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

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posted on 2021-03-01, 10:40 authored by Simone Cardoni, Roberta PireddaRoberta Piredda, Thomas DenkThomas Denk, Guido GrimmGuido Grimm, Aristotelis C. PapageorgiouAristotelis C. Papageorgiou, Ernst-Detlef Schulze, Anna Scoppola, Parvin Salehi Shanjani, Yoshihisa Suyama, Nobuhiro Tomaru, James R.P. Worth, Marco Cosimo SimeoneMarco Cosimo Simeone
Data dump of and supplement to Cardoni et al. (2021) High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species. bioRxiv.

This fileset reports intra-/inter-genomic variation of the nuclear-encoded ribosomal 5S region in Fagus (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 F. crenata – F. sylvatica s.str. lineage, and including F. japonica 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.

The fileset includes:

Graphical abstract:
5S_IGS...png—Doodle summarising results of the study and distribution of sampled 5S-IGS variants.
GC_length...png—Violin and scatterplots of the GC content and length of 5S-IGS amplicons, sorted by samples and sequence major types.

Data dump—Zipped online data archive prodiving used phylogenetic data and analysis files. See archive’s ReadMe.txt for content and archive structure.

Supplementary information
Also included are Cardoni et al. (2021) supplementary files S1–S4, which provide extended materials, results and discussion (File S1; PDF); 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 (File S2, spread-sheet XLSX; optimised for and using Excel autoformatting); graphical representation of the EPA analysis of 4007 5S-IGS variants with a total abundance < 25 (File S3, PDF); and a fully annotated alignment of select-sequence subset in tabulated, graphically enhanced form (File S4, spread-sheet XLSX, includes colouration).


FZT 118:  German Centre for Integrative Biodiversity Research (iDiv)

Deutsche Forschungsgemeinschaft

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MIUR (Italian Ministry for Education, University and Research), Law 232/2016, “Department of excellence”