Whole-genome sequencing and comparative genome analysis of Xanthomonas fragariae YM2 causing angular leaf spot disease in strawberry

Yue Qiu; Fangjun Wei; Han Meng; Menglin Peng; Jinhao Zhang; Yilu He; Lanfang Wei; Waqar Ahmed; Guanghai Ji

doi:10.3389/fpls.2023.1267132

Whole-genome sequencing and comparative genome analysis of Xanthomonas fragariae YM2 causing angular leaf spot disease in strawberry

Front Plant Sci. 2023 Dec 18:14:1267132. doi: 10.3389/fpls.2023.1267132. eCollection 2023.

Authors

Yue Qiu^{1

2

3}, Fangjun Wei^{1

3}, Han Meng^{1

3}, Menglin Peng^{1

3}, Jinhao Zhang^{1

3}, Yilu He^{1

3}, Lanfang Wei^{1

4}, Waqar Ahmed⁵, Guanghai Ji^{1

3}

Affiliations

¹ State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China.
² College of Agriculture, Anshun University, Anshun, Guizhou, China.
³ Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China.
⁴ Agricultural Foundation Experiment Teaching Center, Yunnan Agricultural University, Kunming, Yunnan, China.
⁵ College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China.

Abstract

Background: Angular leaf spot disease caused by plant pathogenic bacterium Xanthomonas fragariae seriously threatens strawberry crop production globally.

Methods: In this study, we sequenced the whole genome of X. fragariae YM2, isolated from Yunnan Province, China. In addition, we performed a comparative genome analysis of X. fragariae YM2 with two existing strains of X. fragariae YL19 and SHQP01 isolated from Liaoning and Shanghai, respectively.

Results: The results of Nanopore sequencing showed that X. fragariae YM2 comprises one single chromosome with a contig size of 4,263,697 bp, one plasmid contig size of 0.39 Mb, a GC content ratio of 62.27%, and 3,958 predicted coding genes. The genome of YM2 comprises gum, hrp, rpf, and xps gene clusters and lipopolysaccharide (LPS), which are typical virulence factors in Xanthomonas species. By performing a comparative genomic analysis between X. fragariae strains YM2, YL19, and SHQP01, we found that strain YM2 is similar to YL19 and SHQP01 regarding genome size and GC contents. However, there are minor differences in the composition of major virulence factors and homologous gene clusters. Furthermore, the results of collinearity analysis demonstrated that YM2 has lower similarity and longer evolutionary distance with YL19 and SHQP01, but YL19 is more closely related to SHQP01.

Conclusions: The availability of this high-quality genetic resource will serve as a basic tool for investigating the biology, molecular pathogenesis, and virulence of X. fragariae YM2. In addition, unraveling the potential vulnerabilities in its genetic makeup will aid in developing more effective disease suppression control measures.

Keywords: Xanthomonas fragariae; collinearity analysis; functional annotation; genome comparison; virulence factors.

Grants and funding

The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article. This study was financially supported by the Yunnan Provincial Science and Technology Department, Basic Research Project-Key Project (202301AS070080), National Natural Science Foundation of China (No. 32060601 and No. 32350410423), and the Yunnan Ten Thousand Talents Plan Leading Talents of Industrial Technology Project of China (YNWR-CYJS-2019-046).