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Aphelenchoides bicaudatus

BioProject PRJNA834627 | Data Source Academia Sinica | Taxonomy ID 293665

About Aphelenchoides bicaudatus

A. bicaudatus has previously been considered a primarily mycophagous species and is known to feed on mushroom mycelium. However, it has also been found living on buds and leaves of crops and plants.

Genome Assembly & Annotation


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.


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.

Key Publications

Assembly Statistics

AssemblyAbicaudatus.fasta, GCA_024699845.1
Database VersionWBPS19
Genome Size46,428,382
Data SourceAcademia Sinica
Annotation Version2022-08-WormBase

Gene counts

Coding genes10,675
Gene transcripts11,699

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