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Purayil GP, Saeed EE, Mathai AM, El-Tarabily KA, AbuQamar SF. A high-quality genome assembly and annotation of Thielaviopsis punctulata DSM102798. Sci Data 2024; 11:745. [PMID: 38982096 PMCID: PMC11233662 DOI: 10.1038/s41597-024-03458-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/31/2024] [Indexed: 07/11/2024] Open
Abstract
Black scorch disease (BSD), caused by the fungal pathogen Thielaviopsis punctulata (Tp) DSM102798, poses a significant threat to date palm cultivation in the United Arab Emirates (UAE). In this study, Chicago and Hi-C libraries were prepared as input for the Dovetail HiRise pipeline to scaffold the genome of Tp DSM102798. We generated an assembly with a total length of 28.23 Mb comprising 1,256 scaffolds, and the assembly had a contig N50 of 18.56 kb, L50 of three, and a BUSCO completeness score of 98.6% for 758 orthologous genes. Annotation of this assembly produced 7,169 genes and 3,501 Gene Ontology (GO) terms. Compared to five other Thielaviopsis genomes, Tp DSM102798 exhibited the highest continuity with a cumulative size of 27.598 Mb for the first seven scaffolds, surpassing the assemblies of all examined strains. These findings offer a foundation for targeted strategies that enhance date palm resistance against BSD, and foster more sustainable and resilient agricultural systems.
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Affiliation(s)
- Gouthaman P Purayil
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Archana M Mathai
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
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Kwon JS, Shilpha J, Lee J, Yeom SI. Beyond NGS data sharing for plant ecological resilience and improvement of agronomic traits. Sci Data 2024; 11:466. [PMID: 38719829 PMCID: PMC11079010 DOI: 10.1038/s41597-024-03305-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Decoding complex plant omics is essential for advancing our understanding of plant biology, evolution, and breeding as well as for practical applications in agriculture, conservation, and biotechnology. The advent of Next-Generation Sequencing (NGS) has revolutionized global plant genomic research, offering high-throughput, cost-effective, and accurate methods for generating genomic data. However, challenges still exist that suggest an entirely unresolved genome characterized by high heterozygosity, extensive repetitive sequences, and complex ploidy features. In addition, individual investigation of genomic information from various genetic resources is essential for omics research, as there are differences in traits within a single breed beyond a species due to the uniqueness of sequence variation. This article provides high-quality genomic and transcriptomic insights targeted at the agronomical background.
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Affiliation(s)
- Ji-Su Kwon
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Jayabalan Shilpha
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Junesung Lee
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Seon-In Yeom
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea.
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Li X, Ma Y, Zhang N, Li Y, Liang Z, Luo Y, Lin L, Zhang D, He Y, Wang Z, Zhang Z, Deng Y. Whole-genome sequencing of Fusarium spp. causing sugarcane root rot on both chewing cane and sugar-making cane. STRESS BIOLOGY 2024; 4:7. [PMID: 38270818 PMCID: PMC10811303 DOI: 10.1007/s44154-023-00145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/24/2023] [Indexed: 01/26/2024]
Abstract
Previously we isolated three Fusarium strains (a F. sacchari strain namely GXUF-1, and another two F. commune strains namely GXUF-2 and GXUF-3), and we verified that GXUF-3 was able to cause sugarcane root rot to the chewing cane cultivar Badila. Considering that Fusarium spp. are a group of widely distributed fungal pathogens, we tested whether these three Fusarium isolates were able to cause root rot to Badila as well as sugar-making cane cultivar (Guitang42), using a suitable inoculation method established based on infection assays using Badila. We found that the three Fusarium strains were able to cause root rot symptoms to both Badila and Guitang42, to different extents. To better investigate the potential pathogenicity mechanisms, we performed Illumina high-throughput sequencing and analyzed the whole genomic sequence data of these three Fusarium strains. The results reveal that the assembly sizes of the three Fusarium strains were in a range of 44.7-48.2 Mb, with G + C contents of 48.0-48.5%, and 14,154-15,175 coding genes. The coding genes were annotated by multiple public databases, and potential pathogenic genes were predicted using proprietary databases (such as PHI, DFVF, CAZy, etc.). Furthermore, based on evolutionary analysis of the coding sequence, we found that contraction and expansion of gene families occurred in the three Fusarium strains. Overall, our results suggest a potential risk that the root rot disease may occur to the sugar-making canes although it was initially spotted from fruit cane, and provide clues to understand the pathogenic mechanisms of Fusarium spp. causing sugarcane root rot.
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Affiliation(s)
- Xinyang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuming Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Na Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Yiming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Zhibin Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Yibao Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Longxin Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Dongliang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yongqiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Ziting Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Zhiquan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yizhen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China.
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