Description

Citrus × aurantium f. aurantium (Syn: Citrus × sinensis), a hybrid between pomelo (Citrus maxima) and mandarin (Citrus reticulata), also known as the sweet oranges, is a commonly cultivated species of orange that includes Valencia oranges, blood oranges and navel oranges.

Whole Genomes

Whole Genome Sequences & Annotations for Citrus sinensis

• Citrus sinensis cv. Valencia DVS v1.0

S genes

Citrus sinensis cv. Valencia DVS v1.0 S genes

Query	Chr	Size(bp)	Coordinates	BLASTn Hit	BLASTn %ID	Domain
SLF13	CM039167.1	29493366	1099357-1098281	PP719853.1, S30-SLF13	98.607	F-box; F_box_assoc
SLF12	CM039167.1	29493366	1110704-1111825	ASM2964120v1, SLF12_cds	99.198	F-box; F_box_assoc
SLF11	CM039167.1	29493366	1115084-1116259	ASM2964120v1, SLF11_cds	98.81	F-box; F_box_assoc
SLF10	CM039167.1	29493366	1118733-1117588	ASM2964120v1, SLF10_cds	99.476	F-box; F_box_assoc
SLF8	CM039167.1	29493366	1140261-1139122	ASM2964120v1, SLF8-2_cds	98.509	F-box; F_box_assoc
SLF9	CM039167.1	29493366	1144296-1143154	ASM2964120v1, SLF9_cds	93.613	F-box; F_box_assoc
SLF7	CM039167.1	29493366	1170672-1171802	PP719832.1, S2-SLF7	93.546	F-box; F_box_assoc
SLF6	CM039167.1	29493366	1180476-1181612	ASM2964120v1, SLF6_cds	91.645	F-box; F_box_assoc
SLF5	CM039167.1	29493366	1232501-1231377	ASM2964120v1, SLF5_cds	90.311	F-box; F_box_assoc
SLF4	CM039167.1	29493366	1299068-1297947	PP719843.1, S30-SLF4	90.446	F-box; F_box_assoc
SLF3	CM039167.1	29493366	1325939-1324827	PP719842.1, S30-SLF3	90.999	F-box; F_box_assoc
SLF2	CM039167.1	29493366	1360020-1358926	PP719841.1, S30-SLF2	91.065	F-box; F_box_assoc
S-RNaseψ	CM039167.1	29493366	1250582-1250346, 1250224-1249797	MN652912.1, SmR-RNase	99.9	-
SLF13-2	CM039176.1	31234485	932558-931482	PP719853.1, S30-SLF13	98.422	F-box; F_box_assoc
SLF12-2	CM039176.1	31234485	943595-944716	PP719852.1, S30-SLF12	99.02	F-box; F_box_assoc
SLF11-2	CM039176.1	31234485	947732-948907	ASM2964120v1, SLF11_cds	99.49	F-box; F_box_assoc
SLF10-2	CM039176.1	31234485	951327-950182	ASM2964120v1, SLF10_cds	99.738	F-box; F_box_assoc
SLF8-2	CM039176.1	31234485	978606-977467	ASM2964120v1, SLF8-2_cds	98.509	F-box; F_box_assoc
SLF9-2	CM039176.1	31234485	982506-981364	ASM2964120v1, SLF9_cds	93.613	F-box; F_box_assoc
SLF7-2	CM039176.1	31234485	985115-986245	PP719832.1, S2-SLF7	92.927	F-box; F_box_assoc
SLF8-3	CM039176.1	31234485	988433-987294	ASM2964120v1, SLF8_cds	96.74	F-box; F_box_assoc
SLF2-2	CM039176.1	31234485	995049-996161	PP719841.1, S30-SLF2	88.839	F-box; F_box_assoc
SLF5-2	CM039176.1	31234485	1007849-1008976	PB533_SCSK_HAP2, SLF5	86.833	F-box; F_box_assoc
SLF4-2	CM039176.1	31234485	1050013-1048898	PP719843.1, S30-SLF4	91.667	F-box; F_box_assoc
SLF3-2	CM039176.1	31234485	1054087-1052966	PP719842.1, S30-SLF3	95.455	F-box; F_box_assoc
SLF2-3	CM039176.1	31234485	1060109-1058985	ASM2964120v1, SLF2_cds	98.933	F-box; F_box_assoc
SLF1	CM039176.1	31234485	1063192-1062092	ASM2964120v1, SLF1_cds	98.093	F-box; F_box_assoc
S-RNase-2	CM039176.1	31234485	1045922-1046164, 1046258-1046710	MN652903.1, S7-RNase	99.7	Ribonuclease T2

Downloads

The Citrus sinensis S gene sequences are available in FASTA format.

CDS and Protein (FASTA file)

S-gene_Citrus_sinensis

Publications

Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y. The draft genome of sweet orange (Citrus sinensis). Nat Genet. 2013 Jan;45(1):59-66. doi: 10.1038/ng.2472.

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.

Xiong Z, Yin H, Wang N, Han G, Gao Y. Chromosome-level genome assembly of navel orange cv. Gannanzao (Citrus sinensis Osbeck cv. Gannanzao). G3 (Bethesda). 2024 Feb 7;14(2):jkad268. doi: 10.1093/g3journal/jkad268.

Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astúa J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol. 2014 Jul;32(7):656-62. doi: 10.1038/nbt.2906.

Wang L, Huang Y, Liu Z, He J, Jiang X, He F, Lu Z, Yang S, Chen P, Yu H, Zeng B, Ke L, Xie Z, Larkin RM, Jiang D, Ming R, Buckler ES, Deng X, Xu Q. Somatic variations led to the selection of acidic and acidless orange cultivars. Nat Plants. 2021 Jul;7(7):954-965. doi: 10.1038/s41477-021-00941-x.