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WormBase ParaSite HomeVersion: WBPS19 (WS291)-  Archive: WBPS18

Ptycholaimellus sp. GST1_10

BioProject PRJNA953805 | Data Source Academia Sinica | Taxonomy ID 3043725

About Ptycholaimellus sp. GST1_10

Ptycholaimellus gst110 is a free-living marine nematode from the family Chromadoridae

Genome Assembly & Annotation

Assembly

The full assembly process is described in Lee et al., (2023). The Flye assembler (ver. 2.9.1) was used to assemble the raw ONT reads. These were then polished by four iterations of Racon (ver. 1.4.11), followed by Medaka (ver. 1.2.0; option: -m r941_min_sup_g507 or r103_sup_g507). The consensus sequences were further corrected with Illumina reads using NextPolish(ver. 1.4.0), and haplotigs were removed using HaploMerger2 (ver. 20180603). Assemblies were mapped to the reference genome with minimap2 (option: -ax asm5). Raw Illumina reads were assembled using the Spades assembler (ver. v3.14.1; option: spades_sc).

Annotation

The full annotation process is described in Lee et al., (2023). Single-worm transcriptome reads were mapped to the corresponding genome assemblies using STAR (ver. 2.7.7a). The gene models were predicted using BRAKER2 (ver. 2.1.6; option: –etpmode) with proteomes and RNA-seq mappings as evidence hints. Transcript predictions were mapped to the reference genome using Minimap2 (-ax splice), converted to gff format and compared against the reference proteome using Gffcompare (ver. v0.11.2).

Key Publications

Assembly Statistics

AssemblyASM3024809v1, GCA_030248095.1
StrainGST1_10
Database VersionWBPS19
Genome Size219,745,496
Data SourceAcademia Sinica
Annotation Version2023-09-WormBase

Gene counts

Coding genes29,035
Gene transcripts29,035

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