Reference target files for Species delimitation and diversification of the Doum palms (Hyphaene; Arecaceae) in Africa

The file PhyloPalms_loci_renamed.fasta was obtained by combining the palm reference sequences used to develop the baits to capture 176 loci as described in Heyduk et al 2016 with the Elaeis guineensis reference sequences used to develop the baits to capture 793 other loci selected to be part of the PhyloPalms kit described in Loiseau et al., 2019. It is build to be used with the program Hybpiper (Johnson et al. 2016). The PhyloPalms_Exons300_and_Heyduk.fasta file was obtained by removing exons <300 bp from the PhyloPalm references included in the PhyloPalms_loci_renamed.fasta file. These files were communicated by Sidonie Bellot. The New_ref.fasta was generated after the first run of Hybpiper (using the file PhyloPalms_loci_renamed.fasta) by selecting the longest exonic contig retrieved for each locus for the Hyphaene species and for the outgroup and was used as a reference in a second run of Hybpiper.文件PhyloPalms_loci_renamed.fasta的构建方式为：将Heyduk等人2016年研究中，用于开发捕获176个基因座（locus，复数形式为loci）的捕获探针的棕榈科参考序列，与Loiseau等人2019年报道的PhyloPalms试剂盒中选定的、用于开发捕获其余793个基因座的捕获探针的油棕（Elaeis guineensis）参考序列进行合并。该文件专为与Hybpiper工具（Johnson等人2016年开发）配合使用而构建。 文件PhyloPalms_Exons300_and_Heyduk.fasta的构建方式为：从PhyloPalms_loci_renamed.fasta文件包含的PhyloPalms参考序列中，移除长度小于300碱基对（base pair，缩写bp）的外显子（exon）区域。 上述文件由Sidonie Bellot提供。 文件New_ref.fasta的生成流程为：首次使用PhyloPalms_loci_renamed.fasta运行Hybpiper后，针对酒椰属（Hyphaene）物种及外类群的每个基因座，选取其检索到的最长外显子重叠群（contig），以此作为参考序列开展第二次Hybpiper运行。