Description

Sugarcane or sugar cane is a species of tall, perennial grass (in the genus Saccharum, tribe Andropogoneae) that is used for sugar production. The plants are 2–6 m (6–20 ft) tall with stout, jointed, fibrous stalks that are rich in sucrose, which accumulates in the stalk internodes. Sugarcanes belong to the grass family, Poaceae, an economically important flowering plant family that includes maize, wheat, rice, and sorghum, and many forage crops. It is native to the warm temperate and tropical regions of India, Southeast Asia, and New Guinea.

Whole Genomes

Whole Genome Sequences & Annotations for Saccharum officinarum x spontaneum

• Saccharum officinarum x spontaneum R570 v2.1

S genes

Saccharum officinarum x spontaneum R570 v2.1 S genes

Query	Chromosome	Size(bp)	Coordinates	tBLASTn Hit	tBLASTn %ID	Domain
DUF247I-S1	Chr4A	82147227	45451459-45453150	Pnotatum	68	DUF247
DUF247I-S2	Chr4B	67335593	35359872-35361542	Pnotatum	72	DUF247
DUF247I-S3Ψ	Chr4B	67335593	35352426-35353532	Pnotatum	76	DUF247
DUF247I-S4	Chr4C	66740618	34973006-34974700	Pnotatum	62	DUF247
DUF247I-S5	Chr4E	51224956	17425601-17427268	Pnotatum	64	DUF247
DUF247I-S6	Chr4F	50041630	18076523-18078217	Pnotatum	62	DUF247
DUF247II-S1	Chr4A	82147227	45118168-45119784	Pnotatum	64	DUF247
DUF247II-S2	Chr4B	67335593	35646182-35647807	Pnotatum	71	DUF247
DUF247II-S3	Chr4C	66740618	34944043-34945665	Pnotatum	65	DUF247
DUF247II-S4	Chr4D	56614552	37553438-37555051	Pnotatum	60	DUF247
DUF247II-S5	Chr4E	51224956	17162933-17164552	Pnotatum	61	DUF247
DUF247II-S6	Chr4F	50041630	16872511-16874133	Pnotatum	65	DUF247
HPS10-S1	Chr4A	82147227	46096791-46096953, 46097063-46097160	Pvaginatum	62	-
HPS10-S2	Chr4B	67335593	35356085-35356194, 35356279-35356444	Pvaginatum	47	-
HPS10-S3	Chr4B	67335593	35348653-35348762, 35348847-35349012	Pvaginatum	47	-
HPS10-S4	Chr4C	66740618	34988926-34989044, 34989165-34989303	Pvaginatum	51	-
HPS10-S5	Chr4E	51224956	17723108-17723220, 17723323-17723464	Pvaginatum	50	-
HPS10-S6	Chr4F	50041630	18096861-18096979, 18097100-18097268	Pvaginatum	51	-
DUF247I-Z1Ψ	Chr7A	71344650	63428166-63428759	Pnotatum	60	DUF247
DUF247I-Z2	Chr7B	68479205	61210945-61212525	Pnotatum	58	DUF247
DUF247I-Z3	Chr7C	63301622	56642183-56643748	Pnotatum	61	DUF247
DUF247I-Z4	Chr7D	62522272	55330487-55332142	Pnotatum	53	DUF247
DUF247I-Z5Ψ	Chr7E	57896127	50081317-50082054	Pvaginatum	71	DUF247
DUF247I-Z6	Chr7_10A	92477847	86187493-86189121	Pvaginatum	47	DUF247
DUF247I-Z7	Chr7os1	28450685	24061534-24063138	Pnotatum	59	DUF247
DUF247II-Z1Ψ	Chr7A	71344650	63465565-63465750	Trufipilum	53	DUF247
DUF247II-Z2	Chr7B	68479205	61216457-61218127	Pnotatum	49	DUF247
DUF247II-Z3	Chr7C	63301622	56674475-56676148	Pnotatum	51	DUF247
DUF247II-Z4	Chr7D	62522272	55326178-55327854	Pnotatum	50	DUF247
DUF247II-Z5	Chr7_10A	92477847	86233541-86235211	Pnotatum	47	DUF247
DUF247II-Z6	Chr7os1	28450685	24109889-24111520	Pnotatum	48	DUF247
HPS10-Z1	Chr7B	68479205	61214485-61214656, 61214963-61215117	Pvaginatum	52	-
HPS10-Z2	Chr7C	63301622	56646243-56646334, 56646512-56646650	Olongistaminata	75	-
HPS10-Z3	Chr7D	62522272	55328126-55328211, 55328481-55328667	Ocoarctata	53	-
HPS10-Z4	Chr7E	57896127	50083900-50083994, 50084317-50084455	Orufipogon	46	-
HPS10-Z5	Chr7_10A	92477847	86232194-86232356, 86232455-86232564	Pnotatum	61	-
HPS10-Z6	Chr7os1	28450685	24100177-24100348, 24100476-24100582	Pvaginatum	60	-

Downloads

The Saccharum officinarum x spontaneum S gene sequences are available in FASTA format.

CDS and Protein (FASTA file)

S-gene_Saccharum_officinarum x spontaneum

Publications

Healey AL, Garsmeur O, Lovell JT, Shengquiang S, Sreedasyam A, Jenkins J, Plott CB, Piperidis N, Pompidor N, Llaca V, Metcalfe CJ, Doležel J, Cápal P, Carlson JW, Hoarau JY, Hervouet C, Zini C, Dievart A, Lipzen A, Williams M, Boston LB, Webber J, Keymanesh K, Tejomurthula S, Rajasekar S, Suchecki R, Furtado A, May G, Parakkal P, Simmons BA, Barry K, Henry RJ, Grimwood J, Aitken KS, Schmutz J, D'Hont A. The complex polyploid genome architecture of sugarcane. Nature. 2024 Apr;628(8009):804-810. doi: 10.1038/s41586-024-07231-4.

Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, Hervouet C, Costet L, Yahiaoui N, Healey A, Sims D, Cherukuri Y, Sreedasyam A, Kilian A, Chan A, Van Sluys MA, Swaminathan K, Town C, Bergès H, Simmons B, Glaszmann JC, van der Vossen E, Henry R, Schmutz J, D'Hont A. A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nat Commun. 2018 Jul 6;9(1):2638. doi: 10.1038/s41467-018-05051-5.

Trujillo-Montenegro JH, Rodríguez Cubillos MJ, Loaiza CD, Quintero M, Espitia-Navarro HF, Salazar Villareal FA, Viveros Valens CA, González Barrios AF, De Vega J, Duitama J, Riascos JJ. Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid. Front Plant Sci. 2021 Aug 13;12:694859. doi: 10.3389/fpls.2021.694859.

Shearman JR, Pootakham W, Sonthirod C, Naktang C, Yoocha T, Sangsrakru D, Jomchai N, Tongsima S, Piriyapongsa J, Ngamphiw C, Wanasen N, Ukoskit K, Punpee P, Klomsa-Ard P, Sriroth K, Zhang J, Zhang X, Ming R, Tragoonrung S, Tangphatsornruang S. A draft chromosome-scale genome assembly of a commercial sugarcane. Sci Rep. 2022 Nov 28;12(1):20474. doi: 10.1038/s41598-022-24823-0.