Supporting files generated during the genome project of Baronia brevicornis from "The genome of the short-horned baronia (Baronia brevicornis), an endangered relict and key lineage in swallowtail butterfly evolution"

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:<br>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

本数据集隶属于研究论文：《短角凤蝶（Baronia brevicornis）的基因组——一种濒危孑遗物种，亦是凤蝶演化历程中的关键支系》
作者：Alba Marino 1,†, Eliette L. Reboud 1†, Emmanuelle Chevalier 1, Marie-Ka Tilak 1, Jorge Contreras-Garduño 2, Benoit Nabholz 1,3† 与 Fabien L. Condamine 1,*†，其中†表示作者贡献均等，* 为通讯作者
单位：
1 蒙彼利埃进化科学研究所（法国蒙彼利埃大学 | 法国国家科学研究中心 | 法国发展研究院 | 法国高等研究实践学院），欧仁·巴塔永广场，34095 蒙彼利埃，法国
2 墨西哥国立自治大学高等研究学院莫雷利亚分校，安提瓜·帕茨夸罗公路#8701，圣何塞德瓦尔特前庄园社区，58190 莫雷利亚，米却肯州，墨西哥
3 法国大学研究所（IUF），巴黎，法国
基因组组装数据可通过以下链接获取：https://www.ncbi.nlm.nih.gov/nuccore/JASFAT000000000.1/
文件说明如下：
Baronia_brevicornis_FC897_final_version.fasta_masked.fasta：经重复序列屏蔽的基因组组装文件
Baronia_brevicornis_FC897_braker2.gtf：通过BRAKER2流程完成的基因组注释GTF（Gene Transfer Format）文件
Baronia_brevicornis_FC897_braker2.codingseq.fasta：BRAKER2流程注释得到的编码序列（CDS, Coding Sequence）文件
Baronia_brevicornis_FC897_braker2.proteins.fasta：BRAKER2流程注释得到的蛋白质序列文件
Baronia_brevicornis_FC897_rnd3.all.maker.noseq.gff：通过MAKER流程完成的基因组注释GFF3（General Feature Format Version 3）文件
Baronia_brevicornis_FC897_rnd3.all.maker.proteins.fasta：MAKER流程注释得到的蛋白质序列文件
Baronia_brevicornis_FC897_rnd3.all.maker.transcripts.fasta：MAKER流程注释得到的编码序列（CDS）文件
createMaskFile.py：用于为MSMC2生成屏蔽文件的Python脚本。使用方法：python3 createMaskFile.py coverage_file.txt 15 100 contig_name output.bed.gz。其中coverage_file.txt可通过"samtools depth"工具生成。
AlgnRM2Fasta：一款可从RepeatMasker结果中提取转座因子（TE, Transposable Element）序列与其序列共识联配结果的工具
Nucleodite_diversity_coding_sequences_scripts.zip：用于计算同义替换位点、非同义替换位点及四倍简并位点核苷酸多样性的脚本与程序