Aphelenchoides bicaudatus

Genome Assembly & Annotation

Assembly

For this assembly, the Aphelenchoides bicaudatus Fsh strain was used, which was collected from ornamental nurseries of bird’s-nest fern in Taiwan and a strawberry field in Dali, Taichung.

According to Lai, C.-K., et al., 2023, raw Oxford Nanopore long-read sequencing reads were assembled using the flye (version 2.8.2) assembler. The assembly was corrected using racon (version 1.4.6) and medaka version 0.10.0. The assembly was further corrected using Illumina reads using pilon (version 1.22) with five iterations. The genome was reference-scaffolded based on this assembly using ragtag.

Annotation

RNA-sequencing (RNA-seq) data were aligned to the assembly and used to infer transcripts. The RNA-seq mappings were also used in braker to train species parameters and generate an initial set of annotations. Proteomes of Bursaphelenchus xylophilus and Caenorhabditis elegans were used as homology guides to pick the best transcripts for each putative locus using mikado and were also used to train MAKER2. Finally, MAKER2 was invoked to generate a final set of gene annotations. Full details can be found on Lai, C.-K., et al., 2023.

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

• Lai CK, Lee YC, Ke HM, Lu MR, Liu WA, Lee HH, Liu YC, Yoshiga T, Kikuchi T, Chen PJ, Tsai IJ. The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant-parasitic nematodes. Mol Ecol Resour, 2023;23(4):905-919

Navigation

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Genome Browser (Ensembl)

Example gene page

Example gene tree