Data for Cardoni et al. (2021): High-Throughput Sequencing of 5S-IGS rDNA in Fagus L.

Data dump of and supplement to <b>Cardoni et al. (2021)</b> High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species. <i>bioRxiv</i>. https://doi.org/10.1101/2021.02.26.433057<br> <br>This fileset reports intra-/inter-genomic variation of the nuclear-encoded ribosomal 5S region in <i>Fagus</i> (beech). We used a multi-copy, potentially multi-locus marker, the non-transcribed intergenic spacer (IGS) of the 5S nuclear ribosomal DNA, and high-throughput target sequencing to address taxonomy, diversity, and evolution of the <i>F. crenata – F. sylvatica</i> s.str. lineage, and including <i>F. japonica</i> as outgroup. The collected data detail the distribution of divergent main 5S sequence types in the studied species pointing to deep polymorphism (allopolyploid origins), incomplete lineage sorting and repeated phases of reticulation. <br><br>The fileset includes:<br><b>Graphical abstract</b>: <br><i>5S_IGS...png</i>—Doodle summarising results of the study and distribution of sampled 5S-IGS variants.<i>GC_length...png</i>—Violin and scatterplots of the GC content and length of 5S-IGS amplicons, sorted by samples and sequence major types.<br><b>Data dump</b><i><br></i><i>ODA.zip</i>—Zipped online data archive prodiving used phylogenetic data and analysis files. See archive’s ReadMe.txt for content and archive structure.<br><b>Supplementary information</b><br>Also included are Cardoni et al. (2021) supplementary files S1–S4, which provide extended materials, results and discussion (<b>File S1; PDF</b>); basic information about samples, obtained HTS reads, an annotated lists for the 4,693 variants with an abundance of ≥ 4 summarised also as Pivot tables (<b>File S2, spread-sheet XLSX</b>; optimised for and using Excel autoformatting); graphical representation of the EPA analysis of 4007 5S-IGS variants with a total abundance &lt; 25 (<b>File S3, PDF</b>); and a fully annotated alignment of select-sequence subset in tabulated, graphically enhanced form (<b>File S4, spread-sheet XLSX</b>, includes colouration).<br>