DOI: 10.5061/dryad.xsj3tx9cq
title: The genome of the Xingu Scale-backed Antbird (Willisornis vidua nigrigula) reveals lineage-specific adaptations

description: Antbirds (Thamnophilidae) are a large neotropical family of passerine bird
 renowned for the ant-following foraging strategies of several members of
 this clade. The high diversity of antbirds provides ample opportunity for
 speciation studies, however these studies can be hindered by the lack of
 an annotated antbird reference genome. In this study, we produced a
 high-quality annotated reference genome for the
 Xingu Scale-backed Antbird (Willisornis vidua nigrigula) using
 10X Genomics Chromium linked-reads technology. The assembly is
 1.09 Gb, with a scaffold N50 of 12.1 Mb and 17,475 annotated
 protein coding genes. We compare the proteome of W. v.
 nigrigula to several other passerines, and produce annotations
 for two additional antbird genomes in order to identify genes under
 lineage-specific positive selection and gene families with evidence for
 significant expansions in antbirds. Several of these genes have functions
 potentially related to the lineage-specific traits of antbirds, including
 adaptations for thermoregulation in a humid tropical environment.
description: This dataset provides the genome assembly and annotation of
 Willisornis poecilinotus vidua from the manuscript "The genome of the
 common scale-backed Antbird (Willisornis poecilinotus) reveals
 lineage-specific adaptations". It contains the following
 files: 1) GFF format annotations of Willisornis vidua
 nigrigula, Hypocnemis ochrogyna, and Rhegmatorhina melanosticta
 These files are named
 "Willisornis_vidua.genome_annotation.gff",
 "Hypocnemis_ochrogyna.genome_annotation.gff", and
 "Rhegmatorhina_melanosticta.genome_annotation.gff"
 These GFF files contain annotation information for the locations
 of protein-coding genes in the genome, as well as locations of
 repeat-masked sequences. They also contain the
 genomic locations of alignments to known protein-coding genes used for
 protein prediction during the Maker2 pipeline. It
 also contains functional annotation information listing GO terms and
 functions predicted for the proteins by Interproscan. 
 It also contains the locations of raw ab-initio gene predictions
 (snap_masked and augustus_masked) which were used to produce the final set
 of protein predictions 2) Protein-coding
 gene annotations sequences, provided in fasta format for both the protein
 (Willisornis.proteins.fasta) and transcripts
 (Willisornis.transcripts.fasta) sequences for Willisornis, Rhegmatorhina,
 and Hypocnemis. Genes for Willisornis vidua
 nigrigula were named with the prefix "WilPoe" followed by a
 unique 5-digit number. The Gene identifier is followed by the name of the
 closest BLAST hit to known proteins in the Swiss-prot or Trembl
 database. 3) Curated transposable element
 library in fasta format:
 "Willisornis_curated_TE_library.fasta" 
 The curated elements are named with the prefix
 "Wilpoe" followed by a 3-digit unique number. This is followed
 by a "#" symbol, and then the name of the transposable element
 class, if identified. If identified below the level of class, this
 identity is given after a "/" symbol. The
 raw uncurated transposable element library is also provided as
 "Willisornis_uncurated_TE_library.fasta", but it should be used
 with caution as it contains sequences that were discarded and
 misclassifications that were corrected during curation.
 4) The pseudohaploid reference genome in compressed
 fasta.gz format:
 "Willisornis_vidua_nigrigula_JTW1144_700mill.fasta.gz". This is
 the genome sequenced used for annotation and in all analyses.
 5) All the code used to run the pipeline from genome assembly to
 analysis are provided in a series of markdown files with code and
 instructions explaining the code. Note that the scripts are kept as they
 were run in this project, and so paths to programs and folders are
 hard-coded and would need to be modified to run on a different computer or
 dataset. Steps of the pipeline are split into several
 pages detailing each step in order (steps can not run out of order as they
 use intermediate files of the previous step):
 1.1_Genome_Assembly_With_Supernova
 1.2_Genome_Quality_Assessment
 1.3_Genome_Size_Estimation
 2.0_Reference_protein_databases 2.1_Repeat
 Library Construction 2.2_Repeat_curation
 2.3_Repeat_analyses
 3.1.2_Reference_transcript_database
 3.2_Gene_Prediction_with_MAKER
 3.3_Protein_Functional_Annotation
 4.1_Obtaining_comparative_data
 4.1.2_Hypocnemis_and_Rhegmatorhina_Annotation
 4.2_Positive_selection
 4.3_Gene_Family_Expansions