BioProject PRJNA834627 | Data Source Academia Sinica | Taxonomy ID 269767
About Aphelenchoides besseyi
The foliar nematode Aphelenchoides besseyi, a.k.a. the rice white tip, infects more than 200 plant species in 35 genera including rice, wheat, soybeans and strawberries. This nematode is 0.4–0.8 mm in body size, has a life cycle of around 10–12 days and it can reproduce in extreme environments, making it hard to eliminate.
There are 3 alternative strains from this genome project for Aphelenchoides besseyi available in WormBase ParaSite: AORJ AORT APFT
Genome Assembly & Annotation
For this assembly, the Aphelenchoides pseudobesseyi VT strain was used, which was collected from the rice field of Linnei, Nantou and Hiroshima, Japan.
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. The training models for the prefiction were also based on the manual curation of 975 genes. Full details can be found on Lai, C.-K., et al., 2023
- 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
|Data Source||Academia Sinica|
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