| Analysis Name | Citrus medica C_medica_denovo_2 Assembly & Annotation |
| Sequencing technology | Illumina HiSeq |
| Assembly method | SOAPdenovo v. 2 |
| Release Date | 2018-01-24 |
Wang X, Xu Y, Zhang S, Cao L, Huang Y, Cheng J, Wu G, Tian S, Chen C, Liu Y, Yu H, Yang X, Lan H, Wang N, Wang L, Xu J, Jiang X, Xie Z, Tan M, Larkin RM, Chen LL, Ma BG, Ruan Y, Deng X, Xu Q. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nat Genet. 2017 May;49(5):765-772. doi: 10.1038/ng.3839.
AbstractThe emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.
Assembly statistics
| Genome size | 406.1 Mb |
| Total ungapped length | 369.6 Mb |
| Number of scaffolds | 32,732 |
| Scaffold N50 | 369.5 kb |
| Scaffold L50 | 304 |
| Number of contigs | 45,671 |
| Contig N50 | 70.6 kb |
| Contig L50 | 1,428 |
| GC percent | 35 |
| Genome coverage | 171.0x |
| Assembly level | Scaffold |
The Citrus medica C_medica_denovo_2 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | C.medica_v1_XZ.scaffold.fa.gz |
The Citrus medica C_medica_denovo_2 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | C.medica_v1_XZ.gene.models.gff3.gz |
| CDS sequences (FASTA file) | C.medica_v1_XZ.CDS.fasta.gz |
| Protein sequences (FASTA file) | C.medica_v1_XZ.peptide.fasta.gz |
Functional annotation for the Citrus medica C_medica_denovo_2 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Citrus_medica_C_medica_denovo_2.Pfam.tsv.gz |
Citrus S genes Nucleotide
Citrus S genes Protein