DOI: 10.5061/dryad.j6q573nqw
title: Reference genome and annotation for Teleopsis dalmanni

description: This dataset provides a reference genome assembly and sequencing data for
 Teleopsis dalmanni (stalk-eyed fly). T. dalmanni is an important
 model organism for the study of sexual selection, sexual conflicts, and
 selfish genetic elements; however, only more recently have high-quality
 genomes become more readily available for understanding the genetic basis
 of these processes.  Here, we present a whole genome assembly
 (three chromosomes with GFF annotation). The assembly was generated from
 PacBio HiFi reads from two runs (BAM, FASTQ, and FASTA formats) and
 Iso-Seq transcript data for annotation. The genome was assembled with
 HiFiasm, haplotigs removed with purge_dups, and scaffolds generated using
 publicly available chromatin conformation capture data. This data also
 showcases the use of the novel annotation method OMAnnotator that
 uses the OMA algorithm, utilising the evolutionary relationships among
 genes across species. 
description: # Reference genome and sequencing data for Teleopsis dalmanni
 [https://doi.org/10.5061/dryad.j6q573nqw](https://doi.org/10.5061/dryad.j6q573nqw) ## Description of the data and file structure Reference genome and sequencing data for Teleopsis dalmanni 
 
 **ST_FINAL.fa** Fasta file for three chromosomes 1,2, and X.  
 
 **ST_FINAL.gff** Genome annotation in gff format 
 
 **m64157e_210730_141553.hifi_reads.bam (8.41 GB)** HiFi reads from
 sequencing run *210730_141553* in BAM format.
 **m64157e_210730_141553.hifi_reads.fastq.gz (8.90 GB)**\ FASTQ reads for
 sequencing run *210730_141553 *in FASTQ format with sequences.
 **m64157e_210730_141553.hifi_reads.fasta.gz (4.43 GB)**\ FASTA version of
 the sequencing run *210730_141553*. **m64157e_211024_013127.hifi_reads.bam
 (4.93 GB)**\ HiFi reads from sequencing run *211024_013127* in BAM format.
 **m64157e_211024_013127.hifi_reads.fastq.gz (5.24 GB)**\ FASTQ reads of
 the sequencing run *210730_141553* .
 **m64157e_211024_013127.hifi_reads.fasta.gz (2.74 GB)**\ FASTA version of
 the sequencing run *210730_141553 *. 
 
 **Methods: Genome sequence** PacBio HiFi reads were generated from pooled
 female larvae. Reads were then assembled with HiFiasm [(Cheng et al.,
 2021)](https://www.zotero.org/google-docs/?ZJ81RP) before applying the
 purge_dups pipeline [(Guan et al.,
 2020)](https://www.zotero.org/google-docs/?WL9DOp). Contigs were
 scaffolded with chromatin conformation capture data previously produced by
 Reinhardt et al [(2023; ncbi BioSample
 SRX9103577) ](https://www.zotero.org/google-docs/?4xbdyt)with the Arima
 pipeline
 ([https://github.com/ArimaGenomics/mapping_pipeline](https://github.com/ArimaGenomics/mapping_pipeline)).  **Methods: Annotation** PacBio Iso-seq was generated from a mixture of adults and larvae. Reads were processed using the Isoseq3 pipeline  ([https://github.com/ylipacbio/IsoSeq3](https://github.com/ylipacbio/IsoSeq3)). The OMAnnotator pipeline was used to build a consensus annotation based on the homology of transcripts and features identified [(Bates et al., 2024;](https://www.zotero.org/google-docs/?b3VBFF) https://doi.org/10.1101/2024.12.04.626846[)](https://www.zotero.org/google-docs/?b3VBFF).