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Series GSE254853 Query DataSets for GSE254853
Status Public on Mar 18, 2024
Title A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous transposon insertions
Organisms Prunus dulcis; Prunus persica
Experiment type Expression profiling by high throughput sequencing
Summary The vast majority of traditional almond varieties are self-incompatible and the level of variability of the species is very high, resulting in a highly heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here we present a phased assembly of genome of the almond cv. Texas. Our analysis shows that the “Texas” genome has a high degree of heterozygosity, both as SNPs, short indels, and structural variants (SV) level. Many of the SVs are due to heterozygous Transposable Element (TE) insertions, and in many cases they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes tend to be associated with allele-specific gene expression (ASE), which highlights the importance of heterozygous SVs in almond.
 
Overall design Flowers (pink stage) and immature fruits of Prunus dulcis cv Texas and Prunus persica cv Early Gold were collected. For RNA-seq analysis, we used three biological replicates per genotype.
Web link https://academic.oup.com/hr/article/11/6/uhae106/7642723
 
Contributor(s) de Tomás C, Castanera R, Vicient CM, Casacuberta JM
Citation(s) 38883330
Submission date Feb 01, 2024
Last update date Jul 01, 2024
Contact name Carlos de Tomás
Organization name CRAG
Street address Carrer de la Vall Moronta
City Cerdanyola del Vallès
State/province Barcelona
ZIP/Postal code 08193
Country Spain
 
Platforms (2)
GPL21993 Illumina HiSeq 2500 (Prunus persica)
GPL27530 Illumina HiSeq 2500 (Prunus dulcis)
Samples (12)
GSM8059059 ALMOND_FLOWER_1
GSM8059060 ALMOND_FLOWER_2
GSM8059061 ALMOND_FLOWER_3
Relations
BioProject PRJNA1072089

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE254853_Texas_F0_transcripts.fasta.gz 13.7 Mb (ftp)(http) FASTA
GSE254853_rawdata_generalanalysis_RNAseq.txt.gz 423.1 Kb (ftp)(http) TXT
GSE254853_rawmatrix_ASE_RNAseq.txt.gz 178.4 Kb (ftp)(http) TXT
GSE254853_rlogmatrix_ASE_RNAseq.txt.gz 781.9 Kb (ftp)(http) TXT
GSE254853_rlogmatrix_generalanalysis_RNAseq.txt.gz 1.7 Mb (ftp)(http) TXT
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Raw data are available in SRA

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