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

Microlaimidae sp. YZB2_3

BioProject PRJNA953805 | Data Source Academia Sinica | Taxonomy ID 3043722

About Microlaimidae sp. YZB2_3

Microlaimidae yzb23 is a species from the family microlaimidae. These are nematodes belonging to the order Desmodorida.

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

AssemblyASM3024817v1, GCA_030248175.1
StrainYZB2_3
Database VersionWBPS19
Genome Size540,312,977
Data SourceAcademia Sinica
Annotation Version2023-09-WormBase

Gene counts

Coding genes27,483
Gene transcripts27,483

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