DOI: 10.6084/m9.figshare.7775810
title: Datasets for Tetep genome analysis

description: <br><b>## Genome sequences</b><b><br></b>Tetep-1.1_pseudomolecule.fasta.gz: Tetep genome sequences (chromosome pseudomolecules) in fasta format, gzip compressed, corresponding to the DDBJ/ENA/GenBank accession GCA_004348155.2 or QQAJ00000000.<br>Tetep-1.1_pseudomolecule.softmasked.fasta.gz: Repeat masked (lowercased) sequences in fasta format, gzip compressed.<br>Tetep-1.1b_pseudomolecule.fasta.gz: A modified version with contig tig00011498 manually anchored to chr11:21344774-21363909, yet to be confirmed.<br><br><b>## Predicted gene sets</b><br>Tetep-1.1_fgenesh.tar.gz: Gene set predicted by Fgenesh.<br>Tetep-1.1b_maker.tar.gz: Gene set predicted by MAKER-P (note the MAKER annotation is based on the genome version 1.1b).<br><br><b>## NLR sequences predicted for 4 rice cultivars and Brachypodium distachyon</b><i>Files are given in fasta format, including full coding sequences (nucleotide), full protein sequences, nucleotide sequences of NB-ARC domain regions, and protein sequences of NB-ARC domain regions. All NB-ARC type genes are provided, and the NB-LRR type genes are marked by "NLR".</i><br>Tetep.NLRs.tar.gz: NLR genes predicted in Tetep genome.<br>Nipponbare.NLRs.tar.gz: NLR genes predicted in Nipponbare genome (genome [IRGSP-1.0]: https://rapdb.dna.affrc.go.jp/download/irgsp1.html, annotation [MSU RGAP7]: http://rice.plantbiology.msu.edu/).<br>MH63.NLRs.tar.gz: NLR genes predicted in Minghui63 genome (genome and annotation [MH63RS1]: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/623/365/GCA_001623365.1_MH63RS1/)<br>R498.NLRs.tar.gz: NLR genes predicted in R498 genome (genome and annotation [V3]: http://www.mbkbase.org/R498/).<br>Bdistachyon.NLRs.tar.gz: NLR genes predicted in Brachypodium distachyon (genome [v3.0] and annotation [v3.1]: https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Bdistachyon).<br><br><br><br><b>## Files for phylogenetic analysis</b><br>Figure_4c<i>This tarball contains phylogenetic trees constructed for "Figure 4c. Paired NLRs identified in the Nipponbare genome that are Pi-ta or Pi-kh homologs"</i><br> Figure_4c.Pita_Pikh_pairs.full_cds.clustalw2.fas: ClutalW2 aligned coding sequences (codon-based alignments). Fasta format.<br> Figure_4c.Pita_Pikh_pairs.full_cds.FastTree.nwk: Phylogenetic tree constructed using FastTree with full coding sequences. Newick format.<br> Figure_4c.Pita_Pikh_pairs.NB-ARC.cds.clustalw2.fas: ClutalW2 aligned nucleotide sequences of NB-ARC domain (codon-based alignments). Fasta format.<br> Figure_4c.Pita_Pikh_pairs.NB-ARC_cds.FastTree.nwk: Phylogenetic tree constructed using FastTree with nucleotide sequences of NB-ARC domain alone. Newick format.<br> Figure_4c.Pita_Pikh_pairs.NB-ARC_pep.clustalw2.fas: ClutalW2 aligned protein sequences of NB-ARC domain. Fasta format.<br> Figure_4c.Pita_Pikh_pairs.NB-ARC_pep.RAxML.nwk: Phylogenetic tree constructed using RAxML with protein sequences of NB-ARC domain alone. Newick format.<br>Figure_6<i>This tarball contains phylogenetic trees constructed for "Figure 6. Phylogenetic tree of paired NLRs".</i><br> Figure_6.NLR_pairs.full_cds.clustalw2.fas: ClutalW2 aligned coding sequences (codon-based alignments). Fasta format.<br> Figure_6.NLR_pairs.full_cds.FastTree.nwk: Phylogenetic tree constructed using FastTree with full coding sequences. Newick format.<br> Figure_6.NLR_pairs.NB-ARC_cds.clustalw2.fas: ClutalW2 aligned nucleotide sequences of NB-ARC domain (codon-based alignments). Fasta format.<br> Figure_6.NLR_pairs.NB-ARC_cds.FastTree.nwk: Phylogenetic tree constructed using FastTree with nucleotide sequences of NB-ARC domain alone. Newick format.<br> Figure_6.NLR_pairs.NB-ARC_pep.clustalw2.fas: ClutalW2 aligned protein sequences of NB-ARC domain. Fasta format.<br> Figure_6.NLR_pairs.NB-ARC_pep.RAxML.nwk: Phylogenetic tree constructed using RAxML with protein sequences of NB-ARC domain alone. Newick format.<br>Supplementary_Figure_2<i>This tarball contains phylogenetic trees constructed for "Supplementary Figure 2. Phylogenetic tree of all NLRs identified in Tetep (*.fgenesh*), Nipponbare (LOC_Os*) and B. distachyon (Brad*)".</i><br> Supplementary_Figure_2.NLR_phylogeny.full_cds.clustalw2.fas: ClutalW2 aligned coding sequences (codon-based alignments). Fasta format.<br> Supplementary_Figure_2.NLR_phylogeny.full_cds.FastTree.nwk: Phylogenetic tree constructed using FastTree with full coding sequences. Newick format.<br> Supplementary_Figure_2.NLR_phylogeny.NB-ARC_cds.clustalw2.fas: ClutalW2 aligned nucleotide sequences of NB-ARC domain (codon-based alignments). Fasta format.<br> Supplementary_Figure_2.NLR_phylogeny.NB-ARC_cds.FastTree.nwk: Phylogenetic tree constructed using FastTree with nucleotide sequences of NB-ARC domain alone. Newick format.<br> Supplementary_Figure_2.NLR_phylogeny.NB-ARC_cds.RAxML.nwk: Phylogenetic tree constructed using RAxML with nucleotide sequences of NB-ARC domain alone. Newick format.<br> Supplementary_Figure_2.NLR_phylogeny.NB-ARC_pep.clustalw2.fas: ClutalW2 aligned protein sequences of NB-ARC domain. Fasta format.<br> Supplementary_Figure_2.NLR_phylogeny.NB-ARC_pep.RAxML.nwk: Phylogenetic tree constructed using RAxML with protein sequences of NB-ARC domain alone. Newick format.<br><br><b>## Miscellanies</b><br>Tetep.NLR.Sanger.sequences.fasta: Assembled sanger sequences for 93 cloned NLRs.<br>Tetep_Illumina.mapped.to.Nipponbare.snpEff.vcf.gz: Variants with predicted effects after mapping Tetep Illumina reads to Nipponbare genome. The variants were called by GATK HaplotypeCaller (https://software.broadinstitute.org/gatk/), and the effects were predicted using SnpEff (http://snpeff.sourceforge.net/) based on the MSU RGAP7 gene models (http://rice.plantbiology.msu.edu/). The file was compressed with bgzip (http://www.htslib.org/doc/bgzip.html).<br>Tetep_Illumina.mapped.to.Nipponbare.snpEff.vcf.gz.tbi: Tabix (http://www.htslib.org/doc/tabix.html) index file for "Tetep_Illumina.mapped.to.Nipponbare.snpEff.vcf.gz".<br>Tetep_Illumina.mapped.to.Nipponbare.snpEff.genes.txt.gz: Predicted effects for each gene in txt format.<br>OrthoFinder.Orthogroups.csv: Tab separated text file contains orthogroups identified using Orthofinder (https://github.com/davidemms/OrthoFinder) among all predicted NB-ARC type genes in Tetep, Nipponbare, MH63, R498 and Brachypodium distachyon.<br>OrthoFinder.Orthologues_Tetep.tar.gz: Orthologues between Tetep and each of other 4 genomes reported by OrthoFinder.<br><br>