A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants

# Genomic datasets associated to the publication: 

# Gene-ID conversion with previous genome version

Texasv3_vs_Texasv2_GeneID.txt -- gene ID conversion between Texasv3 and Texasv2 (https://www.rosaceae.org/analysis/295)

pdulcis26_to_F1_liftoff_polished.gff3 -- Texasv2 gene annotation liftoff on Phase-1 assembly (Phase-1 coordinates)

# Phase-1

Texas_F1_K80_chr.fasta  -- genome asssembly, phase-1 
Texas_F1_gene_models.gff3 --  phase-1  gene annotation (de novo annotation)
Functional_annotation_TexasF1.csv --  phase-1 gene functions  
Texas_F1_ref_SV.vcf --- Structural variations relative to phase-0 (This file uses Phase-1 as reference)

# Phase-0

Texas_F0_K80_chr.fasta -- genome asssembly, phase-0 
Texas_F0_gene_models.gff3 --  phase-0  gene annotation (liftoff from Phase-1)
Functional_annotation_TexasF0.csv --  phase-0  gene functions  
Texas_F0_ref_SV.vcf --- Structural variations relative to phase-1 (This file uses Phase-0 as reference)

# Transposable element annotation

Texas_F0_HiConf_TE_v3.gff3 --- TE annotation in Phase-0
Texas_F1_HiConf_TE_v3.gff3 --- TE annotation in Phase-1
Texasv3_TElib.fa --- TE library of TexasV3 (non-redundant repeat consensuses taking the account the two genome phases)