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

<h2># Genomic datasets associated to the publication:&nbsp;</h2> <h3># Gene-ID conversion with previous genome version</h3> <p>Texasv3_vs_Texasv2_GeneID.txt -- gene ID conversion between Texasv3 and Texasv2 (https://www.rosaceae.org/analysis/295)</p> <p>pdulcis26_to_F1_liftoff_polished.gff3 -- Texasv2 gene annotation liftoff on Phase-1 assembly (Phase-1 coordinates)</p> <h3># Phase-1</h3> <p>Texas_F1_K80_chr.fasta &nbsp;-- genome asssembly, phase-1&nbsp;<br>Texas_F1_gene_models.gff3 -- &nbsp;phase-1 &nbsp;gene annotation (de novo annotation)<br>Functional_annotation_TexasF1.csv -- &nbsp;phase-1 gene functions &nbsp;<br>Texas_F1_ref_SV.vcf --- Structural variations relative to phase-0 (This file uses Phase-1 as reference)</p> <h3># Phase-0</h3> <p>Texas_F0_K80_chr.fasta -- genome asssembly, phase-0&nbsp;<br>Texas_F0_gene_models.gff3 -- &nbsp;phase-0 &nbsp;gene annotation (liftoff from Phase-1)<br>Functional_annotation_TexasF0.csv -- &nbsp;phase-0 &nbsp;gene functions &nbsp;<br>Texas_F0_ref_SV.vcf --- Structural variations relative to phase-1 (This file uses Phase-0 as reference)</p> <h3># Transposable element annotation</h3> <p>Texas_F0_HiConf_TE_v3.gff3 --- TE annotation in Phase-0<br>Texas_F1_HiConf_TE_v3.gff3 --- TE annotation in Phase-1<br>Texasv3_TElib.fa --- TE library of TexasV3 (non-redundant repeat consensuses taking the account the two genome phases)</p> <h3># Gene sequences in fasta</h3> <p>Transcript, CDS and protein sequences in fasta format for phase-0 (F0) and phase-1 (F1)&nbsp;</p>