Necator americanus

Genome Assembly & Annotation

Assembly

The N. americanus genome was sequenced by the Mitreva laboratory at the Genome Institute of Washington University, as described by Tang et al (2014).

Annotation

The gene predictions for this assembly were drastically updated in WBPS17 by Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, as described by Logan et al (2020). Gene models were generated using the MAKER pipeline. Publicly available RNASeq data, protein sequences of related species from SwissProt UniRef100 and WormBase ParaSite, previously generated models by Tang et. al. and ab initio gene predictions were provided to MAKER and BRAKER as further evidence. Final gene models were created using GeneMark and Augustus within BRAKER.

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

• Tang YT, Gao X, Rosa BA, Abubucker S, Hallsworth-Pepin K, Martin J, Tyagi R, Heizer E, Zhang X, Bhonagiri-Palsikar V, Minx P, Warren WC, Wang Q, Zhan B, Hotez PJ, Sternberg PW, Dougall A, Gaze ST, Mulvenna J, Sotillo J, Ranganathan S, Rabelo EM, Wilson RW, Felgner PL, Bethony J, Hawdon JM, Gasser RB, Loukas A, Mitreva M. Genome of the human hookworm Necator americanus. Nat Genet, 2014;46(3):261-269
• Logan J, Pearson MS, Manda SS, Choi YJ, Field M, Eichenberger RM, Mulvenna J, Nagaraj SH, Fujiwara RT, Gazzinelli-Guimaraes P, Bueno L, Mati V, Bethony JM, Mitreva M, Sotillo J, Loukas A. Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms. PLoS Negl Trop Dis, 2020;14(5):e0008237

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression