| Analysis Name | Citrus trifoliata ASM1835013v1 Assembly & Annotation |
| Sequencing technology | PacBio Sequel |
| Assembly method | FALCON v. MAY-2017 |
| Release Date | 2021-05-13 |
Huang Y, Xu Y, Jiang X, Yu H, Jia H, Tan C, Hu G, Hu Y, Rao MJ, Deng X, Xu Q. Genome of a citrus rootstock and global DNA demethylation caused by heterografting. Hortic Res. 2021 Apr 1;8(1):69. doi: 10.1038/s41438-021-00505-2.
AbstractGrafting is an ancient technique used for plant propagation and improvement in horticultural crops for at least 1,500 years. Citrus plants, with a seed-to-seed cycle of 5–15 years, are among the fruit crops that were probably domesticated by grafting. Poncirus trifoliata, a widely used citrus rootstock, can promote early flowering, strengthen stress tolerance, and improve fruit quality via scion–rootstock interactions. Here, we report its genome assembly using PacBio sequencing. We obtained a final genome of 303 Mb with a contig N50 size of 1.17 Mb and annotated 25,680 protein-coding genes. DNA methylome and transcriptome analyses indicated that the strong adaptability of P. trifoliata is likely attributable to its special epigenetic modification and expression pattern of resistance-related genes. Heterografting by using sweet orange as scion and P. trifoliata as rootstock and autografting using sweet orange as both scion and rootstock were performed to investigate the genetic effects of the rootstock. Single-base methylome analysis indicated that P. trifoliata as a rootstock caused DNA demethylation and a reduction in 24-nt small RNAs (sRNAs) in scions compared to the level observed with autografting, implying the involvement of sRNA-mediated graft-transmissible epigenetic modifications in citrus grafting. Taken together, the assembled genome for the citrus rootstock and the analysis of graft-induced epigenetic modifications provide global insights into the genetic effects of rootstock–scion interactions and grafting biology.
Assembly statistics
| Genome size | 303.1 Mb |
| Total ungapped length | 303 Mb |
| Gaps between scaffolds | 222 |
| Number of chromosomes | 9 |
| Number of scaffolds | 707 |
| Scaffold N50 | 1.2 Mb |
| Scaffold L50 | 64 |
| Number of contigs | 707 |
| Contig N50 | 1.2 Mb |
| Contig L50 | 64 |
| GC percent | 34 |
| Genome coverage | 91.0x |
| Assembly level | Chromosome |
The Citrus trifoliata ASM1835013v1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | P.trifoliata_ZK8_v1.scaffolds.fa.gz |
The Citrus trifoliata ASM1835013v1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | P.trifoliata_ZK8_v1.geneModels.fa.gz |
| CDS sequences (FASTA file) | P.trifoliata_ZK8_v1.CDS.fa.gz |
| Protein sequences (FASTA file) | P.trifoliata_ZK8_v1.protein.fa.gz |
Functional annotation for the Citrus trifoliata ASM1835013v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Poncirus_trifoliata_ASM1835013v1.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF1 | chr7_ZK8 | 21477625 | 20096284-20097384 | ASM2964120v1, SLF1-2 | 98.183 | F-box; F_box_assoc |
| SLF2 | chr7_ZK8 | 21477625 | 20099121-20100245 | PP719841.1, S30-SLF2 | 96.178 | F-box; F_box_assoc |
| SLF3 | chr7_ZK8 | 21477625 | 20161181-20162281 | PB533_SCSK_HAP2, SLF3 | 95.924 | F-box; F_box_assoc |
| SLF4 | chr7_ZK8 | 21477625 | 20165826-20166941 | PP719843.1, S30-SLF4 | 93.548 | F-box; F_box_assoc |
| SLF5 | chr7_ZK8 | 21477625 | 20190703-20189576 | PP719830.1, S2-SLF5 | 87.433 | F-box; F_box_assoc |
| SLF9 | chr7_ZK8 | 21477625 | 20224035-20222911 | PB533_SCSK_HAP2, SLF9 | 91.133 | F-box; F_box_assoc |
| SLF6 | chr7_ZK8 | 21477625 | 20259439-20260575 | ASM2964120v1, SLF6 | 88.506 | F-box; F_box_assoc |
| SLF7 | chr7_ZK8 | 21477625 | 20292206-20291076 | PP719832.1, S2-SLF7 | 89.92 | F-box; F_box_assoc |
| SLF8 | chr7_ZK8 | 21477625 | 20313045-20314184 | ASM2964120v1, SLF8 | 95.066 | F-box; F_box_assoc |
| SLF10 | chr7_ZK8 | 21477625 | 20335102-20336247 | ASM2964120v1, SLF10 | 99.215 | F-box; F_box_assoc |
| SLF11ψ | chr7_ZK8 | 21477625 | 20338687-20337513 | ASM2964120v1, SLF11-2 | 98.98 | F-box; F_box_assoc |
| SLF12 | chr7_ZK8 | 21477625 | 20342845-20341721 | PP719852.1, S30-SLF12 | 96.533 | F-box; F_box_assoc |
| SLF13 | chr7_ZK8 | 21477625 | 20354308-20355384 | ASM2964120v1, SLF13 | 99.257 | F-box; F_box_assoc |
| SLF3-2 | chr7_ZK8 | 21477625 | 20420999-20422120 | PP719828.1, S2-SLF3 | 98.841 | F-box; F_box_assoc |
| SLF4-2 | chr7_ZK8 | 21477625 | 20436136-20437239 | PP719829.1, S2-SLF4 | 99.366 | F-box; F_box_assoc |
| SLF5-2 | chr7_ZK8 | 21477625 | 20453124-20452000 | PP719830.1, S2-SLF5 | 93.956 | F-box; F_box_assoc |
| SLF6-2 | chr7_ZK8 | 21477625 | 20480127-20479003 | PP719831.1, S2-SLF6 | 93.789 | F-box; F_box_assoc |
| SLF7-2 | chr7_ZK8 | 21477625 | 20492378-20491248 | PP719832.1, S2-SLF7 | 92.75 | F-box; F_box_assoc |
| SLF9-2 | chr7_ZK8 | 21477625 | 20494954-20496096 | ASM2964120v1, SLF9 | 92.913 | F-box; F_box_assoc |
| SLF8-2 | chr7_ZK8 | 21477625 | 20500668-20501807 | ASM2964120v1, SLF8-2 | 98.421 | F-box; F_box_assoc |
| SLF10-2 | chr7_ZK8 | 21477625 | 20523585-20524730 | ASM2964120v1, SLF10 | 98.866 | F-box; F_box_assoc |
| SLF11-2 | chr7_ZK8 | 21477625 | 20527280-20526105 | ASM2964120v1, SLF11 | 98.724 | F-box; F_box_assoc |
| SLF12-2 | chr7_ZK8 | 21477625 | 20531427-20530306 | ASM2964120v1, SLF12 | 99.287 | F-box; F_box_assoc |
| SLF13-2 | chr7_ZK8 | 21477625 | 20542919-20543995 | ASM2964120v1, SLF13 | 99.35 | F-box; F_box_assoc |
| S-RNase-1 | chr7_ZK8 | 21477625 | 20175555-20175313,20175211-20174759 | OR359668.1, S31-RNase | 99.1 | Ribonuclease T2 |
| S-RNase-2 | chr7_ZK8 | 21477625 | 20469272-20469526,20469618-20470061 | OQ672696.1, S2-RNase | 100 | Ribonuclease T2 |
Citrus S genes Nucleotide
Citrus S genes Protein