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

Mesodorylaimus sp. YZB2_4

BioProject PRJNA953805 | Data Source Academia Sinica | Taxonomy ID 3043728

About Mesodorylaimus sp. YZB2_4

Mesodorylaimus sp. YZB2_4 is a free-living nematode.

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

AssemblyASM3024829v1, GCA_030248295.1
StrainYZB2_4
Database VersionWBPS19
Genome Size142,543,121
Data SourceAcademia Sinica
Annotation Version2023-08-WormBase

Gene counts

Coding genes22,630
Gene transcripts22,630

Learn more about this widget in our help section

This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh