A chromosome-level genome assembly for Erianthus fulvus provides insights into its biofuel potential and facilitates breeding for improvement of sugarcane

Ling Kui; Aasim Majeed; Xianhong Wang; Zijiang Yang; Jian Chen; Lilian He; Yining Di; Xuzhen Li; Zhenfeng Qian; Yinming Jiao; Guoyun Wang; Lufeng Liu; Rong Xu; Shujie Gu; Qinghui Yang; Shuying Chen; Hongbo Lou; Yu Meng; Linyan Xie; Fu Xu; Qingqing Shen; Amit Singh; Karl Gruber; Yunbing Pan; Tingting Hao; Yang Dong; Fusheng Li

doi:10.1016/j.xplc.2023.100562

A chromosome-level genome assembly for Erianthus fulvus provides insights into its biofuel potential and facilitates breeding for improvement of sugarcane

Plant Commun. 2023 Jul 10;4(4):100562. doi: 10.1016/j.xplc.2023.100562. Epub 2023 Feb 21.

Authors

Ling Kui¹, Aasim Majeed², Xianhong Wang³, Zijiang Yang⁴, Jian Chen⁵, Lilian He⁶, Yining Di⁴, Xuzhen Li⁷, Zhenfeng Qian⁴, Yinming Jiao⁸, Guoyun Wang⁸, Lufeng Liu⁹, Rong Xu⁴, Shujie Gu⁴, Qinghui Yang⁶, Shuying Chen⁶, Hongbo Lou⁶, Yu Meng⁴, Linyan Xie⁴, Fu Xu⁴, Qingqing Shen⁴, Amit Singh¹⁰, Karl Gruber¹⁰, Yunbing Pan⁷, Tingting Hao⁷, Yang Dong¹¹, Fusheng Li¹²

Affiliations

¹ Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518067, China.
² Plant Molecular Genetics Laboratory, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
³ Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan 650201, China.
⁴ College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China.
⁵ International Genome Center, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
⁶ Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China.
⁷ State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China.
⁸ Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518067, China.
⁹ Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan 650201, China.
¹⁰ Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria.
¹¹ State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China. Electronic address: loyalyang@163.com.
¹² Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan 650201, China. Electronic address: lfs810@sina.com.

Abstract

Erianthus produces substantial biomass, exhibits a good Brix value, and shows wide environmental adaptability, making it a potential biofuel plant. In contrast to closely related sorghum and sugarcane, Erianthus can grow in degraded soils, thus releasing pressure on agricultural lands used for biofuel production. However, the lack of genomic resources for Erianthus hinders its genetic improvement, thus limiting its potential for biofuel production. In the present study, we generated a chromosome-scale reference genome for Erianthus fulvus Nees. The genome size estimated by flow cytometry was 937 Mb, and the assembled genome size was 902 Mb, covering 96.26% of the estimated genome size. A total of 35 065 protein-coding genes were predicted, and 67.89% of the genome was found to be repetitive. A recent whole-genome duplication occurred approximately 74.10 million years ago in the E. fulvus genome. Phylogenetic analysis showed that E. fulvus is evolutionarily closer to S. spontaneum and diverged after S. bicolor. Three of the 10 chromosomes of E. fulvus formed through rearrangements of ancestral chromosomes. Phylogenetic reconstruction of the Saccharum complex revealed a polyphyletic origin of the complex and a sister relationship of E. fulvus with Saccharum sp., excluding S. arundinaceum. On the basis of the four amino acid residues that provide substrate specificity, the E. fulvus SWEET proteins were classified as mono- and disaccharide sugar transporters. Ortho-QTL genes identified for 10 biofuel-related traits may aid in the rapid screening of E. fulvus populations to enhance breeding programs for improved biofuel production. The results of this study provide valuable insights for breeding programs aimed at improving biofuel production in E. fulvus and enhancing sugarcane introgression programs.

Keywords: Erianthus fulvus; QTLs; SWEET family; biofuel; cold stress; reference genome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biofuels
Chromosomes, Plant / genetics
Phylogeny
Plant Breeding
Saccharum* / genetics

Substances

Biofuels