Dataset for "Nanopore-based genome assembly and the evolutionary genomics of basmati rice"

Description of uploaded files:

Basmati334.basmati.not_scaffolded.fa

- Polished genome assembly for Basmati 334 but not scaffolded.

 

Basmati334.basmati.not_scaffolded.sorted.gff

- Gene annotation for the assembly Basmati334.basmati.not_scaffolded.fa

 

Basmati334.basmati.ragoo_scaffold.fa

- Polished genome assembly for Basmati 334 and scaffolding with RaGOO using the Nipponbare RAPDB1.0 as reference genome.

 

Basmati334.basmati.ragoo_scaffold.sorted.gff

- Gene annotation for the assembly Basmati334.basmati.ragoo_scaffold.fa

 

Basmati334.basmati.ragoo_scaffold.repeatmasker.bed

- Repetitive DNA coordinates for the assembly Basmati334.basmati.ragoo_scaffold.fa

 

CONSEL.tar.gz

- Files used for CONSEL analysis

   - Folder CONSEL/PHYLOGENY_TEST/ contains the input files for CONSEL

   - Folder CONSEL/CONSEL_RESULT/ contains the CONSEL test results

 

DADI_ANALYSIS.tar.gz

- Input file for dadi analysis and scripts used for dadi modeling

 

DomSufid.sadri.not_scaffolded.fa

- Polished genome assembly for Dom Sufid but not scaffolded.

 

DomSufid.sadri.not_scaffolded.sorted.gff

- Gene annotation for the assembly DomSufid.sadri.not_scaffolded.fa

 

DomSufid.sadri.ragoo_scaffold.fa

- Polished genome assembly for Dom Sufid and scaffolding with RaGOO using the Nipponbare RAPDB1.0 as reference genome.

 

DomSufid.sadri.ragoo_scaffold.sorted.gff

- Gene annotation for the assembly DomSufid.sadri.ragoo_scaffold.fa

 

DomSufid.sadri.ragoo_scaffold.repeatmasker.bed

- Repetitive DNA coordinates for the assembly DomSufid.sadri.ragoo_scaffold.fa

 

Four_rice_population.vcf.gz

- Filtered SNP VCF file used in the basmati population relationship with japonica and aus.

 

MULTIZ_ALIGNMENT.tar.gz

- Reference genome alignment using Nipponbare RAPDB1.0 as reference and aligning various Oryza de novo genome assemblies

 

Multi_Oryza_gene_FASTAs.tar.gz

- Using the alignments from MULTIZ_ALIGNMENT/ pulled out coding DNA sequences of each Nipponbare RAPDB1.0 gene

 

Obarthii_outgroup_AlignedToBasmatiScaffolded_genome.fa

- O. barthii reference genome sequence was aligned to scaffolded Basmati 334 reference genome. For every Basmati 334 genome coordinate was converted into a O. barthii sequence resulting in a basmati-ized O. barthii genome sequence. Not alignable regions were indicated as 'N'. 

 

Only_basmati_rice_population.vcf.gz

- Filtered SNP VCF file used in the basmati population analysis.

 

Oryza_LTR_DivergenceTime.txt

- LTR retrotransposon annotated in various Oryza reference genomes and their estimated insertion time (based on the divergence between the LTRs).

 

TWISST.tar.gz 

- TWISST input and results file.

   - Four_rice_population.geno.gz, genotype file generated from the genomic_general from S. Martin and used as input for TWISST analysis.

   - *.trees.gz phylogenetic trees generated from sliding windows

   - *.data.tsv sliding window coordinates

   - *.weights.csv.gz topology weights