| Analysis Name | Citrus mangshanensis ASM3044989v1 Assembly & Annotation |
| Sequencing technology | Oxford Nanopore |
| Assembly method | SMARTdenovo v. default |
| Release Date | 2023-07-13 |
Huang Y, He J, Xu Y, Zheng W, Wang S, Chen P, Zeng B, Yang S, Jiang X, Liu Z, Wang L, Wang X, Liu S, Lu Z, Liu Z, Yu H, Yue J, Gao J, Zhou X, Long C, Zeng X, Guo YJ, Zhang WF, Xie Z, Li C, Ma Z, Jiao W, Zhang F, Larkin RM, Krueger RR, Smith MW, Ming R, Deng X, Xu Q. Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. Nat Genet. 2023 Nov;55(11):1964-1975. doi: 10.1038/s41588-023-01516-6.
AbstractThe orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide, such as sweet orange and lemon. The origin of Citrus species has long been debated and less is known about the Aurantioideae. Here, we compiled the genome sequences of 314 accessions, de novo assembled the genomes of 12 species and constructed a graph-based pangenome for Aurantioideae. Our analysis indicates that the ancient Indian Plate is the ancestral area for Citrus-related genera and that South Central China is the primary center of origin of the Citrus genus. We found substantial variations in the sequence and expression of the PH4 gene in Citrus relative to Citrus-related genera. Gene editing and biochemical experiments demonstrate a central role for PH4 in the accumulation of citric acid in citrus fruits. This study provides insights into the origin and evolution of the orange subfamily and a regulatory mechanism underpinning the evolution of fruit taste.
Assembly statistics
| Genome size | 371 Mb |
| Total ungapped length | 371 Mb |
| Number of contigs | 376 |
| Contig N50 | 3.6 Mb |
| Contig L50 | 24 |
| GC percent | 37.5 |
| Genome coverage | 77.0x |
| Assembly level | Contig |
The Citrus mangshanensis ASM3044989v1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | MSYG.v1.0.genome.fa.gz |
The Citrus mangshanensis ASM3044989v1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | MSYG.v1.0.gene.model.gff3.gz |
| CDS sequences (FASTA file) | MSYG.v1.0.CDS.fa.gz |
| Protein sequences (FASTA file) | MSYG.v1.0.protein.fa.gz |
Functional annotation for the Citrus mangshanensis ASM3044989v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Citrus_mangshanensis_ASM3044989v1.Pfam.tsv.gz |
Summary
| Query | Contig | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF13ψ | contig135 | 520690 | 46320-45244 | ASM2964120v1, SLF13 | 98.795 | - |
| SLF3 | contig135 | 520690 | 64230-65339 | PB533_SCSK_HAP2, SLF3 | 96.216 | F-box; F_box_assoc |
| SLF4 | contig135 | 520690 | 78761-79876 | PP719843.1, S30-SLF4 | 94.176 | F-box; F_box_assoc |
| SLF5 | contig135 | 520690 | 158103-159227 | ASM2964120v1, SLF5 | 92.851 | F-box; F_box_assoc |
| SLF6 | contig135 | 520690 | 182860-183999 | ASM2964120v1, SLF6 | 93.634 | F-box; F_box_assoc |
| SLF7 | contig135 | 520690 | 222200-221073 | ASM2964120v1, SLF7 | 91.851 | F-box; F_box_assoc |
| SLF9 | contig135 | 520690 | 250132-251271 | ASM2964120v1, SLF9 | 91.373 | F-box; F_box_assoc |
| SLF8 | contig135 | 520690 | 266274-267413 | ASM2964120v1, SLF8-2 | 93.684 | F-box; F_box_assoc |
| SLF10ψ | contig135 | 520690 | 347044-348079 | ASM2964120v1, SLF10 | 92.954 | - |
| SLF11 | contig135 | 520690 | 364830-363676 | ASM2964120v1, SLF11 | 94.934 | F-box; F_box_assoc |
| SLF12 | contig135 | 520690 | 374773-373654 | ASM2964120v1, SLF12 | 90.893 | F-box; F_box_assoc |
| SLF13 | contig135 | 520690 | 390406-391521 | ASM2964120v1, SLF13 | 92.242 | F-box; F_box_assoc |
| SLF2 | contig135 | 520690 | 400446-399322 | PP719841.1, S30-SLF2 | 96.622 | F-box; F_box_assoc |
| SLF1 | contig135 | 520690 | 409463-408363 | PP719840.1, S30-SLF1 | 97.366 | F-box; F_box_assoc |
| SLF1-2 | contig285 | 9003745 | 7859314-7860414 | Citrus maxima SLF_S2C | 98.547 | F-box; F_box_assoc |
| SLF2-2 | contig285 | 9003745 | 7870101-7871216 | PP719827.1, S2-SLF2 | 99.104 | F-box; F_box_assoc |
| SLF3-2 | contig285 | 9003745 | 7892799-7893920 | PP719828.1, S2-SLF3 | 98.841 | F-box; F_box_assoc |
| SLF4-2 | contig285 | 9003745 | 7904196-7905299 | PP719843.1, S30-SLF4 | 91.561 | F-box; F_box_assoc |
| SLF5-2 | contig285 | 9003745 | 7921796-7920672 | PP719830.1, S2-SLF5 | 99.2 | F-box; F_box_assoc |
| SLF6-2 | contig285 | 9003745 | 7961077-7959944 | PP719831.1, S2-SLF6 | 98.942 | F-box; F_box_assoc |
| SLF7-2 | contig285 | 9003745 | 7966329-7965199 | PP719832.1, S2-SLF7 | 99.293 | F-box; F_box_assoc |
| SLF9-2 | contig285 | 9003745 | 7975089-7976234 | PP719834.1, S2-SLF9 | 99.302 | F-box; F_box_assoc |
| SLF8-2 | contig285 | 9003745 | 7980615-7981754 | PP719833.1, S2-SLF8 | 98.509 | F-box; F_box_assoc |
| SLF10-2 | contig285 | 9003745 | 8002841-8003965 | ASM2964120v1, SLF10 | 99.564 | F-box; F_box_assoc |
| SLF11-2 | contig285 | 9003745 | 8006447-8005272 | ASM2964120v1, SLF11 | 98.895 | F-box; F_box_assoc |
| SLF12-2 | contig285 | 9003745 | 8010578-8009457 | ASM2964120v1, SLF12 | 98.93 | F-box; F_box_assoc |
| SLF13-2 | contig285 | 9003745 | 8021118-8022173 | ASM2964120v1, SLF13 | 99.071 | F-box; F_box_assoc |
| S-RNase-1 | contig135 | 520690 | 131165-131404,131508-131945 | OQ672689.1, S23-RNase | 100 | Ribonuclease T2 |
| S-RNase-2 | contig285 | 9003745 | 7938886-7939140,7939233-7939676 | OQ672700.1, S2-RNase | 100 | Ribonuclease T2 |
Citrus S genes Nucleotide
Citrus S genes Protein