Résumé
These files are part of the manuscript:The genome of the short-horned baronia (Baronia brevicornis), an endangered relict and key lineage in swallowtail butterfly evolutionAlba Marino 1,†, Eliette L. Reboud 1†, Emmanuelle Chevalier 1, Marie-Ka Tilak 1, Jorge Contreras-Garduño 2, Benoit Nabholz 1,3† and Fabien L. Condamine 1,*†1 Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France2 Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores, campus Morelia, Antigua Carretera a Pátzcuaro #8701, Col. Ex-Hacienda San José de la Huerta, 58190 Morelia, Michoacán, Mexico3 Institut Universitaire de France (IUF), Paris, France† These authors contributed equally.Genome assembly is available here : https://www.ncbi.nlm.nih.gov/nuccore/JASFAT000000000.1/Files descriptions:Baronia_brevicornis_FC897_final_version.fasta_masked.fasta : Masked genome assemblyBaronia_brevicornis_FC897_braker2.gtf : GTF file of the annotation performed with BRAKER2 pipelineBaronia_brevicornis_FC897_braker2.codingseq.fasta : CDS of the annotation performed with BRAKER2 pipelineBaronia_brevicornis_FC897_braker2.proteins.fasta : Proteins of the annotation performed with BRAKER2 pipelineBaronia_brevicornis_FC897_rnd3.all.maker.noseq.gff : GFF3 file of the annotation performed with MAKER pipelineBaronia_brevicornis_FC897_rnd3.all.maker.proteins.fasta : Proteins of the annotation performed with MAKER pipelineBaronia_brevicornis_FC897_rnd3.all.maker.transcripts.fasta : CDS of the annotation performed with MAKER pipelinecreateMaskFile.py is a python script to create mask files for MSMC2. Usage : python3 createMaskFile.py coverage_file.txt 15 100 contig_name output.bed.gz. The coverage_file.txt is create using "samtools depth" program.AlgnRM2Fasta : is a program to extract the alignment of TE sequences with their sequence consensus from RepeatMaskerNucleodite_diversity_coding_sequences_scripts.zip : Script and program compute the synonymous, non-synonymous and four-fold degenerated sites nucleotide diversity