DOI: 10.5281/zenodo.8016647
title: Haplotype-aware reference genome reveals hidden somatic mutations of sweet orange

description: <strong>Filename: </strong>ASE_in_five_fruit_development.txt <strong>Description: </strong>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. <strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv <strong>Description: </strong>The biallelic genes were identified using the Genespace program. <strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw <strong>Description: </strong>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. <strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw <strong>Description:</strong> The peaks generated from Control chip-seq. <strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf <strong>Description: </strong>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). <strong>Filename: </strong>HaplotypeA_CuteSV.vcf <strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program. <strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv <strong>Description: </strong>The gene annotations of haplotype A. <strong>Filename: </strong>HaplotypeA_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype A. <strong>Filename: </strong>HaplotypeA_genome.fa <strong>Description:</strong> The genome sequences of haplotype A. <strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip <strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome. <strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype A. <strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv <strong>Description:</strong> The gene annotations of haplotype B. <strong>Filename: </strong>HaplotypeB_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype B. <strong>Filename: </strong>HaplotypeB_genome.fa <strong>Filename: </strong>ASE_in_five_fruit_development.txt <strong>Description: </strong>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. <strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv <strong>Description: </strong>The biallelic genes were identified using the Genespace program. <strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw <strong>Description: </strong>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. <strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw <strong>Description:</strong> The peaks generated from Control chip-seq. <strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf <strong>Description: </strong>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). <strong>Filename: </strong>HaplotypeA_CuteSV.vcf <strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program. <strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv <strong>Description: </strong>The gene annotations of haplotype A. <strong>Filename: </strong>HaplotypeA_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype A. <strong>Filename: </strong>HaplotypeA_genome.fa <strong>Description:</strong> The genome sequences of haplotype A. <strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip <strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome. <strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype A. <strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv <strong>Description:</strong> The gene annotations of haplotype B. <strong>Filename: </strong>HaplotypeB_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype B. <strong>Filename: </strong>HaplotypeB_genome.fa <strong>Description:</strong> The genome sequences of haplotype B. <strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype B. <strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf <strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A). <strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt <strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). <strong>Filename: </strong>ASE_in_five_fruit_development.txt <strong>Description: </strong>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. <strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv <strong>Description: </strong>The biallelic genes were identified using the Genespace program. <strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw <strong>Description: </strong>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. <strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw <strong>Description:</strong> The peaks generated from Control chip-seq. <strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf <strong>Description: </strong>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). <strong>Filename: </strong>HaplotypeA_CuteSV.vcf <strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program. <strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv <strong>Description: </strong>The gene annotations of haplotype A. <strong>Filename: </strong>HaplotypeA_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype A. <strong>Filename: </strong>HaplotypeA_genome.fa <strong>Description:</strong> The genome sequences of haplotype A. <strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip <strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome. <strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype A. <strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv <strong>Description:</strong> The gene annotations of haplotype B. <strong>Filename: </strong>HaplotypeB_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype B. <strong>Filename: </strong>HaplotypeB_genome.fa <strong>Description:</strong> The genome sequences of haplotype B. <strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype B. <strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf <strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A). <strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt <strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). <strong>Filename: </strong>ASE_in_five_fruit_development.txt <strong>Description: </strong>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. <strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv <strong>Description: </strong>The biallelic genes were identified using the Genespace program. <strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw <strong>Description: </strong>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. <strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw <strong>Description:</strong> The peaks generated from Control chip-seq. <strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf <strong>Description: </strong>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). <strong>Filename: </strong>HaplotypeA_CuteSV.vcf <strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program. <strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv <strong>Description: </strong>The gene annotations of haplotype A. <strong>Filename: </strong>HaplotypeA_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype A. <strong>Filename: </strong>HaplotypeA_genome.fa <strong>Description:</strong> The genome sequences of haplotype A. <strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip <strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome. <strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype A. <strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv <strong>Description:</strong> The gene annotations of haplotype B. <strong>Filename: </strong>HaplotypeB_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype B. <strong>Filename: </strong>HaplotypeB_genome.fa <strong>Description:</strong> The genome sequences of haplotype B. <strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype B. <strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf <strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A). <strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt <strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). <strong>Filename: </strong>ASE_in_five_fruit_development.txt <strong>Description: </strong>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. <strong>Filename: </strong>Biallelic_genes_haplogenomes.tsv <strong>Description: </strong>The biallelic genes were identified using the Genespace program. <strong>Filename: </strong>Haplogenomes_CENH3_chip_peaks.bw <strong>Description: </strong>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. <strong>Filename: </strong>Haplogenomes_Control_chip_peaks.bw <strong>Description:</strong> The peaks generated from Control chip-seq. <strong>Filename: </strong>Haplotype_based_79accessions_somatic_variations.vcf <strong>Description: </strong>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). <strong>Filename: </strong>HaplotypeA_CuteSV.vcf <strong>Description: </strong>The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program. <strong>Filename: </strong>HaplotypeA_gene_function_annotation.tsv <strong>Description: </strong>The gene annotations of haplotype A. <strong>Filename: </strong>HaplotypeA_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype A. <strong>Filename: </strong>HaplotypeA_genome.fa <strong>Description:</strong> The genome sequences of haplotype A. <strong>Filename: </strong>HaplotypeA_PEPPER_OUTPUT.zip <strong>Description: </strong>The small variations of sweet orange using the haplotype A as the reference genome. <strong>Filename: </strong>HaplotypeA_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype A. <strong>Filename: </strong>HaplotypeB_gene_function_annotation.tsv <strong>Description:</strong> The gene annotations of haplotype B. <strong>Filename: </strong>HaplotypeB_gene_model.gff3 <strong>Description:</strong> The gene structure model of haplotype B. <strong>Filename: </strong>HaplotypeB_genome.fa <strong>Description:</strong> The genome sequences of haplotype B. <strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype B. <strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf <strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A). <strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt <strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). <strong>Description:</strong> The genome sequences of haplotype B. <strong>Filename: </strong>HaplotypeB_TEs_annotation.gff3 <strong>Description:</strong> The TE annotations of haplotype B. <strong>Filename: </strong>Single_reference_87accessions_somatic_variations.vcf <strong>Description:</strong> The small somatic variations generated based on the single reference genome (Haplotype A). <strong>Filename: </strong>Somatic_material_RNA_seq_matrix.txt <strong>Description: </strong>The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).