DOI: 10.5061/dryad.x0k6djhng
title: Draft genome assembly of alpine carnations Dianthus sylvestris and D. carthusianorum (Caryophyllaceae)

description: Draft reference sequences for the alpine carnations Dianthus sylvestris
 and D. carthusianorum were assembled. The assemblies are complemented with
 linkage maps to anchor scaffolds to chromosomes, and with a structural and
 functional annotation of coding sequences.
description: # Draft genome assembly of alpine carnations Dianthus sylvestris and D.
 carthusianorum (Caryophyllaceae)
 [https://doi.org/10.5061/dryad.x0k6djhng](https://doi.org/10.5061/dryad.x0k6djhng) ## Description of the data and file structure 1\) Fasta sequence of genome assemblies Dianthus_sylvestris_assembly_v1.fa.gz Dianthus_carthusian_assembly_v1.fa.gz The assemblies were obtained from a combination of paired-end and mate-pair Illumina libraries implemented in the Allpath-LG assembler. The initial assembly was improved through nucleotide correction, gap filling and the assessment of misassemblies.  The final assembly for D. sylvestris/D. carthusianorum consists of ca. 21 K scaffolds, N50 of 61/47 Kb, contig length of 354/288 Mb, scaffold length of 444/354 Mb, covering 73/54% of the estimated genome size (ca. 600 MB) and 86/87% of Busco eukaryotic genes. 2\) Structural annotation Dianthus_sylvestris_assembly_v1_annot.gff3.gz Dianthus_carthusian_assembly_v1_annot.gff3.gz Structural annotation was obtained through the Maker2 pipeline with the support of RNA-seq data. The inferred coding sequences for D.sylvestris/D. carthusianorum include ~22/16 K predicted genes (N50 ~1.8/1.9 Kb).   3\) Functional annotation Dianthus_sylvestris_assembly_v1_maker_blast2go.txt.gz Dianthus_sylvestris_assembly_v1_abinitio_blast2go.txt.gz Dianthus_carthusian_assembly_v1_maker_blast2go.txt.gz Dianthus_carthusian_assembly_v1_abinitio_blast2go.txt.gz Functional annotation for D. sylvestris and D. carthusianorum was obtained with Blast2go. Annotation for maker-approved and ab-inition genes are available in separate files. 4\) Protein sequences Dianthus_sylvestris_assembly_v1_maker_proteins.fa.gz Dianthus_sylvestris_assembly_v1_abinitio_proteins.fa.gz Dianthus_carthusian_assembly_v1_maker_proteins.fa.gz Dianthus_carthusian_assembly_v1_abinitio_proteins.fa.gz Protein sequences as translated from gene model predictions for D. sylvestris and D. carthusianorum. Sequences for maker-approved and ab-inition genes are available in separate files. 5\) Linkage map Dsylvestris_Dcarthusian_linkageMaps.xlsx A linkage map was obtained from a controlled F2 cross for each species genotyped with ddRAD sequencing. The linkage map was built in Joinmap and anchored 1359/1172 scaffold to the chromosomes of D. sylvestris/D. carthusianorum. ## Sharing/Access information Sequencing data used in the assemblies and annotations are available in ENA. D. sylvestris Assembly (DNA): ERS7647936, ERS7647937, ERS7647938, ERS7647939, ERS7647940, ERS7647941, ERS7647942 Annotation (RNAseq): ERS7667052, ERS7667053, ERS7667054, ERS7667055, ERS7667056 D. carthusianorum Assembly (DNA): ERS7647943, ERS7647944, ERS7647945, ERS7647946, ERS7647947, ERS7647948 Annotation (RNAseq): ERS7667057, ERS7667058, ERS7667059, ERS7667060, ERS7667061, ERS7667062