Levipalatum texanum

Genome Assembly & Annotation

Assembly

The full assembly process is outline in Casasa et al., (2021). Paired-end reads between 150- and 500-bp in length were trimmed using Cutadapt and error corrected with Reckoner. To check insert size, a preliminary single-end assembly was created with Minia. SPAdes was then used to fully assemble the nuclear genome, and scaffolds that were identified as contamination, at low coverage (<1×), and < 500 bp in length were removed. PlasmidSPAdes was used to assemble the mitochondrial genome.

Annotation

The full annotation process is outlined in Casasa et al., (2021). The genome was annotated using the BRAKER pipeline. The BAM file created by aligning RNA-Seq reads to the genome with STAR was included in this process. The mitochondrial genomes were annotated using MITOS2 on the MITOS Web Server.

Downloads

• Genomic Sequence (FASTA)
• Hard-masked Genomic Sequence (FASTA)
• Soft-masked Genomic Sequence (FASTA)
• Annotations (GFF3)
• Proteins (FASTA)
• Full-length transcripts (FASTA)
• CDS transcripts (FASTA)

Tools

• Search for sequences in the genome and proteome using BLAST
• Work with lists of data using the WormBase ParaSite BioMart data-mining tool
• Programatically access WormBase ParaSite data using the REST API
• Predict the effects of variants using the Variant Effect Predictor

Key Publications

• Casasa S, Biddle JF, Koutsovoulos GD, Ragsdale EJ. Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks. Mol Biol Evol, 2021;38(2):331-343

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree