The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance

doi:10.1016/j.pld.2025.01.001

Plant Diversity ›› 2025, Vol. 47 ›› Issue (02): 201-213.DOI: 10.1016/j.pld.2025.01.001

Special Issue: 虚拟专辑 | 干旱响应与适应 | 整合生物学期刊集群跨刊组建

• Articles • Previous Articles Next Articles

The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance

Gulbar Yisilam^a,b,c,d, Enting Zheng^a,d, Chuanning Li^a,d, Zhiyong Zhang^a,d, Ying Su^b, Zhenzhou Chu^b, Pan Li^c, Xinmin Tian^a,b,d

a. Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin 541006, China;
b. Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
c. Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
d. Guangxi University Enginering Research Center of Bioinformation and Genetic Improvement of Speciaty Crops, Guangxi Normal University, Guilin 541006, China

Received:2024-10-07 Revised:2024-12-30 Online:2025-04-03 Published:2025-03-25
Contact: Pan Li,E-mail:panli_zju@126.com;Xinmin Tian,E-mail:tianxm333333@foxmail.com
Supported by:
This work was supported by the National Natural Science Foundation of China (32360058), and the Central Government Guides Local Science and Technology Development Projects, China (2023ZYZX1224), and Xinjiang University Excellent Doctoral Student Innovation Project (XJU2022BS051).

The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance

Gulbar Yisilam^a,b,c,d, Enting Zheng^a,d, Chuanning Li^a,d, Zhiyong Zhang^a,d, Ying Su^b, Zhenzhou Chu^b, Pan Li^c, Xinmin Tian^a,b,d

a. Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin 541006, China;
b. Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
c. Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
d. Guangxi University Enginering Research Center of Bioinformation and Genetic Improvement of Speciaty Crops, Guangxi Normal University, Guilin 541006, China

通讯作者: Pan Li,E-mail:panli_zju@126.com;Xinmin Tian,E-mail:tianxm333333@foxmail.com
作者简介:Gulbar Yisilam,E-mail:Gulbaryisilam@163.com;Enting Zheng,E-mail:zz15219585505@163.com;Chuanning Li,E-mail:Lichuanning228@163.com;Zhiyong Zhang,E-mail:zhangzy@gxnu.edu.cn;Ying Su,E-mail:15109159670@163.com;Zhenzhou Chu,E-mail:chuzhenzhou@outlook.com
基金资助:
This work was supported by the National Natural Science Foundation of China (32360058), and the Central Government Guides Local Science and Technology Development Projects, China (2023ZYZX1224), and Xinjiang University Excellent Doctoral Student Innovation Project (XJU2022BS051).

Abstract

Abstract: The black wolfberry (Lycium ruthenicum; 2n = 2x = 24) is an important medicinal plant with ecological and economic value. Its fruits have numerous beneficial pharmacological activities, especially those of anthocyanins, polysaccharides, and alkaloids, and have high nutritional value. However, the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms. In this study, we developed the telomere-to-telomere (T2T) nearly gapless genome of L. ruthenicum (2.26 Gb) by integrating PacBio HiFi, Nanopore Ultra-Long, and Hi-C technologies. The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated. Approximately 80% of the repetitive sequences were identified, of which long terminal repeats (LTRs) were the most abundant, accounting for 73.01%. The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species. The species-specific genes of L. ruthenicum were related to defense mechanisms, salt tolerance, drought resistance, and oxidative stress, further demonstrating their superior adaptability to arid environments. Based on the assembled genome and fruit transcriptome data, we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L. ruthenicum, most of which were highly expressed at a later stage in fruit development. Furthermore, 154 potential disease resistance-related nucleotide-binding genes have been identified in the L. ruthenicum genome. The whole-genome and proximal, dispersed, and tandem duplication genes in the L. ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways. These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.

Key words: Lycium ruthenicum, Genome, Anthocyanin biosynthesis, Gene duplication, Comparative genomics

摘要： The black wolfberry (Lycium ruthenicum; 2n = 2x = 24) is an important medicinal plant with ecological and economic value. Its fruits have numerous beneficial pharmacological activities, especially those of anthocyanins, polysaccharides, and alkaloids, and have high nutritional value. However, the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms. In this study, we developed the telomere-to-telomere (T2T) nearly gapless genome of L. ruthenicum (2.26 Gb) by integrating PacBio HiFi, Nanopore Ultra-Long, and Hi-C technologies. The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated. Approximately 80% of the repetitive sequences were identified, of which long terminal repeats (LTRs) were the most abundant, accounting for 73.01%. The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species. The species-specific genes of L. ruthenicum were related to defense mechanisms, salt tolerance, drought resistance, and oxidative stress, further demonstrating their superior adaptability to arid environments. Based on the assembled genome and fruit transcriptome data, we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L. ruthenicum, most of which were highly expressed at a later stage in fruit development. Furthermore, 154 potential disease resistance-related nucleotide-binding genes have been identified in the L. ruthenicum genome. The whole-genome and proximal, dispersed, and tandem duplication genes in the L. ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways. These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.

关键词: Lycium ruthenicum, Genome, Anthocyanin biosynthesis, Gene duplication, Comparative genomics

Gulbar Yisilam, Enting Zheng, Chuanning Li, Zhiyong Zhang, Ying Su, Zhenzhou Chu, Pan Li, Xinmin Tian. The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance[J]. Plant Diversity, 2025, 47(02): 201-213.

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The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance

The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance

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