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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 Venn diagram showing the overlapping genes between B. pahangi and other similar species prior to filtering of Wolbachia genes. b Relative arrangements of B. pahangi genes and their orthologs on B. malayi. Forward and reverse strands are distinguished based on position (i.e., forward on top and reverse below). c A phylogenetic tree constructed based on B. pahangi and other sequenced genomes using single-copy orthologous genes. The different molecular clocks (i.e., divergence rates) might be explained by the body size or generation time hypotheses, which suggest that larger body size or longer generation time result in a slower molecular clock
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Fig2: a Venn diagram showing the overlapping genes between B. pahangi and other similar species prior to filtering of Wolbachia genes. b Relative arrangements of B. pahangi genes and their orthologs on B. malayi. Forward and reverse strands are distinguished based on position (i.e., forward on top and reverse below). c A phylogenetic tree constructed based on B. pahangi and other sequenced genomes using single-copy orthologous genes. The different molecular clocks (i.e., divergence rates) might be explained by the body size or generation time hypotheses, which suggest that larger body size or longer generation time result in a slower molecular clock

Mentions: Comparison between draft genome sequences of B. pahangi and those of B. malayi, C. briggsae [44], and C. elegans [45] was performed (Additional file 1: Table S4). We found that B. pahangi genome shows the highest sequence similarity to those of B. malayi. From the predicted B. pahangi genes, 90 % (8681 genes) appears to have orthologs (BLASTp cut-off: 10-5) in B. malayi, as compared to that in C. elegans (n = 7424; 77 %) and C. briggsae (n = 7271; 75 %). Overall, 6795 genes were found to be orthologous among all 4 species under comparison. Another 62 predicted B. pahangi genes were found to be shared among B. malayi and C. briggsae, and 1624 B. pahangi genes were shared exclusively with B. malayi. A total of 569 genes were predicted to be unique to B. pahangi (Fig. 2a). Via whole genome conserved synteny analysis using LASTZ pairwise genome alignment [19], we observed high rates of agreement upon comparison between B. pahangi and B. malayi genomes, with a genome coverage range of 70-75 % (Fig. 2b).Fig. 2


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 Venn diagram showing the overlapping genes between B. pahangi and other similar species prior to filtering of Wolbachia genes. b Relative arrangements of B. pahangi genes and their orthologs on B. malayi. Forward and reverse strands are distinguished based on position (i.e., forward on top and reverse below). c A phylogenetic tree constructed based on B. pahangi and other sequenced genomes using single-copy orthologous genes. The different molecular clocks (i.e., divergence rates) might be explained by the body size or generation time hypotheses, which suggest that larger body size or longer generation time result in a slower molecular clock
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: a Venn diagram showing the overlapping genes between B. pahangi and other similar species prior to filtering of Wolbachia genes. b Relative arrangements of B. pahangi genes and their orthologs on B. malayi. Forward and reverse strands are distinguished based on position (i.e., forward on top and reverse below). c A phylogenetic tree constructed based on B. pahangi and other sequenced genomes using single-copy orthologous genes. The different molecular clocks (i.e., divergence rates) might be explained by the body size or generation time hypotheses, which suggest that larger body size or longer generation time result in a slower molecular clock
Mentions: Comparison between draft genome sequences of B. pahangi and those of B. malayi, C. briggsae [44], and C. elegans [45] was performed (Additional file 1: Table S4). We found that B. pahangi genome shows the highest sequence similarity to those of B. malayi. From the predicted B. pahangi genes, 90 % (8681 genes) appears to have orthologs (BLASTp cut-off: 10-5) in B. malayi, as compared to that in C. elegans (n = 7424; 77 %) and C. briggsae (n = 7271; 75 %). Overall, 6795 genes were found to be orthologous among all 4 species under comparison. Another 62 predicted B. pahangi genes were found to be shared among B. malayi and C. briggsae, and 1624 B. pahangi genes were shared exclusively with B. malayi. A total of 569 genes were predicted to be unique to B. pahangi (Fig. 2a). Via whole genome conserved synteny analysis using LASTZ pairwise genome alignment [19], we observed high rates of agreement upon comparison between B. pahangi and B. malayi genomes, with a genome coverage range of 70-75 % (Fig. 2b).Fig. 2

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