| Analysis Name | Citrus limon cv. Eureka v1.0 Assembly & Annotation |
| Sequencing technology | PacBio, ONT, Hi-C, Illumina |
| Assembly method | Hifiasm |
| Release Date | 2023-04-28 |
Bao Y, Zeng Z, Yao W, Chen X, Jiang M, Sehrish A, Wu B, Powell CA, Chen B, Xu J, Zhang X, Zhang M. A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance. Hortic Res. 2023 Feb 14;10(4):uhad020. doi: 10.1093/hr/uhad020.
AbstractThe lemon (Citrus limon; family Rutaceae) is one of the most important and popular fruits worldwide. Lemon also tolerates huanglongbing (HLB) disease, which is a devastating citrus disease. Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing, Oxford Nanopore 50-kb ultra-long, and high-throughput chromatin conformation capture technologies. The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps, while a total of 633.0 Mb genomic sequences were generated. The origination analysis identified 338.5 Mb genomic sequences originating from citron (53.5%), 147.4 Mb from mandarin (23.3%), and 147.1 Mb from pummelo (23.2%). The genome included 30 528 protein-coding genes, and most of the assembled sequences were found to be repetitive sequences. Several significantly expanded gene families were associated with plant-pathogen interactions, plant hormone signal transduction, and the biosynthesis of major active components, such as terpenoids and flavor compounds. Most HLB-tolerant genes were expanded in the lemon genome, such as 2-oxoglutarate (2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1, cell wall-related genes, and lignin synthesis genes. Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon. Our results provide insight into lemon genome evolution, active component biosynthesis, and genes associated with HLB tolerance.
Assembly statistics
| Total length (Mb) | 633.0 |
| Total number of contigs | 18 |
| Longest contig (Mb) | 52.6 |
| Contig N50 (Mb) | 35.6 |
| Anchor rate | 100% |
The Citrus limon cv. Eureka v1.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GWHCBFQ00000000.1.genome.fasta.gz |
The Citrus limon cv. Eureka v1.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | GWHCBFQ00000000.1.gff.gz |
| CDS sequences (FASTA file) | GWHCBFQ00000000.1.RNA.fasta.gz |
| Protein sequences (FASTA file) | GWHCBFQ00000000.1.Protein.faa.gz |
Functional annotation for the Citrus limon cv. Eureka v1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Citrus_limon_cv.Eureka_v1.0.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF13 | ChrA1 | 34398103 | 948946-947870 | ASM2964120v1, SLF13 | 98.7 | F-box; F_box_assoc |
| SLF12 | ChrA1 | 34398103 | 957488-958609 | PP719852.1, S30-SLF12 | 99.02 | F-box; F_box_assoc |
| SLF11 | ChrA1 | 34398103 | 961586-962761 | ASM2964120v1, SLF11 | 98.469 | F-box; F_box_assoc |
| SLF10 | ChrA1 | 34398103 | 965182-964037 | ASM2964120v1, SLF10 | 99.564 | F-box; F_box_assoc |
| SLF8 | ChrA1 | 34398103 | 986903-985764 | ASM2964120v1, SLF8-2 | 97.719 | F-box; F_box_assoc |
| SLF9 | ChrA1 | 34398103 | 990683-989541 | ASM2964120v1, SLF9-2 | 92.301 | F-box; F_box_assoc |
| SLF7 | ChrA1 | 34398103 | 993301-994431 | PP719832.1, S2-SLF7 | 92.838 | F-box; F_box_assoc |
| SLF6 | ChrA1 | 34398103 | 999636-1000778 | PP719831.1, S2-SLF6 | 94.144 | F-box; F_box_assoc |
| S-RNase | ChrA1 | 34398103 | 1009492-1009238,1009146-1008703 | WWV94842.1, S2-ribonuclease | 98.71 | Ribonuclease T2 |
| SLF5 | ChrA1 | 34398103 | 1077414-1078538 | PP719830.1, S2-SLF5 | 94.133 | F-box; F_box_assoc |
| SLF4 | ChrA1 | 34398103 | 1099176-1098073 | PP719829.1, S2-SLF4 | 97.826 | F-box; F_box_assoc |
| SLF3 | ChrA1 | 34398103 | 1131767-1130646 | PP719828.1, S2-SLF3 | 97.772 | F-box; F_box_assoc |
| SLF2 | ChrA1 | 34398103 | 1155500-1154385 | PP719827.1, S2-SLF2 | 99.104 | F-box; F_box_assoc |
| SLF1 | ChrA1 | 34398103 | 1170737-1169637 | KR363148.1, SLF_S2C | 98.274 | F-box; F_box_assoc |
| SLF13-2 | ChrB1 | 29532049 | 1001794-1000718 | ASM2964120v1, SLF13 | 98.793 | F-box; F_box_assoc |
| SLF12-2 | ChrB1 | 29532049 | 1013141-1014262 | ASM2964120v1, SLF12 | 99.198 | F-box; F_box_assoc |
| SLF11-2 | ChrB1 | 29532049 | 1017521-1018696 | PP719851.1, S30-SLF11 | 98.775 | F-box; F_box_assoc |
| SLF10-2 | ChrB1 | 29532049 | 1021170-1020025 | ASM2964120v1, SLF10 | 99.476 | F-box; F_box_assoc |
| SLF8-2 | ChrB1 | 29532049 | 1042697-1041558 | PP719833.1, S2-SLF8 | 93.158 | F-box; F_box_assoc |
| SLF9-2 | ChrB1 | 29532049 | 1046732-1045590 | ASM2964120v1, SLF9 | 93.613 | F-box; F_box_assoc |
| SLF7-2 | ChrB1 | 29532049 | 1073108-1074238 | PP719832.1, S2-SLF7 | 93.546 | F-box; F_box_assoc |
| SLF6-2 | ChrB1 | 29532049 | 1082912-1084048 | ASM2964120v1, SLF6 | 91.645 | F-box; F_box_assoc |
| SLF5-2 | ChrB1 | 29532049 | 1134937-1133813 | ASM2964120v1, SLF5 | 90.311 | F-box; F_box_assoc |
| S-RNase-2ψ | ChrB1 | 29532049 | 1153021-1152785,1152663-1152236 | MN652912.1, SmR-ribonuclease | 99.9 | - |
| SLF4-2 | ChrB1 | 29532049 | 1201507-1200386 | PP719843.1, S30-SLF4 | 90.446 | F-box; F_box_assoc |
| SLF3-2 | ChrB1 | 29532049 | 1228378-1227266 | PP719842.1, S30-SLF3 | 90.999 | F-box; F_box_assoc |
| SLF2-2 | ChrB1 | 29532049 | 1262459-1261365 | PP719841.1, S30-SLF2 | 91.065 | F-box; F_box_assoc |
Citrus S genes Nucleotide
Citrus S genes Protein