mb of bacterial (Wolbachia) chromosomal genome sequences (N50 = 155.8 kb; 29,435 scaffolds) (Table 1). The mean GC-content of the B. pahangi genome was 28.5 % (Fig. 1). A Core Eukaryotic Genes Mapping Approach (CEGMA) score of 94.32 % was detected. The generated draft genome was estimated to contain a repeat content of 5.9 % (~4.9 Mb of DNA), which includes 0.924 % DNA transposons, 0.466 % LINE, 0.009 % SINE, 0.774 % LTR, 0.917 % unclassified dispersed elements and 0.008 % other elements (Additional file 1: Table S3). A total of 476,584 LTR, 369,943 LINE, and 7123 SINE were identified across the whole draft genome (Additional file 1: Table S3). In addition, a total of 9687 protein-encoding genes were predicted. The average sizes of exons and introns were found to be 153 bp and 345 bp respectively, with an average of 5.9 exons per gene (Additional file 1: Table S4).Table 1

Bottom Line: Nevertheless, 166 genes were considered to be unique to B. pahangi, which may be responsible for the distinct properties of B. pahangi as compared to other filarial nematodes.The reporting of B. pahangi draft genome contributes to genomic archive.Albeit with high similarity to B. malayi genome, the B. pahangi-unique genes found in this study may serve as new focus to study differences in virulence, vector selection and host adaptability among different Brugia spp.

View Article: PubMed Central - PubMed

Affiliation: Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. lauyeeling@um.edu.my.

ABSTRACT

Background: Efforts to completely eradicate lymphatic filariasis from human population may be challenged by the emergence of Brugia pahangi as another zoonotic lymphatic filarial nematode. In this report, a genomic study was conducted to understand this species at molecular level.

Methods: After blood meal on a B. pahangi-harbouring cat, the Aedes togoi mosquitoes were maintained to harvest infective third stage larvae, which were then injected into male Mongolian gerbils. Subsequently, adult B. pahangi were obtained from the infected gerbil for genomic DNA extraction. Sequencing and subsequently, construction of genomic libraries were performed. This was followed by genomic analyses and gene annotation analysis. By using archived protein sequences of B. malayi and a few other nematodes, clustering of gene orthologs and phylogenetics were conducted.

Results: A total of 9687 coding genes were predicted. The genome of B. pahangi shared high similarity to that B. malayi genome, particularly genes annotated to fundamental processes. Nevertheless, 166 genes were considered to be unique to B. pahangi, which may be responsible for the distinct properties of B. pahangi as compared to other filarial nematodes. In addition, 803 genes were deduced to be derived from Wolbachia, an endosymbiont bacterium, with 44 of these genes intercalate into the nematode genome.

Conclusions: The reporting of B. pahangi draft genome contributes to genomic archive. Albeit with high similarity to B. malayi genome, the B. pahangi-unique genes found in this study may serve as new focus to study differences in virulence, vector selection and host adaptability among different Brugia spp.

No MeSH data available.


Related in: MedlinePlus