Table 1 Overview of data files and data sets used in this study
From: Chromosome-scale assembly of the Verbenaceae species Queen’s Wreath (Petrea volubilis L.)
Label | Data file/Data set name | File types | Data repository and identifier (DOI or accession number) |
|---|---|---|---|
Data file 1 | Petrea volubilis libraries used in this study | Spreadsheet (.xlxs) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data file 2 | Genomescope k-mer frequency distribution plot | Portable Document Files (.pdf) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data file 3 | Hi-C contact map | Portable Document Files (.pdf) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data file 4 | Assembly metrics for the Petrea volubilis assembly | Spreadsheet (.xlxs) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data file 5 | Pseudomolecule lengths and gap content for the Petrea volubulis assembly | Spreadsheet (.xlxs) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data file 6 | KAT k-mer comparison plot | Portable Document Files (.pdf) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data file 7 | BUSCO results on the Petrea volubilis assembly and annotation | Spreadsheet (.xlxs) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data file 8 | Repetitive sequence content in the Petrea volubilis assembly | Spreadsheet (.xlxs) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data file 9 | Petrea volubulis gene annotation summary | Spreadsheet (.xlxs) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 1 | Pac Bio reads from high molecular weight DNA, SRR11516643 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR11516643) [7, 21] |
Data set 2 | Pac Bio reads from high molecular weight DNA, SRR11516644 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR11516644) [7, 22] |
Data set 3 | Illumina whole genome shotgun reads, SRR11516645 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR11516645) [7, 11] |
Data set 4 | Illumina Hi-C DNA sequence reads, SRR15904679 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR15904679) [7, 15] |
Data set 5 | Illumina Hi-C DNA sequence reads, SRR15904680 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR15904680) [7, 16] |
Data set 6 | Illumina RNA-Seq—Root, SRR8937863 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR8937863) [7, 23] |
Data set 7 | Illumina RNA-Seq—Petiole, SRR8937861 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR8937861) [7, 24] |
Data set 8 | Illumina RNA-Seq—Stem, SRR8937862 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR8937862) [7, 25] |
Data set 9 | Illumina RNA-Seq—Immature leaf, SRR8937859 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR8937859) [7, 26] |
Data set 10 | Illumina RNA-Seq—Mature leaf, SRR8937860 | Fastq file (.fastq.gz) | NCBI (https://identifiers.org/ncbi/insdc.sra:SRR8937860) [7, 27] |
Data set 11 | Genome assembly of Petrea volubilis | fasta file (.fa) | NCBI (https://identifiers.org/assembly:GCA_026212405.1) [7, 28] |
Data set 12 | High Confidence Petrea volubilis Gene Models cDNA | fasta file (.fa) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 13 | High Confidence Petrea volubilis Gene Models CDS | fasta file (.fa) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 14 | High Confidence Petrea volubilis Gene Models GFF3 | GFF3 file (.gff3) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 15 | High Confidence Petrea volubilis Gene Models Proteins | fasta file (.fa) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 16 | Representative High Confidence Petrea volubilis Gene Models cDNA | fasta file (.fa) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 17 | Representative High Confidence Petrea volubilis Gene Models CDS | fasta file (.fa) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 18 | Representative High Confidence Petrea volubilis Gene Models GFF3 | GFF3 file (.gff3) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 19 | Representative High Confidence Petrea volubilis Gene Models List | text file (.txt) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 20 | Representative High Confidence Petrea volubilis Gene Models Proteins | fasta file (.fa) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 21 | Petrea volubilis Working Gene Models cDNA | fasta file (.fa) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 22 | Petrea volubilis Working Gene Models CDS | fasta file (.fa) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 23 | Petrea volubilis Working Gene Models GFF3 | GFF3 file (.gff3) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 24 | Petrea volubilis Working Gene Models Proteins | fasta file (.fa) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |
Data set 25 | Petrea volubilis Working Gene Models Functional Annotation | text file (.txt) | Figshare (https://doi.org/10.6084/m9.figshare.21429219.v3) [7] |