README: Draft genome assembly of alpine carnations Dianthus sylvestris and D. carthusianorum (Caryophyllaceae)

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