Citrus sinensis cv. Valencia DVS v1.0 Assembly & Annotation

Overview

Analysis Name Citrus sinensis cv. Valencia DVS v1.0 Assembly & Annotation
Sequencing technology PacBio Sequel II
Assembly method FALCON-Unzip v. 2.0; CANU v. 2.0
Release Date 2022-02-11
Reference Publication(s)

Wu B, Yu Q, Deng Z, Duan Y, Luo F, Gmitter F Jr. A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance. Hortic Res. 2022 Nov 3;10(1):uhac247. doi: 10.1093/hr/uhac247.

Abstract

Sweet orange originated from the introgressive hybridizations of pummelo and mandarin resulting in a highly heterozygous genome. How alleles from the two species cooperate in shaping sweet orange phenotypes under distinct circumstances is unknown. Here, we assembled a chromosome-level phased diploid Valencia sweet orange (DVS) genome with over 99.999% base accuracy and 99.2% gene annotation BUSCO completeness. DVS enables allele-level studies for sweet orange and other hybrids between pummelo and mandarin. We first configured an allele-aware transcriptomic profiling pipeline and applied it to 740 sweet orange transcriptomes. On average, 32.5% of genes have a significantly biased allelic expression in the transcriptomes. Different cultivars, transgenic lineages, tissues, development stages, and disease status all impacted allelic expressions and resulted in diversified allelic expression patterns in sweet orange, but particularly citrus Huanglongbing (HLB) shifted the allelic expression of hundreds of genes in leaves and calyx abscission zones. In addition, we detected allelic structural mutations in an HLB-tolerant mutant (T19) and a more sensitive mutant (T78) through long-read sequencing. The irradiation-induced structural mutations mostly involved double-strand breaks, while most spontaneous structural mutations were transposon insertions. In the mutants, most genes with significant allelic expression ratio alterations (≥1.5-fold) were directly affected by those structural mutations. In T19, alleles located at a translocated segment terminal were upregulated, including CsDnaJ, CsHSP17.4B, and CsCEBPZ. Their upregulation is inferred to keep phloem protein homeostasis under the stress from HLB and enable subsequent stress responses observed in T19. DVS will advance allelic level studies in citrus.

Assembly statistics

DVS_A1.0DVS_B1.0
Genome size299 Mb299.6 Mb
Total ungapped length299 Mb299.6 Mb
Number of chromosomes99
Number of scaffolds99
Scaffold N5032.9 Mb32.3 Mb
Scaffold L5044
Number of contigs99
Contig N5032.9 Mb32.3 Mb
Contig L5044
GC percent3434
Genome coverage117.0x117.0x
Assembly levelComplete GenomeComplete Genome

Assembly

The Citrus sinensis cv. Valencia DVS v1.0 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) GCA_022201045.1_DVS_A1.0_genomic.fna.gz GCA_022201065.1_DVS_B1.0_genomic.fna.gz

Gene Predictions

The Citrus sinensis cv. Valencia DVS v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) GCA_022201045.1_DVS_A1.0_genomic.gff.gz GCA_022201065.1_DVS_B1.0_genomic.gff.gz
CDS sequences (FASTA file) GCA_022201045.1_DVS_A1.0_cds_from_genomic.fna.gz GCA_022201065.1_DVS_B1.0_cds_from_genomic.fna.gz
Protein sequences (FASTA file) GCA_022201045.1_DVS_A1.0_protein.faa.gz GCA_022201065.1_DVS_B1.0_protein.faa.gz

Functional Analysis

Functional annotation for the Citrus sinensis cv. Valencia DVS v1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Citrus_sinensis_DVS_A_v1.0.Pfam.tsv.gz Citrus_sinensis_DVS_B_v1.0.Pfam.tsv.gz

S genes

Summary

QueryChrSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF13CM039167.1294933661099357-1098281PP719853.1, S30-SLF1398.607F-box; F_box_assoc
SLF12CM039167.1294933661110704-1111825ASM2964120v1, SLF12_cds99.198F-box; F_box_assoc
SLF11CM039167.1294933661115084-1116259ASM2964120v1, SLF11_cds98.81F-box; F_box_assoc
SLF10CM039167.1294933661118733-1117588ASM2964120v1, SLF10_cds99.476F-box; F_box_assoc
SLF8CM039167.1294933661140261-1139122ASM2964120v1, SLF8-2_cds98.509F-box; F_box_assoc
SLF9CM039167.1294933661144296-1143154ASM2964120v1, SLF9_cds93.613F-box; F_box_assoc
SLF7CM039167.1294933661170672-1171802PP719832.1, S2-SLF793.546F-box; F_box_assoc
SLF6CM039167.1294933661180476-1181612ASM2964120v1, SLF6_cds91.645F-box; F_box_assoc
SLF5CM039167.1294933661232501-1231377ASM2964120v1, SLF5_cds90.311F-box; F_box_assoc
SLF4CM039167.1294933661299068-1297947PP719843.1, S30-SLF490.446F-box; F_box_assoc
SLF3CM039167.1294933661325939-1324827PP719842.1, S30-SLF390.999F-box; F_box_assoc
SLF2CM039167.1294933661360020-1358926PP719841.1, S30-SLF291.065F-box; F_box_assoc
S-RNaseψCM039167.1294933661250582-1250346,
1250224-1249797		MN652912.1, SmR-RNase99.9-
SLF13-2CM039176.131234485932558-931482PP719853.1, S30-SLF1398.422F-box; F_box_assoc
SLF12-2CM039176.131234485943595-944716PP719852.1, S30-SLF1299.02F-box; F_box_assoc
SLF11-2CM039176.131234485947732-948907ASM2964120v1, SLF11_cds99.49F-box; F_box_assoc
SLF10-2CM039176.131234485951327-950182ASM2964120v1, SLF10_cds99.738F-box; F_box_assoc
SLF8-2CM039176.131234485978606-977467ASM2964120v1, SLF8-2_cds98.509F-box; F_box_assoc
SLF9-2CM039176.131234485982506-981364ASM2964120v1, SLF9_cds93.613F-box; F_box_assoc
SLF7-2CM039176.131234485985115-986245PP719832.1, S2-SLF792.927F-box; F_box_assoc
SLF8-3CM039176.131234485988433-987294ASM2964120v1, SLF8_cds96.74F-box; F_box_assoc
SLF2-2CM039176.131234485995049-996161PP719841.1, S30-SLF288.839F-box; F_box_assoc
SLF5-2CM039176.1312344851007849-1008976PB533_SCSK_HAP2, SLF586.833F-box; F_box_assoc
SLF4-2CM039176.1312344851050013-1048898PP719843.1, S30-SLF491.667F-box; F_box_assoc
SLF3-2CM039176.1312344851054087-1052966PP719842.1, S30-SLF395.455F-box; F_box_assoc
SLF2-3CM039176.1312344851060109-1058985ASM2964120v1, SLF2_cds98.933F-box; F_box_assoc
SLF1CM039176.1312344851063192-1062092ASM2964120v1, SLF1_cds98.093F-box; F_box_assoc
S-RNase-2CM039176.1312344851045922-1046164,
1046258-1046710		MN652903.1, S7-RNase99.7Ribonuclease T2

Citrus S genes Nucleotide

Citrus S genes Protein

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