Brugia malayi

Genome Assembly & Annotation

Assembly

The B.malayi genome was first sequenced at the former TIGR institute and described by Ghedin et al (2007). In 2012 a new genome sequencing, assembly and curation project was conducted on the FR3 strain as a cooperative effort between WormBase and the University of Pittsburgh. An improvement of this assembly by including PacBio and optical mapping data was conducted in 2016, allowing the scaffolding of chromosomes as well as better representation of repetitive regions. This sequenced FR3 strain is available at the Filiarisis Research Reagent Center.

A publication covering the new assembly is in progress, and the consortium reserves itself the right of first publication.

Annotation

The gene structures are actively curated by WormBase.

Downloads

• Genomic Sequence (FASTA)
• Hard-masked Genomic Sequence (FASTA)
• Soft-masked Genomic Sequence (FASTA)
• Annotations (GFF3)
• Proteins (FASTA)
• Full-length transcripts (FASTA)
• CDS transcripts (FASTA)

Tools

• Search for sequences in the genome and proteome using BLAST
• Work with lists of data using the WormBase ParaSite BioMart data-mining tool
• Programatically access WormBase ParaSite data using the REST API
• Predict the effects of variants using the Variant Effect Predictor

Key Publications

• Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL. Draft genome of the filarial nematode parasite Brugia malayi. Science, 2007;317(5845):1756-1760

Resources

• The Blaxter Lab, Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh
• The CDC Foundation helps the Center for Disease Control and Prevention
• The World Health Organisation
• Filariasis Research Reagent Resource Center (FR3)
• Wolbachia endosymbiont strain TRS of Brugia malayi at Ensembl Bacteria

Picture credit: Mark Blaxter (Creative Commons BY-NC-SA 3.0)

Navigation

View karyotype

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression