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Haplotype-aware reference genome reveals hidden somatic mutations of sweet orange

Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).   Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).   Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).

ShareScore

40/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 4
Access: 20
Reuse readiness: 8
Engagement: 0

Topics

Citrus, haplogenomes, somatic mutations, allelic specific expression